diff --git a/package/CHANGELOG b/package/CHANGELOG index 7f6a5b356a4..a1185a3f6bf 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -14,15 +14,19 @@ The rules for this file: ------------------------------------------------------------------------------ ??/??/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst + manuel.nuno.melo * 0.14.0 API Changes + * Offsets files for Gromacs trajectory formats have been changed to a numpy style format '.npz'. Offsets files will be regenerated when you load a xtc/trr trajectory again. (Issue #441) Enhancement + + * XDR file seeking errors now report system errno. (PR #678) * Offsets reading for xtc/trr files has been sped up. (Issue #441) * select_atoms now implicitly ORs multiple values after a keyword for many types of selections (Issue #345) @@ -33,6 +37,8 @@ Changes * util.NamedStream no longer inherits from basestring (Issue #649) Fixes + + * XDR file seeking and telling working again for large files (Issue #677). * ContactAnalysis1 run method now starts at frame index 0 by deafult (Issue #624) * Fixed PrimitivePDBWriter getting atom type column shifted to the right (Issue #639) diff --git a/package/MDAnalysis/lib/formats/src/xdrfile.c b/package/MDAnalysis/lib/formats/src/xdrfile.c index d7eb60ccb1c..6f9b21fca63 100644 --- a/package/MDAnalysis/lib/formats/src/xdrfile.c +++ b/package/MDAnalysis/lib/formats/src/xdrfile.c @@ -41,6 +41,7 @@ #include #include #include +#include /* get fixed-width types if we are using ANSI C99 */ #ifdef HAVE_STDINT_H @@ -2515,8 +2516,8 @@ static int xdrstdio_getlong (XDR *, int32_t *); static int xdrstdio_putlong (XDR *, int32_t *); static int xdrstdio_getbytes (XDR *, char *, unsigned int); static int xdrstdio_putbytes (XDR *, char *, unsigned int); -static unsigned int xdrstdio_getpos (XDR *); -static int xdrstdio_setpos (XDR *, unsigned int, int); +static off_t xdrstdio_getpos (XDR *); +static int xdrstdio_setpos (XDR *, off_t, int); static void xdrstdio_destroy (XDR *); /* @@ -2598,16 +2599,22 @@ xdrstdio_putbytes (XDR *xdrs, char *addr, unsigned int len) } -static unsigned int +static off_t xdrstdio_getpos (XDR *xdrs) { return ftello((FILE *) xdrs->x_private); } static int -xdrstdio_setpos (XDR *xdrs, unsigned int pos, int whence) +xdrstdio_setpos (XDR *xdrs, off_t pos, int whence) { - return fseeko((FILE *) xdrs->x_private, pos, whence) < 0 ? exdrNR : exdrOK; + /* A reason for failure can be filesystem limits on allocation units, + * before the actual off_t overflow (ext3, with a 4K clustersize, + * has a 16TB limit).*/ + /* We return errno relying on the fact that it is never set to 0 on + * success, which means that if an error occurrs it'll never be the same + * as exdrOK, and xdr_seek won't be confused.*/ + return fseeko((FILE *) xdrs->x_private, pos, whence) < 0 ? errno : exdrOK; } @@ -2621,7 +2628,7 @@ int xdr_seek(XDRFILE *xd, int64_t pos, int whence) /* Seeks to position in file */ { int result; - if ((result = xdrstdio_setpos(xd->xdr, (off_t) pos, whence)) != exdrOK) + if ((result = xdrstdio_setpos(xd->xdr, (off_t) pos, whence)) != 0) return result; return exdrOK; diff --git a/package/MDAnalysis/lib/formats/xdrlib.c b/package/MDAnalysis/lib/formats/xdrlib.c index 22fbdf15add..d53d9211cd2 100644 --- a/package/MDAnalysis/lib/formats/xdrlib.c +++ b/package/MDAnalysis/lib/formats/xdrlib.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.23.4 */ +/* Generated by Cython 0.23.2 */ /* BEGIN: Cython Metadata { @@ -18,8 +18,8 @@ ] ], "depends": [ - "/home/max/.virtualenvs/mda-p2/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h", - "/home/max/.virtualenvs/mda-p2/local/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h", + "/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h", + "/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ufuncobject.h", "MDAnalysis/lib/formats/include/trr_seek.h", "MDAnalysis/lib/formats/include/xdrfile.h", "MDAnalysis/lib/formats/include/xdrfile_trr.h", @@ -27,7 +27,7 @@ "MDAnalysis/lib/formats/include/xtc_seek.h" ], "include_dirs": [ - "/home/max/.virtualenvs/mda-p2/local/lib/python2.7/site-packages/numpy/core/include", + "/usr/local/lib/python2.7/dist-packages/numpy/core/include", "MDAnalysis/lib/formats/include", "MDAnalysis/lib/formats" ] @@ -42,7 +42,7 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) #error Cython requires Python 2.6+ or Python 3.2+. #else -#define CYTHON_ABI "0_23_4" +#define CYTHON_ABI "0_23_2" #include #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) @@ -224,7 +224,7 @@ typedef struct { #define CYTHON_RESTRICT #endif #endif -#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) +#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None) #ifndef CYTHON_INLINE #if defined(__GNUC__) @@ -339,10 +339,10 @@ typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; #define __Pyx_sst_abs(value) abs(value) #elif SIZEOF_LONG >= SIZEOF_SIZE_T #define __Pyx_sst_abs(value) labs(value) -#elif defined (_MSC_VER) && defined (_M_X64) - #define __Pyx_sst_abs(value) _abs64(value) #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L #define __Pyx_sst_abs(value) llabs(value) +#elif defined (_MSC_VER) && defined (_M_X64) + #define __Pyx_sst_abs(value) _abs64(value) #elif defined (__GNUC__) #define __Pyx_sst_abs(value) __builtin_llabs(value) #else @@ -611,7 +611,7 @@ typedef volatile __pyx_atomic_int_type __pyx_atomic_int; #endif -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":725 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -620,7 +620,7 @@ typedef volatile __pyx_atomic_int_type __pyx_atomic_int; */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":726 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -629,7 +629,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":727 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":727 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -638,7 +638,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":728 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":728 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -647,7 +647,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":732 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -656,7 +656,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":733 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -665,7 +665,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":734 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":734 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -674,7 +674,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":735 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":735 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -683,7 +683,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":739 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":739 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -692,7 +692,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":740 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -701,7 +701,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":749 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -710,7 +710,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":750 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":750 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -719,7 +719,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":751 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -728,7 +728,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":753 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":753 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -737,7 +737,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":754 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -746,7 +746,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":755 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -755,7 +755,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":757 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":757 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -764,7 +764,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":758 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -773,7 +773,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -782,7 +782,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":761 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":761 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -791,7 +791,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -800,7 +800,7 @@ typedef npy_double __pyx_t_5numpy_double_t; */ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; -/* "MDAnalysis/lib/formats/xdrlib.pyx":86 +/* "MDAnalysis/lib/formats/xdrlib.pyx":88 * np.import_array() * * ctypedef np.float32_t DTYPE_T # <<<<<<<<<<<<<< @@ -838,7 +838,7 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":764 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":764 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -847,7 +847,7 @@ struct __pyx_memoryviewslice_obj; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":765 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":765 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -856,7 +856,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":766 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -865,7 +865,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":768 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":768 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -874,7 +874,7 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; */ typedef npy_cdouble __pyx_t_5numpy_complex_t; -/* "MDAnalysis/lib/formats/xdrlib.pyx":59 +/* "MDAnalysis/lib/formats/xdrlib.pyx":61 * * * cdef enum: # <<<<<<<<<<<<<< @@ -894,10 +894,10 @@ enum { __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EMAGIC = 9, __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EMEMORY = 10, __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EENDOFFILE = 11, - __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_ENOTFOUND = 11 + __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_ENOTFOUND = 12 }; -/* "MDAnalysis/lib/formats/xdrlib.pyx":94 +/* "MDAnalysis/lib/formats/xdrlib.pyx":96 * * * cdef class _XDRFile: # <<<<<<<<<<<<<< @@ -919,7 +919,7 @@ struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile { }; -/* "MDAnalysis/lib/formats/xdrlib.pyx":292 +/* "MDAnalysis/lib/formats/xdrlib.pyx":349 * * * cdef class TRRFile(_XDRFile): # <<<<<<<<<<<<<< @@ -931,7 +931,7 @@ struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib_TRRFile { }; -/* "MDAnalysis/lib/formats/xdrlib.pyx":505 +/* "MDAnalysis/lib/formats/xdrlib.pyx":561 * * * cdef class XTCFile(_XDRFile): # <<<<<<<<<<<<<< @@ -1220,6 +1220,11 @@ static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, long intval, i PyObject_RichCompare(op1, op2, Py_EQ) #endif +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); + +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); + static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, @@ -1297,11 +1302,6 @@ static CYTHON_INLINE PyObject* __Pyx_decode_c_string( const char* encoding, const char* errors, PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); -static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); -static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); - -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); - static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); @@ -1424,12 +1424,16 @@ typedef struct { static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); +static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int64_t(int64_t value); + #if CYTHON_CCOMPLEX #ifdef __cplusplus #define __Pyx_CREAL(z) ((z).real()) @@ -1691,6 +1695,7 @@ static PyObject *__pyx_builtin_IOError; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_RuntimeError; +static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_MemoryError; static PyObject *__pyx_builtin_enumerate; @@ -1726,6 +1731,7 @@ static char __pyx_k_obj[] = "obj"; static char __pyx_k_xyz[] = "xyz"; static char __pyx_k_atol[] = "atol"; static char __pyx_k_base[] = "base"; +static char __pyx_k_keys[] = "keys"; static char __pyx_k_main[] = "__main__"; static char __pyx_k_mode[] = "mode"; static char __pyx_k_name[] = "name"; @@ -1768,9 +1774,11 @@ static char __pyx_k_lambda[] = "_lambda"; static char __pyx_k_memory[] = "memory"; static char __pyx_k_name_2[] = "__name__"; static char __pyx_k_natoms[] = "natoms"; +static char __pyx_k_offset[] = "offset"; static char __pyx_k_string[] = "string"; static char __pyx_k_struct[] = "struct"; static char __pyx_k_unpack[] = "unpack"; +static char __pyx_k_whence[] = "whence"; static char __pyx_k_IOError[] = "IOError"; static char __pyx_k_exc_val[] = "exc_val"; static char __pyx_k_float32[] = "float32"; @@ -1780,6 +1788,10 @@ static char __pyx_k_memview[] = "memview"; static char __pyx_k_offsets[] = "offsets"; static char __pyx_k_os_path[] = "os.path"; static char __pyx_k_Ellipsis[] = "Ellipsis"; +static char __pyx_k_KeyError[] = "KeyError"; +static char __pyx_k_SEEK_CUR[] = "SEEK_CUR"; +static char __pyx_k_SEEK_END[] = "SEEK_END"; +static char __pyx_k_SEEK_SET[] = "SEEK_SET"; static char __pyx_k_TRRFrame[] = "TRRFrame"; static char __pyx_k_XTCFrame[] = "XTCFrame"; static char __pyx_k_allclose[] = "allclose"; @@ -1801,6 +1813,7 @@ static char __pyx_k_MemoryError[] = "MemoryError"; static char __pyx_k_calc_natoms[] = "_calc_natoms"; static char __pyx_k_collections[] = "collections"; static char __pyx_k_compression[] = "compression"; +static char __pyx_k_whence_vals[] = "_whence_vals"; static char __pyx_k_RuntimeError[] = "RuntimeError"; static char __pyx_k_calc_offsets[] = "calc_offsets"; static char __pyx_k_StopIteration[] = "StopIteration"; @@ -1815,7 +1828,7 @@ static char __pyx_k_unsigned_integer[] = "unsigned integer"; static char __pyx_k_XDRLIB_read_error[] = "XDRLIB read error: {}"; static char __pyx_k_ascontiguousarray[] = "ascontiguousarray"; static char __pyx_k_strided_and_direct[] = ""; -static char __pyx_k_File_does_not_exists[] = "File does not exists: {}"; +static char __pyx_k_File_does_not_exist[] = "File does not exist: {}"; static char __pyx_k_strided_and_indirect[] = ""; static char __pyx_k_x_box_step_time_prec[] = "x box step time prec"; static char __pyx_k_contiguous_and_direct[] = ""; @@ -1835,9 +1848,9 @@ static char __pyx_k_Step_may_not_be_zero_axis_d[] = "Step may not be zero (axis static char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; static char __pyx_k_Couldn_t_read_number_of_atoms[] = "Couldn't read number of atoms: {}"; -static char __pyx_k_XDR_seek_failed_error_message[] = "XDR seek failed, error-message={}"; static char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; static char __pyx_k_strided_and_direct_or_indirect[] = ""; +static char __pyx_k_Parameter_whence_must_be_one_of[] = "Parameter 'whence' must be one of {}"; static char __pyx_k_Previous_frames_contained_atoms[] = "Previous frames contained {} atoms. You are trying to write {} atoms."; static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; static char __pyx_k_All_dimensions_preceding_dimensi[] = "All dimensions preceding dimension %d must be indexed and not sliced"; @@ -1863,6 +1876,7 @@ static char __pyx_k_Reached_last_frame_in_XTC_seek_t[] = "Reached last frame in static char __pyx_k_TRR_couldn_t_calculate_offsets_e[] = "TRR couldn't calculate offsets, error={}"; static char __pyx_k_Trying_to_seek_over_max_number_o[] = "Trying to seek over max number of frames"; static char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; +static char __pyx_k_XDR_seek_failed_with_system_errn[] = "XDR seek failed with system errno={}"; static char __pyx_k_XTC_couldn_t_calculate_offsets_e[] = "XTC couldn't calculate offsets, error={}"; static char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; static char __pyx_k_mode_must_be_one_of_r_or_w_you_s[] = "mode must be one of \"r\" or \"w\", you supplied {}"; @@ -1879,7 +1893,7 @@ static PyObject *__pyx_kp_s_Couldn_t_read_number_of_atoms; static PyObject *__pyx_n_s_DTYPE; static PyObject *__pyx_n_s_Ellipsis; static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; -static PyObject *__pyx_kp_s_File_does_not_exists; +static PyObject *__pyx_kp_s_File_does_not_exist; static PyObject *__pyx_kp_s_File_opened_in_mode_Reading_only; static PyObject *__pyx_kp_s_File_opened_in_mode_Writing_only; static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; @@ -1889,6 +1903,7 @@ static PyObject *__pyx_n_s_IndexError; static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; +static PyObject *__pyx_n_s_KeyError; static PyObject *__pyx_n_s_MemoryError; static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; static PyObject *__pyx_kp_s_MemoryView_of_r_object; @@ -1898,6 +1913,7 @@ static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; static PyObject *__pyx_n_b_O; static PyObject *__pyx_n_s_OK; static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; +static PyObject *__pyx_kp_s_Parameter_whence_must_be_one_of; static PyObject *__pyx_kp_s_Previous_frames_contained_atoms; static PyObject *__pyx_kp_s_Previous_frames_contained_box_Yo; static PyObject *__pyx_kp_s_Previous_frames_forces_contained; @@ -1907,6 +1923,9 @@ static PyObject *__pyx_kp_s_Previous_frames_xyz_contained_at; static PyObject *__pyx_kp_s_Reached_last_frame_in_TRR_seek_t; static PyObject *__pyx_kp_s_Reached_last_frame_in_XTC_seek_t; static PyObject *__pyx_n_s_RuntimeError; +static PyObject *__pyx_n_s_SEEK_CUR; +static PyObject *__pyx_n_s_SEEK_END; +static PyObject *__pyx_n_s_SEEK_SET; static PyObject *__pyx_n_s_StopIteration; static PyObject *__pyx_n_s_TRRFrame; static PyObject *__pyx_kp_s_TRR_Read_Error_occured; @@ -1917,7 +1936,7 @@ static PyObject *__pyx_n_s_TypeError; static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; static PyObject *__pyx_n_s_ValueError; static PyObject *__pyx_kp_s_XDRLIB_read_error; -static PyObject *__pyx_kp_s_XDR_seek_failed_error_message; +static PyObject *__pyx_kp_s_XDR_seek_failed_with_system_errn; static PyObject *__pyx_n_s_XTCFrame; static PyObject *__pyx_kp_s_XTC_Read_Error_occured; static PyObject *__pyx_kp_s_XTC_couldn_t_calculate_offsets_e; @@ -1969,6 +1988,7 @@ static PyObject *__pyx_n_s_int64; static PyObject *__pyx_n_s_integer; static PyObject *__pyx_n_s_itemsize; static PyObject *__pyx_kp_s_itemsize_0_for_cython_array; +static PyObject *__pyx_n_s_keys; static PyObject *__pyx_n_s_lambda; static PyObject *__pyx_n_s_magic; static PyObject *__pyx_n_s_main; @@ -1987,6 +2007,7 @@ static PyObject *__pyx_n_s_notfound; static PyObject *__pyx_n_s_np; static PyObject *__pyx_n_s_numpy; static PyObject *__pyx_n_s_obj; +static PyObject *__pyx_n_s_offset; static PyObject *__pyx_n_s_offsets; static PyObject *__pyx_n_s_open; static PyObject *__pyx_n_s_os_path; @@ -2021,6 +2042,8 @@ static PyObject *__pyx_kp_s_unsigned_integer; static PyObject *__pyx_n_s_velocity; static PyObject *__pyx_n_b_w; static PyObject *__pyx_n_s_w; +static PyObject *__pyx_n_s_whence; +static PyObject *__pyx_n_s_whence_vals; static PyObject *__pyx_kp_s_x_box_step_time_prec; static PyObject *__pyx_kp_s_x_v_f_box_step_time_lmbda_hasx_h; static PyObject *__pyx_n_s_xyz; @@ -2034,9 +2057,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_12__iter_ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_14__next__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self); /* proto */ static Py_ssize_t __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_16__len__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self, PyObject *__pyx_v_frame); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20offsets(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22set_offsets(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self, PyObject *__pyx_v_offsets); /* proto */ -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_24tell(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20_bytes_seek(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self, PyObject *__pyx_v_offset, PyObject *__pyx_v_whence); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22offsets(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_24set_offsets(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self, PyObject *__pyx_v_offsets); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_26tell(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_28_bytes_tell(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_7n_atoms___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_5fname___get__(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile__calc_natoms(CYTHON_UNUSED struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib_TRRFile *__pyx_v_self, PyObject *__pyx_v_fname); /* proto */ @@ -2129,7 +2154,7 @@ static PyObject *__pyx_tuple__34; static PyObject *__pyx_tuple__35; static PyObject *__pyx_tuple__36; -/* "MDAnalysis/lib/formats/xdrlib.pyx":130 +/* "MDAnalysis/lib/formats/xdrlib.pyx":132 * cdef int _has_offsets * * def __cinit__(self, fname, mode='r'): # <<<<<<<<<<<<<< @@ -2173,7 +2198,7 @@ static int __pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_1__cinit__(PyOb } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 130; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -2188,7 +2213,7 @@ static int __pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_1__cinit__(PyOb } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 130; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MDAnalysis.lib.formats.xdrlib._XDRFile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); @@ -2214,7 +2239,7 @@ static int __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile___cinit__(struc int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__cinit__", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":131 + /* "MDAnalysis/lib/formats/xdrlib.pyx":133 * * def __cinit__(self, fname, mode='r'): * self.fname = fname # <<<<<<<<<<<<<< @@ -2227,7 +2252,7 @@ static int __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile___cinit__(struc __Pyx_DECREF(__pyx_v_self->fname); __pyx_v_self->fname = __pyx_v_fname; - /* "MDAnalysis/lib/formats/xdrlib.pyx":132 + /* "MDAnalysis/lib/formats/xdrlib.pyx":134 * def __cinit__(self, fname, mode='r'): * self.fname = fname * self.is_open = False # <<<<<<<<<<<<<< @@ -2236,14 +2261,14 @@ static int __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile___cinit__(struc */ __pyx_v_self->is_open = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":133 + /* "MDAnalysis/lib/formats/xdrlib.pyx":135 * self.fname = fname * self.is_open = False * self.open(self.fname, mode) # <<<<<<<<<<<<<< * * def __dealloc__(self): */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 133; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = NULL; __pyx_t_4 = 0; @@ -2257,7 +2282,7 @@ static int __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile___cinit__(struc __pyx_t_4 = 1; } } - __pyx_t_5 = PyTuple_New(2+__pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 133; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(2+__pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); if (__pyx_t_3) { __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3); __pyx_t_3 = NULL; @@ -2268,13 +2293,13 @@ static int __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile___cinit__(struc __Pyx_INCREF(__pyx_v_mode); __Pyx_GIVEREF(__pyx_v_mode); PyTuple_SET_ITEM(__pyx_t_5, 1+__pyx_t_4, __pyx_v_mode); - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 133; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":130 + /* "MDAnalysis/lib/formats/xdrlib.pyx":132 * cdef int _has_offsets * * def __cinit__(self, fname, mode='r'): # <<<<<<<<<<<<<< @@ -2297,7 +2322,7 @@ static int __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile___cinit__(struc return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":135 +/* "MDAnalysis/lib/formats/xdrlib.pyx":137 * self.open(self.fname, mode) * * def __dealloc__(self): # <<<<<<<<<<<<<< @@ -2326,14 +2351,14 @@ static void __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_2__dealloc__(s int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__dealloc__", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":136 + /* "MDAnalysis/lib/formats/xdrlib.pyx":138 * * def __dealloc__(self): * self.close() # <<<<<<<<<<<<<< * * def close(self): */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_2))) { @@ -2346,16 +2371,16 @@ static void __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_2__dealloc__(s } } if (__pyx_t_3) { - __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; } else { - __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":135 + /* "MDAnalysis/lib/formats/xdrlib.pyx":137 * self.open(self.fname, mode) * * def __dealloc__(self): # <<<<<<<<<<<<<< @@ -2374,7 +2399,7 @@ static void __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_2__dealloc__(s __Pyx_RefNannyFinishContext(); } -/* "MDAnalysis/lib/formats/xdrlib.pyx":138 +/* "MDAnalysis/lib/formats/xdrlib.pyx":140 * self.close() * * def close(self): # <<<<<<<<<<<<<< @@ -2397,7 +2422,7 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_5close(Py } static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_4close(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self) { - int __pyx_v_res; + long __pyx_v_res; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -2412,18 +2437,18 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_4close(st int __pyx_clineno = 0; __Pyx_RefNannySetupContext("close", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":146 + /* "MDAnalysis/lib/formats/xdrlib.pyx":148 * If the TRR file can't be closed for some reason * """ - * cdef int res = 1 # <<<<<<<<<<<<<< + * res = 1 # <<<<<<<<<<<<<< * if self.is_open: * res = xdrfile_close(self.xfp) */ __pyx_v_res = 1; - /* "MDAnalysis/lib/formats/xdrlib.pyx":147 + /* "MDAnalysis/lib/formats/xdrlib.pyx":149 * """ - * cdef int res = 1 + * res = 1 * if self.is_open: # <<<<<<<<<<<<<< * res = xdrfile_close(self.xfp) * self.is_open = False @@ -2431,54 +2456,54 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_4close(st __pyx_t_1 = (__pyx_v_self->is_open != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":148 - * cdef int res = 1 + /* "MDAnalysis/lib/formats/xdrlib.pyx":150 + * res = 1 * if self.is_open: * res = xdrfile_close(self.xfp) # <<<<<<<<<<<<<< * self.is_open = False - * if res != 0: + * if res != EOK: */ __pyx_v_res = xdrfile_close(__pyx_v_self->xfp); - /* "MDAnalysis/lib/formats/xdrlib.pyx":149 + /* "MDAnalysis/lib/formats/xdrlib.pyx":151 * if self.is_open: * res = xdrfile_close(self.xfp) * self.is_open = False # <<<<<<<<<<<<<< - * if res != 0: + * if res != EOK: * raise IOError('Couldn\'t close file: {}, Error = XDRLIB-{}'.format( */ __pyx_v_self->is_open = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":150 + /* "MDAnalysis/lib/formats/xdrlib.pyx":152 * res = xdrfile_close(self.xfp) * self.is_open = False - * if res != 0: # <<<<<<<<<<<<<< + * if res != EOK: # <<<<<<<<<<<<<< * raise IOError('Couldn\'t close file: {}, Error = XDRLIB-{}'.format( * self.fname, error_message[res])) */ - __pyx_t_1 = ((__pyx_v_res != 0) != 0); + __pyx_t_1 = ((__pyx_v_res != __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EOK) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":151 + /* "MDAnalysis/lib/formats/xdrlib.pyx":153 * self.is_open = False - * if res != 0: + * if res != EOK: * raise IOError('Couldn\'t close file: {}, Error = XDRLIB-{}'.format( # <<<<<<<<<<<<<< * self.fname, error_message[res])) * # forget old offsets in case we open a different file with the same instance. */ - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Couldn_t_close_file_Error_XDRLIB, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Couldn_t_close_file_Error_XDRLIB, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - /* "MDAnalysis/lib/formats/xdrlib.pyx":152 - * if res != 0: + /* "MDAnalysis/lib/formats/xdrlib.pyx":154 + * if res != EOK: * raise IOError('Couldn\'t close file: {}, Error = XDRLIB-{}'.format( * self.fname, error_message[res])) # <<<<<<<<<<<<<< * # forget old offsets in case we open a different file with the same instance. * self._has_offsets = False */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 152; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 154; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_4, __pyx_v_res, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_4, __pyx_v_res, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_4 = NULL; @@ -2493,7 +2518,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_4close(st __pyx_t_6 = 1; } } - __pyx_t_7 = PyTuple_New(2+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(2+__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_4) { __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_4); __pyx_t_4 = NULL; @@ -2504,49 +2529,49 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_4close(st __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_7, 1+__pyx_t_6, __pyx_t_5); __pyx_t_5 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":151 + /* "MDAnalysis/lib/formats/xdrlib.pyx":153 * self.is_open = False - * if res != 0: + * if res != EOK: * raise IOError('Couldn\'t close file: {}, Error = XDRLIB-{}'.format( # <<<<<<<<<<<<<< * self.fname, error_message[res])) * # forget old offsets in case we open a different file with the same instance. */ - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":150 + /* "MDAnalysis/lib/formats/xdrlib.pyx":152 * res = xdrfile_close(self.xfp) * self.is_open = False - * if res != 0: # <<<<<<<<<<<<<< + * if res != EOK: # <<<<<<<<<<<<<< * raise IOError('Couldn\'t close file: {}, Error = XDRLIB-{}'.format( * self.fname, error_message[res])) */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":147 + /* "MDAnalysis/lib/formats/xdrlib.pyx":149 * """ - * cdef int res = 1 + * res = 1 * if self.is_open: # <<<<<<<<<<<<<< * res = xdrfile_close(self.xfp) * self.is_open = False */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":154 + /* "MDAnalysis/lib/formats/xdrlib.pyx":156 * self.fname, error_message[res])) * # forget old offsets in case we open a different file with the same instance. * self._has_offsets = False # <<<<<<<<<<<<<< @@ -2555,7 +2580,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_4close(st */ __pyx_v_self->_has_offsets = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":155 + /* "MDAnalysis/lib/formats/xdrlib.pyx":157 * # forget old offsets in case we open a different file with the same instance. * self._has_offsets = False * return True # <<<<<<<<<<<<<< @@ -2567,7 +2592,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_4close(st __pyx_r = Py_True; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":138 + /* "MDAnalysis/lib/formats/xdrlib.pyx":140 * self.close() * * def close(self): # <<<<<<<<<<<<<< @@ -2590,7 +2615,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_4close(st return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":157 +/* "MDAnalysis/lib/formats/xdrlib.pyx":159 * return True * * def open(self, fname, mode): # <<<<<<<<<<<<<< @@ -2630,11 +2655,11 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_7open(PyO case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_mode)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("open", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("open", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "open") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "open") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; @@ -2647,7 +2672,7 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_7open(PyO } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("open", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("open", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MDAnalysis.lib.formats.xdrlib._XDRFile.open", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); @@ -2681,7 +2706,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str int __pyx_clineno = 0; __Pyx_RefNannySetupContext("open", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":176 + /* "MDAnalysis/lib/formats/xdrlib.pyx":178 * Couldn't read the file * """ * if self.is_open: # <<<<<<<<<<<<<< @@ -2691,14 +2716,14 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str __pyx_t_1 = (__pyx_v_self->is_open != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":177 + /* "MDAnalysis/lib/formats/xdrlib.pyx":179 * """ * if self.is_open: * self.close() # <<<<<<<<<<<<<< * self.fname = fname * self.n_atoms = 0 */ - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_3))) { @@ -2711,16 +2736,16 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str } } if (__pyx_t_4) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; } else { - __pyx_t_2 = __Pyx_PyObject_CallNoArg(__pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallNoArg(__pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":176 + /* "MDAnalysis/lib/formats/xdrlib.pyx":178 * Couldn't read the file * """ * if self.is_open: # <<<<<<<<<<<<<< @@ -2729,7 +2754,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":178 + /* "MDAnalysis/lib/formats/xdrlib.pyx":180 * if self.is_open: * self.close() * self.fname = fname # <<<<<<<<<<<<<< @@ -2742,7 +2767,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str __Pyx_DECREF(__pyx_v_self->fname); __pyx_v_self->fname = __pyx_v_fname; - /* "MDAnalysis/lib/formats/xdrlib.pyx":179 + /* "MDAnalysis/lib/formats/xdrlib.pyx":181 * self.close() * self.fname = fname * self.n_atoms = 0 # <<<<<<<<<<<<<< @@ -2751,7 +2776,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str */ __pyx_v_self->n_atoms = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":180 + /* "MDAnalysis/lib/formats/xdrlib.pyx":182 * self.fname = fname * self.n_atoms = 0 * self.reached_eof = False # <<<<<<<<<<<<<< @@ -2760,7 +2785,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str */ __pyx_v_self->reached_eof = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":181 + /* "MDAnalysis/lib/formats/xdrlib.pyx":183 * self.n_atoms = 0 * self.reached_eof = False * self.current_frame = 0 # <<<<<<<<<<<<<< @@ -2769,17 +2794,17 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str */ __pyx_v_self->current_frame = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":183 + /* "MDAnalysis/lib/formats/xdrlib.pyx":185 * self.current_frame = 0 * * if mode == 'r': # <<<<<<<<<<<<<< * opening_mode = b'r' * elif mode == 'w': */ - __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_mode, __pyx_n_s_r, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_mode, __pyx_n_s_r, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":184 + /* "MDAnalysis/lib/formats/xdrlib.pyx":186 * * if mode == 'r': * opening_mode = b'r' # <<<<<<<<<<<<<< @@ -2789,7 +2814,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str __Pyx_INCREF(__pyx_n_b_r); __pyx_v_opening_mode = __pyx_n_b_r; - /* "MDAnalysis/lib/formats/xdrlib.pyx":183 + /* "MDAnalysis/lib/formats/xdrlib.pyx":185 * self.current_frame = 0 * * if mode == 'r': # <<<<<<<<<<<<<< @@ -2799,17 +2824,17 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str goto __pyx_L4; } - /* "MDAnalysis/lib/formats/xdrlib.pyx":185 + /* "MDAnalysis/lib/formats/xdrlib.pyx":187 * if mode == 'r': * opening_mode = b'r' * elif mode == 'w': # <<<<<<<<<<<<<< * opening_mode = b'w' * else: */ - __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_mode, __pyx_n_s_w, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_mode, __pyx_n_s_w, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":186 + /* "MDAnalysis/lib/formats/xdrlib.pyx":188 * opening_mode = b'r' * elif mode == 'w': * opening_mode = b'w' # <<<<<<<<<<<<<< @@ -2819,7 +2844,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str __Pyx_INCREF(__pyx_n_b_w); __pyx_v_opening_mode = __pyx_n_b_w; - /* "MDAnalysis/lib/formats/xdrlib.pyx":185 + /* "MDAnalysis/lib/formats/xdrlib.pyx":187 * if mode == 'r': * opening_mode = b'r' * elif mode == 'w': # <<<<<<<<<<<<<< @@ -2829,7 +2854,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str goto __pyx_L4; } - /* "MDAnalysis/lib/formats/xdrlib.pyx":188 + /* "MDAnalysis/lib/formats/xdrlib.pyx":190 * opening_mode = b'w' * else: * raise ValueError('mode must be one of "r" or "w", you ' # <<<<<<<<<<<<<< @@ -2838,14 +2863,14 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str */ /*else*/ { - /* "MDAnalysis/lib/formats/xdrlib.pyx":189 + /* "MDAnalysis/lib/formats/xdrlib.pyx":191 * else: * raise ValueError('mode must be one of "r" or "w", you ' * 'supplied {}'.format(mode)) # <<<<<<<<<<<<<< * self.mode = mode * */ - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_mode_must_be_one_of_r_or_w_you_s, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_mode_must_be_one_of_r_or_w_you_s, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_3))) { @@ -2858,50 +2883,50 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str } } if (!__pyx_t_4) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_v_mode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_v_mode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); } else { - __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4); __pyx_t_4 = NULL; __Pyx_INCREF(__pyx_v_mode); __Pyx_GIVEREF(__pyx_v_mode); PyTuple_SET_ITEM(__pyx_t_5, 0+1, __pyx_v_mode); - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":188 + /* "MDAnalysis/lib/formats/xdrlib.pyx":190 * opening_mode = b'w' * else: * raise ValueError('mode must be one of "r" or "w", you ' # <<<<<<<<<<<<<< * 'supplied {}'.format(mode)) * self.mode = mode */ - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_L4:; - /* "MDAnalysis/lib/formats/xdrlib.pyx":190 + /* "MDAnalysis/lib/formats/xdrlib.pyx":192 * raise ValueError('mode must be one of "r" or "w", you ' * 'supplied {}'.format(mode)) * self.mode = mode # <<<<<<<<<<<<<< * * if self.mode == 'r': */ - if (!(likely(PyString_CheckExact(__pyx_v_mode))||((__pyx_v_mode) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_v_mode)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(PyString_CheckExact(__pyx_v_mode))||((__pyx_v_mode) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_v_mode)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 192; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = __pyx_v_mode; __Pyx_INCREF(__pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); @@ -2910,25 +2935,25 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str __pyx_v_self->mode = ((PyObject*)__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":192 + /* "MDAnalysis/lib/formats/xdrlib.pyx":194 * self.mode = mode * * if self.mode == 'r': # <<<<<<<<<<<<<< * if not exists(self.fname): - * raise IOError('File does not exists: {}'.format(self.fname)) + * raise IOError('File does not exist: {}'.format(self.fname)) */ - __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_self->mode, __pyx_n_s_r, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 192; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_self->mode, __pyx_n_s_r, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_6 = (__pyx_t_1 != 0); if (__pyx_t_6) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":193 + /* "MDAnalysis/lib/formats/xdrlib.pyx":195 * * if self.mode == 'r': * if not exists(self.fname): # <<<<<<<<<<<<<< - * raise IOError('File does not exists: {}'.format(self.fname)) + * raise IOError('File does not exist: {}'.format(self.fname)) * */ - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_exists); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_exists); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_3))) { @@ -2941,33 +2966,33 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str } } if (!__pyx_t_5) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_v_self->fname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_v_self->fname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); } else { - __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5); __pyx_t_5 = NULL; __Pyx_INCREF(__pyx_v_self->fname); __Pyx_GIVEREF(__pyx_v_self->fname); PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_v_self->fname); - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_1 = ((!__pyx_t_6) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":194 + /* "MDAnalysis/lib/formats/xdrlib.pyx":196 * if self.mode == 'r': * if not exists(self.fname): - * raise IOError('File does not exists: {}'.format(self.fname)) # <<<<<<<<<<<<<< + * raise IOError('File does not exist: {}'.format(self.fname)) # <<<<<<<<<<<<<< * * return_code, self.n_atoms = self._calc_natoms(fname); */ - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_does_not_exists, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_does_not_exist, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_3))) { @@ -2980,49 +3005,49 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str } } if (!__pyx_t_4) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_v_self->fname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_v_self->fname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); } else { - __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4); __pyx_t_4 = NULL; __Pyx_INCREF(__pyx_v_self->fname); __Pyx_GIVEREF(__pyx_v_self->fname); PyTuple_SET_ITEM(__pyx_t_5, 0+1, __pyx_v_self->fname); - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":193 + /* "MDAnalysis/lib/formats/xdrlib.pyx":195 * * if self.mode == 'r': * if not exists(self.fname): # <<<<<<<<<<<<<< - * raise IOError('File does not exists: {}'.format(self.fname)) + * raise IOError('File does not exist: {}'.format(self.fname)) * */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":196 - * raise IOError('File does not exists: {}'.format(self.fname)) + /* "MDAnalysis/lib/formats/xdrlib.pyx":198 + * raise IOError('File does not exist: {}'.format(self.fname)) * * return_code, self.n_atoms = self._calc_natoms(fname); # <<<<<<<<<<<<<< * - * if return_code != 0: + * if return_code != EOK: */ - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_calc_natoms); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_calc_natoms); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_3))) { @@ -3035,16 +3060,16 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str } } if (!__pyx_t_5) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_v_fname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_v_fname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); } else { - __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5); __pyx_t_5 = NULL; __Pyx_INCREF(__pyx_v_fname); __Pyx_GIVEREF(__pyx_v_fname); PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_v_fname); - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; } @@ -3059,7 +3084,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str if (unlikely(size != 2)) { if (size > 2) __Pyx_RaiseTooManyValuesError(2); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -3072,15 +3097,15 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str __Pyx_INCREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_4); #else - __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); #endif __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; } else { Py_ssize_t index = -1; - __pyx_t_5 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_7 = Py_TYPE(__pyx_t_5)->tp_iternext; @@ -3088,7 +3113,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str __Pyx_GOTREF(__pyx_t_3); index = 1; __pyx_t_4 = __pyx_t_7(__pyx_t_5); if (unlikely(!__pyx_t_4)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_4); - if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_5), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_5), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_7 = NULL; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; goto __pyx_L8_unpacking_done; @@ -3096,105 +3121,108 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_7 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L8_unpacking_done:; } - __pyx_t_8 = __Pyx_PyInt_As_int(__pyx_t_4); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_PyInt_As_int(__pyx_t_4); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_v_return_code = __pyx_t_3; __pyx_t_3 = 0; __pyx_v_self->n_atoms = __pyx_t_8; - /* "MDAnalysis/lib/formats/xdrlib.pyx":198 + /* "MDAnalysis/lib/formats/xdrlib.pyx":200 * return_code, self.n_atoms = self._calc_natoms(fname); * - * if return_code != 0: # <<<<<<<<<<<<<< + * if return_code != EOK: # <<<<<<<<<<<<<< * raise IOError('XDRLIB read error: {}'.format( * error_message[return_code])) */ - __pyx_t_2 = PyObject_RichCompare(__pyx_v_return_code, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EOK); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_return_code, __pyx_t_2, Py_NE); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":199 + /* "MDAnalysis/lib/formats/xdrlib.pyx":201 * - * if return_code != 0: + * if return_code != EOK: * raise IOError('XDRLIB read error: {}'.format( # <<<<<<<<<<<<<< * error_message[return_code])) * if self.n_atoms <= 0: */ - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_XDRLIB_read_error, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_XDRLIB_read_error, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); - /* "MDAnalysis/lib/formats/xdrlib.pyx":200 - * if return_code != 0: + /* "MDAnalysis/lib/formats/xdrlib.pyx":202 + * if return_code != EOK: * raise IOError('XDRLIB read error: {}'.format( * error_message[return_code])) # <<<<<<<<<<<<<< * if self.n_atoms <= 0: * raise IOError('Couldn\'t read number of atoms: {}'.format( */ - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_5 = PyObject_GetItem(__pyx_t_3, __pyx_v_return_code); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_5 = PyObject_GetItem(__pyx_t_3, __pyx_v_return_code); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_3 = NULL; - if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_4))) { - __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_4); + if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2); if (likely(__pyx_t_3)) { - PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); __Pyx_INCREF(__pyx_t_3); __Pyx_INCREF(function); - __Pyx_DECREF_SET(__pyx_t_4, function); + __Pyx_DECREF_SET(__pyx_t_2, function); } } if (!__pyx_t_3) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(__pyx_t_4); } else { - __pyx_t_9 = PyTuple_New(1+1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyTuple_New(1+1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_3); __pyx_t_3 = NULL; __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_9, 0+1, __pyx_t_5); __pyx_t_5 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_9, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_9, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } - __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":199 + /* "MDAnalysis/lib/formats/xdrlib.pyx":201 * - * if return_code != 0: + * if return_code != EOK: * raise IOError('XDRLIB read error: {}'.format( # <<<<<<<<<<<<<< * error_message[return_code])) * if self.n_atoms <= 0: */ - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); - __Pyx_GIVEREF(__pyx_t_2); - PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); - __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_GIVEREF(__pyx_t_4); + PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4); + __pyx_t_4 = 0; + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_Raise(__pyx_t_4, 0, 0, 0); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":198 + /* "MDAnalysis/lib/formats/xdrlib.pyx":200 * return_code, self.n_atoms = self._calc_natoms(fname); * - * if return_code != 0: # <<<<<<<<<<<<<< + * if return_code != EOK: # <<<<<<<<<<<<<< * raise IOError('XDRLIB read error: {}'.format( * error_message[return_code])) */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":201 + /* "MDAnalysis/lib/formats/xdrlib.pyx":203 * raise IOError('XDRLIB read error: {}'.format( * error_message[return_code])) * if self.n_atoms <= 0: # <<<<<<<<<<<<<< @@ -3204,17 +3232,17 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str __pyx_t_1 = ((__pyx_v_self->n_atoms <= 0) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":202 + /* "MDAnalysis/lib/formats/xdrlib.pyx":204 * error_message[return_code])) * if self.n_atoms <= 0: * raise IOError('Couldn\'t read number of atoms: {}'.format( # <<<<<<<<<<<<<< * fname)) * */ - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Couldn_t_read_number_of_atoms, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Couldn_t_read_number_of_atoms, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); - /* "MDAnalysis/lib/formats/xdrlib.pyx":203 + /* "MDAnalysis/lib/formats/xdrlib.pyx":205 * if self.n_atoms <= 0: * raise IOError('Couldn\'t read number of atoms: {}'.format( * fname)) # <<<<<<<<<<<<<< @@ -3222,51 +3250,51 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str * self.xfp = xdrfile_open(fname, opening_mode) */ __pyx_t_9 = NULL; - if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_4))) { - __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_4); + if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_9 = PyMethod_GET_SELF(__pyx_t_2); if (likely(__pyx_t_9)) { - PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); __Pyx_INCREF(__pyx_t_9); __Pyx_INCREF(function); - __Pyx_DECREF_SET(__pyx_t_4, function); + __Pyx_DECREF_SET(__pyx_t_2, function); } } if (!__pyx_t_9) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_v_fname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_v_fname); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); } else { - __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_9); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_9); __pyx_t_9 = NULL; __Pyx_INCREF(__pyx_v_fname); __Pyx_GIVEREF(__pyx_v_fname); PyTuple_SET_ITEM(__pyx_t_5, 0+1, __pyx_v_fname); - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } - __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":202 + /* "MDAnalysis/lib/formats/xdrlib.pyx":204 * error_message[return_code])) * if self.n_atoms <= 0: * raise IOError('Couldn\'t read number of atoms: {}'.format( # <<<<<<<<<<<<<< * fname)) * */ - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); - __Pyx_GIVEREF(__pyx_t_2); - PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); - __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_GIVEREF(__pyx_t_4); + PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4); + __pyx_t_4 = 0; + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_Raise(__pyx_t_4, 0, 0, 0); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":201 + /* "MDAnalysis/lib/formats/xdrlib.pyx":203 * raise IOError('XDRLIB read error: {}'.format( * error_message[return_code])) * if self.n_atoms <= 0: # <<<<<<<<<<<<<< @@ -3275,27 +3303,27 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":192 + /* "MDAnalysis/lib/formats/xdrlib.pyx":194 * self.mode = mode * * if self.mode == 'r': # <<<<<<<<<<<<<< * if not exists(self.fname): - * raise IOError('File does not exists: {}'.format(self.fname)) + * raise IOError('File does not exist: {}'.format(self.fname)) */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":205 + /* "MDAnalysis/lib/formats/xdrlib.pyx":207 * fname)) * * self.xfp = xdrfile_open(fname, opening_mode) # <<<<<<<<<<<<<< * if self.xfp is NULL: * raise IOError('error opening xtf file: {}'.format(self.fname)) */ - __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_fname); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_11 = __Pyx_PyObject_AsString(__pyx_v_opening_mode); if (unlikely((!__pyx_t_11) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = __Pyx_PyObject_AsString(__pyx_v_fname); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = __Pyx_PyObject_AsString(__pyx_v_opening_mode); if (unlikely((!__pyx_t_11) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_self->xfp = xdrfile_open(__pyx_t_10, __pyx_t_11); - /* "MDAnalysis/lib/formats/xdrlib.pyx":206 + /* "MDAnalysis/lib/formats/xdrlib.pyx":208 * * self.xfp = xdrfile_open(fname, opening_mode) * if self.xfp is NULL: # <<<<<<<<<<<<<< @@ -3305,53 +3333,53 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str __pyx_t_1 = ((__pyx_v_self->xfp == NULL) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":207 + /* "MDAnalysis/lib/formats/xdrlib.pyx":209 * self.xfp = xdrfile_open(fname, opening_mode) * if self.xfp is NULL: * raise IOError('error opening xtf file: {}'.format(self.fname)) # <<<<<<<<<<<<<< * self.is_open = True * */ - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_error_opening_xtf_file, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_error_opening_xtf_file, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __pyx_t_5 = NULL; - if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_4))) { - __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_4); + if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_2))) { + __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_2); if (likely(__pyx_t_5)) { - PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2); __Pyx_INCREF(__pyx_t_5); __Pyx_INCREF(function); - __Pyx_DECREF_SET(__pyx_t_4, function); + __Pyx_DECREF_SET(__pyx_t_2, function); } } if (!__pyx_t_5) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_v_self->fname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_v_self->fname); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); } else { - __pyx_t_9 = PyTuple_New(1+1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyTuple_New(1+1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_5); __pyx_t_5 = NULL; __Pyx_INCREF(__pyx_v_self->fname); __Pyx_GIVEREF(__pyx_v_self->fname); PyTuple_SET_ITEM(__pyx_t_9, 0+1, __pyx_v_self->fname); - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_9, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_9, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } - __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); - __Pyx_GIVEREF(__pyx_t_2); - PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); - __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_GIVEREF(__pyx_t_4); + PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4); + __pyx_t_4 = 0; + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_Raise(__pyx_t_4, 0, 0, 0); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":206 + /* "MDAnalysis/lib/formats/xdrlib.pyx":208 * * self.xfp = xdrfile_open(fname, opening_mode) * if self.xfp is NULL: # <<<<<<<<<<<<<< @@ -3360,7 +3388,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":208 + /* "MDAnalysis/lib/formats/xdrlib.pyx":210 * if self.xfp is NULL: * raise IOError('error opening xtf file: {}'.format(self.fname)) * self.is_open = True # <<<<<<<<<<<<<< @@ -3369,7 +3397,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str */ __pyx_v_self->is_open = 1; - /* "MDAnalysis/lib/formats/xdrlib.pyx":157 + /* "MDAnalysis/lib/formats/xdrlib.pyx":159 * return True * * def open(self, fname, mode): # <<<<<<<<<<<<<< @@ -3396,7 +3424,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":210 +/* "MDAnalysis/lib/formats/xdrlib.pyx":212 * self.is_open = True * * def __enter__(self): # <<<<<<<<<<<<<< @@ -3423,7 +3451,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_8__enter_ __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__enter__", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":212 + /* "MDAnalysis/lib/formats/xdrlib.pyx":214 * def __enter__(self): * """Support context manager""" * return self # <<<<<<<<<<<<<< @@ -3435,7 +3463,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_8__enter_ __pyx_r = ((PyObject *)__pyx_v_self); goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":210 + /* "MDAnalysis/lib/formats/xdrlib.pyx":212 * self.is_open = True * * def __enter__(self): # <<<<<<<<<<<<<< @@ -3450,7 +3478,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_8__enter_ return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":214 +/* "MDAnalysis/lib/formats/xdrlib.pyx":216 * return self * * def __exit__(self, exc_type, exc_val, exc_tb): # <<<<<<<<<<<<<< @@ -3492,16 +3520,16 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_11__exit_ case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_exc_val)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_exc_tb)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__exit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__exit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { goto __pyx_L5_argtuple_error; @@ -3516,7 +3544,7 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_11__exit_ } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MDAnalysis.lib.formats.xdrlib._XDRFile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); @@ -3540,14 +3568,14 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_10__exit_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__exit__", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":216 + /* "MDAnalysis/lib/formats/xdrlib.pyx":218 * def __exit__(self, exc_type, exc_val, exc_tb): * """Support context manager""" * self.close() # <<<<<<<<<<<<<< * # always propagate exceptions forward * return False */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_2))) { @@ -3560,16 +3588,16 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_10__exit_ } } if (__pyx_t_3) { - __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; } else { - __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":218 + /* "MDAnalysis/lib/formats/xdrlib.pyx":220 * self.close() * # always propagate exceptions forward * return False # <<<<<<<<<<<<<< @@ -3581,7 +3609,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_10__exit_ __pyx_r = Py_False; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":214 + /* "MDAnalysis/lib/formats/xdrlib.pyx":216 * return self * * def __exit__(self, exc_type, exc_val, exc_tb): # <<<<<<<<<<<<<< @@ -3602,7 +3630,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_10__exit_ return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":220 +/* "MDAnalysis/lib/formats/xdrlib.pyx":222 * return False * * def __iter__(self): # <<<<<<<<<<<<<< @@ -3636,14 +3664,14 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_12__iter_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__iter__", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":221 + /* "MDAnalysis/lib/formats/xdrlib.pyx":223 * * def __iter__(self): * self.close() # <<<<<<<<<<<<<< * self.open(self.fname, self.mode) * return self */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_2))) { @@ -3656,23 +3684,23 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_12__iter_ } } if (__pyx_t_3) { - __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; } else { - __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":222 + /* "MDAnalysis/lib/formats/xdrlib.pyx":224 * def __iter__(self): * self.close() * self.open(self.fname, self.mode) # <<<<<<<<<<<<<< * return self * */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = NULL; __pyx_t_4 = 0; @@ -3686,7 +3714,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_12__iter_ __pyx_t_4 = 1; } } - __pyx_t_5 = PyTuple_New(2+__pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(2+__pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); if (__pyx_t_3) { __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3); __pyx_t_3 = NULL; @@ -3697,13 +3725,13 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_12__iter_ __Pyx_INCREF(__pyx_v_self->mode); __Pyx_GIVEREF(__pyx_v_self->mode); PyTuple_SET_ITEM(__pyx_t_5, 1+__pyx_t_4, __pyx_v_self->mode); - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":223 + /* "MDAnalysis/lib/formats/xdrlib.pyx":225 * self.close() * self.open(self.fname, self.mode) * return self # <<<<<<<<<<<<<< @@ -3715,7 +3743,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_12__iter_ __pyx_r = ((PyObject *)__pyx_v_self); goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":220 + /* "MDAnalysis/lib/formats/xdrlib.pyx":222 * return False * * def __iter__(self): # <<<<<<<<<<<<<< @@ -3737,7 +3765,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_12__iter_ return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":225 +/* "MDAnalysis/lib/formats/xdrlib.pyx":227 * return self * * def __next__(self): # <<<<<<<<<<<<<< @@ -3770,7 +3798,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_14__next_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__next__", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":226 + /* "MDAnalysis/lib/formats/xdrlib.pyx":228 * * def __next__(self): * if self.reached_eof: # <<<<<<<<<<<<<< @@ -3780,7 +3808,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_14__next_ __pyx_t_1 = (__pyx_v_self->reached_eof != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":227 + /* "MDAnalysis/lib/formats/xdrlib.pyx":229 * def __next__(self): * if self.reached_eof: * raise StopIteration # <<<<<<<<<<<<<< @@ -3788,9 +3816,9 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_14__next_ * */ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 227; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":226 + /* "MDAnalysis/lib/formats/xdrlib.pyx":228 * * def __next__(self): * if self.reached_eof: # <<<<<<<<<<<<<< @@ -3799,7 +3827,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_14__next_ */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":228 + /* "MDAnalysis/lib/formats/xdrlib.pyx":230 * if self.reached_eof: * raise StopIteration * return self.read() # <<<<<<<<<<<<<< @@ -3807,7 +3835,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_14__next_ * def __len__(self): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_read); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_read); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_3))) { @@ -3820,10 +3848,10 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_14__next_ } } if (__pyx_t_4) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; } else { - __pyx_t_2 = __Pyx_PyObject_CallNoArg(__pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallNoArg(__pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -3831,7 +3859,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_14__next_ __pyx_t_2 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":225 + /* "MDAnalysis/lib/formats/xdrlib.pyx":227 * return self * * def __next__(self): # <<<<<<<<<<<<<< @@ -3852,7 +3880,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_14__next_ return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":230 +/* "MDAnalysis/lib/formats/xdrlib.pyx":232 * return self.read() * * def __len__(self): # <<<<<<<<<<<<<< @@ -3885,7 +3913,7 @@ static Py_ssize_t __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_16__len_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__len__", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":231 + /* "MDAnalysis/lib/formats/xdrlib.pyx":233 * * def __len__(self): * if not self.is_open: # <<<<<<<<<<<<<< @@ -3895,20 +3923,20 @@ static Py_ssize_t __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_16__len_ __pyx_t_1 = ((!(__pyx_v_self->is_open != 0)) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":232 + /* "MDAnalysis/lib/formats/xdrlib.pyx":234 * def __len__(self): * if not self.is_open: * raise RuntimeError('No file currently opened') # <<<<<<<<<<<<<< * return self.offsets.size * */ - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":231 + /* "MDAnalysis/lib/formats/xdrlib.pyx":233 * * def __len__(self): * if not self.is_open: # <<<<<<<<<<<<<< @@ -3917,24 +3945,24 @@ static Py_ssize_t __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_16__len_ */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":233 + /* "MDAnalysis/lib/formats/xdrlib.pyx":235 * if not self.is_open: * raise RuntimeError('No file currently opened') * return self.offsets.size # <<<<<<<<<<<<<< * * def seek(self, frame): */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_offsets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_offsets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_4 = __Pyx_PyIndex_AsSsize_t(__pyx_t_3); if (unlikely((__pyx_t_4 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyIndex_AsSsize_t(__pyx_t_3); if (unlikely((__pyx_t_4 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_r = __pyx_t_4; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":230 + /* "MDAnalysis/lib/formats/xdrlib.pyx":232 * return self.read() * * def __len__(self): # <<<<<<<<<<<<<< @@ -3953,7 +3981,7 @@ static Py_ssize_t __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_16__len_ return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":235 +/* "MDAnalysis/lib/formats/xdrlib.pyx":237 * return self.offsets.size * * def seek(self, frame): # <<<<<<<<<<<<<< @@ -3963,7 +3991,7 @@ static Py_ssize_t __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_16__len_ /* Python wrapper */ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_19seek(PyObject *__pyx_v_self, PyObject *__pyx_v_frame); /*proto*/ -static char __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek[] = "Seek to Frame.\n\n Please note if that this function will generate internal file offsets if\n they haven't been set before. For large file this means the first seek\n can be very slow. Later seeks will be very fast\n\n Parameters\n ----------\n frame : int\n seek the file to given frame\n\n Raises\n ------\n RuntimeError\n If you seek for more frames then are available\n "; +static char __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek[] = "Seek to Frame.\n\n Please note that this function will generate internal file offsets if\n they haven't been set before. For large file this means the first seek\n can be very slow. Later seeks will be very fast.\n\n Parameters\n ----------\n frame : int\n seek the file to given frame\n\n Raises\n ------\n IOError\n If you seek for more frames than are available or if the\n seek fails (the low-level system error is reported).\n "; static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_19seek(PyObject *__pyx_v_self, PyObject *__pyx_v_frame) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations @@ -3976,37 +4004,38 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_19seek(Py } static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self, PyObject *__pyx_v_frame) { - int __pyx_v_offset; + int64_t __pyx_v_offset; int __pyx_v_ok; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_t_2; PyObject *__pyx_t_3 = NULL; - int __pyx_t_4; + int64_t __pyx_t_4; PyObject *__pyx_t_5 = NULL; PyObject *__pyx_t_6 = NULL; PyObject *__pyx_t_7 = NULL; + int __pyx_t_8; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("seek", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":253 + /* "MDAnalysis/lib/formats/xdrlib.pyx":256 * """ - * cdef int offset + * cdef int64_t offset * if frame == 0: # <<<<<<<<<<<<<< * offset = 0 * else: */ - __pyx_t_1 = __Pyx_PyInt_EqObjC(__pyx_v_frame, __pyx_int_0, 0, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 253; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyInt_EqObjC(__pyx_v_frame, __pyx_int_0, 0, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 256; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 253; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 256; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_2) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":254 - * cdef int offset + /* "MDAnalysis/lib/formats/xdrlib.pyx":257 + * cdef int64_t offset * if frame == 0: * offset = 0 # <<<<<<<<<<<<<< * else: @@ -4014,9 +4043,9 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek(st */ __pyx_v_offset = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":253 + /* "MDAnalysis/lib/formats/xdrlib.pyx":256 * """ - * cdef int offset + * cdef int64_t offset * if frame == 0: # <<<<<<<<<<<<<< * offset = 0 * else: @@ -4024,181 +4053,162 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek(st goto __pyx_L3; } - /* "MDAnalysis/lib/formats/xdrlib.pyx":256 + /* "MDAnalysis/lib/formats/xdrlib.pyx":259 * offset = 0 * else: * if frame >= self.offsets.size: # <<<<<<<<<<<<<< - * raise RuntimeError('Trying to seek over max number of frames') + * raise IOError('Trying to seek over max number of frames') * offset = self.offsets[frame] */ /*else*/ { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_offsets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 256; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_offsets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 256; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_RichCompare(__pyx_v_frame, __pyx_t_3, Py_GE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 256; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_frame, __pyx_t_3, Py_GE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 256; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_2) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":257 + /* "MDAnalysis/lib/formats/xdrlib.pyx":260 * else: * if frame >= self.offsets.size: - * raise RuntimeError('Trying to seek over max number of frames') # <<<<<<<<<<<<<< + * raise IOError('Trying to seek over max number of frames') # <<<<<<<<<<<<<< * offset = self.offsets[frame] * self.reached_eof = False */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":256 + /* "MDAnalysis/lib/formats/xdrlib.pyx":259 * offset = 0 * else: * if frame >= self.offsets.size: # <<<<<<<<<<<<<< - * raise RuntimeError('Trying to seek over max number of frames') + * raise IOError('Trying to seek over max number of frames') * offset = self.offsets[frame] */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":258 + /* "MDAnalysis/lib/formats/xdrlib.pyx":261 * if frame >= self.offsets.size: - * raise RuntimeError('Trying to seek over max number of frames') + * raise IOError('Trying to seek over max number of frames') * offset = self.offsets[frame] # <<<<<<<<<<<<<< * self.reached_eof = False * ok = xdr_seek(self.xfp, offset, SEEK_SET) */ - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_offsets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 258; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_offsets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_3 = PyObject_GetItem(__pyx_t_1, __pyx_v_frame); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 258; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_3 = PyObject_GetItem(__pyx_t_1, __pyx_v_frame); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_4 = __Pyx_PyInt_As_int(__pyx_t_3); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 258; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_As_int64_t(__pyx_t_3); if (unlikely((__pyx_t_4 == (int64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_v_offset = __pyx_t_4; } __pyx_L3:; - /* "MDAnalysis/lib/formats/xdrlib.pyx":259 - * raise RuntimeError('Trying to seek over max number of frames') + /* "MDAnalysis/lib/formats/xdrlib.pyx":262 + * raise IOError('Trying to seek over max number of frames') * offset = self.offsets[frame] * self.reached_eof = False # <<<<<<<<<<<<<< * ok = xdr_seek(self.xfp, offset, SEEK_SET) - * if ok != 0: + * if ok != EOK: */ __pyx_v_self->reached_eof = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":260 + /* "MDAnalysis/lib/formats/xdrlib.pyx":263 * offset = self.offsets[frame] * self.reached_eof = False * ok = xdr_seek(self.xfp, offset, SEEK_SET) # <<<<<<<<<<<<<< - * if ok != 0: - * raise RuntimeError("XDR seek failed, error-message={}".format( + * if ok != EOK: + * # errno is the direct system error, not from the XDR library. */ __pyx_v_ok = xdr_seek(__pyx_v_self->xfp, __pyx_v_offset, SEEK_SET); - /* "MDAnalysis/lib/formats/xdrlib.pyx":261 + /* "MDAnalysis/lib/formats/xdrlib.pyx":264 * self.reached_eof = False * ok = xdr_seek(self.xfp, offset, SEEK_SET) - * if ok != 0: # <<<<<<<<<<<<<< - * raise RuntimeError("XDR seek failed, error-message={}".format( - * error_message[ok])) + * if ok != EOK: # <<<<<<<<<<<<<< + * # errno is the direct system error, not from the XDR library. + * # errno=22 can be cryptic, since it means a wrong 'whence' */ - __pyx_t_2 = ((__pyx_v_ok != 0) != 0); + __pyx_t_2 = ((__pyx_v_ok != __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EOK) != 0); if (__pyx_t_2) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":262 - * ok = xdr_seek(self.xfp, offset, SEEK_SET) - * if ok != 0: - * raise RuntimeError("XDR seek failed, error-message={}".format( # <<<<<<<<<<<<<< - * error_message[ok])) - * self.current_frame = frame - */ - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_XDR_seek_failed_error_message, __pyx_n_s_format); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - - /* "MDAnalysis/lib/formats/xdrlib.pyx":263 - * if ok != 0: - * raise RuntimeError("XDR seek failed, error-message={}".format( - * error_message[ok])) # <<<<<<<<<<<<<< + /* "MDAnalysis/lib/formats/xdrlib.pyx":270 + * # offset is negative, or if the offset overflows the filesystem + * # limit (ext3 is 16TB, for instance). + * raise IOError("XDR seek failed with system errno={}".format(ok)) # <<<<<<<<<<<<<< * self.current_frame = frame * */ - __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 263; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_XDR_seek_failed_with_system_errn, __pyx_n_s_format); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_ok); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_5, __pyx_v_ok, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; - __Pyx_GOTREF(__pyx_t_6); - __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = NULL; + __pyx_t_6 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_1))) { - __pyx_t_5 = PyMethod_GET_SELF(__pyx_t_1); - if (likely(__pyx_t_5)) { + __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_1); + if (likely(__pyx_t_6)) { PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_1); - __Pyx_INCREF(__pyx_t_5); + __Pyx_INCREF(__pyx_t_6); __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_1, function); } } - if (!__pyx_t_5) { - __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + if (!__pyx_t_6) { + __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_GOTREF(__pyx_t_3); } else { - __pyx_t_7 = PyTuple_New(1+1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(1+1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5); __pyx_t_5 = NULL; - __Pyx_GIVEREF(__pyx_t_6); - PyTuple_SET_ITEM(__pyx_t_7, 0+1, __pyx_t_6); - __pyx_t_6 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_7, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_6); __pyx_t_6 = NULL; + __Pyx_GIVEREF(__pyx_t_5); + PyTuple_SET_ITEM(__pyx_t_7, 0+1, __pyx_t_5); + __pyx_t_5 = 0; + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_7, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - - /* "MDAnalysis/lib/formats/xdrlib.pyx":262 - * ok = xdr_seek(self.xfp, offset, SEEK_SET) - * if ok != 0: - * raise RuntimeError("XDR seek failed, error-message={}".format( # <<<<<<<<<<<<<< - * error_message[ok])) - * self.current_frame = frame - */ - __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":261 + /* "MDAnalysis/lib/formats/xdrlib.pyx":264 * self.reached_eof = False * ok = xdr_seek(self.xfp, offset, SEEK_SET) - * if ok != 0: # <<<<<<<<<<<<<< - * raise RuntimeError("XDR seek failed, error-message={}".format( - * error_message[ok])) + * if ok != EOK: # <<<<<<<<<<<<<< + * # errno is the direct system error, not from the XDR library. + * # errno=22 can be cryptic, since it means a wrong 'whence' */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":264 - * raise RuntimeError("XDR seek failed, error-message={}".format( - * error_message[ok])) + /* "MDAnalysis/lib/formats/xdrlib.pyx":271 + * # limit (ext3 is 16TB, for instance). + * raise IOError("XDR seek failed with system errno={}".format(ok)) * self.current_frame = frame # <<<<<<<<<<<<<< * - * @property + * def _bytes_seek(self, offset, whence="SEEK_SET"): */ - __pyx_t_4 = __Pyx_PyInt_As_int(__pyx_v_frame); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 264; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->current_frame = __pyx_t_4; + __pyx_t_8 = __Pyx_PyInt_As_int(__pyx_v_frame); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_self->current_frame = __pyx_t_8; - /* "MDAnalysis/lib/formats/xdrlib.pyx":235 + /* "MDAnalysis/lib/formats/xdrlib.pyx":237 * return self.offsets.size * * def seek(self, frame): # <<<<<<<<<<<<<< @@ -4223,85 +4233,467 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek(st return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":267 +/* "MDAnalysis/lib/formats/xdrlib.pyx":273 + * self.current_frame = frame * - * @property - * def offsets(self): # <<<<<<<<<<<<<< - * """get byte offsets from current xdr file + * def _bytes_seek(self, offset, whence="SEEK_SET"): # <<<<<<<<<<<<<< + * """Low-level access to the stream repositioning xdr_seek call. * */ /* Python wrapper */ -static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_21offsets(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ -static char __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20offsets[] = "get byte offsets from current xdr file\n\n See Also\n --------\n set_offsets\n "; -static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_21offsets(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("offsets (wrapper)", 0); - __pyx_r = __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20offsets(((struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *)__pyx_v_self)); - - /* function exit code */ - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20offsets(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self) { - PyObject *__pyx_r = NULL; - __Pyx_RefNannyDeclarations - int __pyx_t_1; - PyObject *__pyx_t_2 = NULL; - PyObject *__pyx_t_3 = NULL; - PyObject *__pyx_t_4 = NULL; +static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_21_bytes_seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20_bytes_seek[] = "Low-level access to the stream repositioning xdr_seek call.\n\n Beware that this function will not update :attr:`current_frame`,\n even on a successful seek, and might render the :class:`Reader`\n unstable.\n\n Parameters\n ----------\n offset : int\n move the stream *offset* bytes relative to *whence*\n (can be negative).\n\n whence : str, optional\n must be one of:\n \"SEEK_SET\": *offset* is applied relative to the beginning\n of the file.\n \"SEEK_CUR\": *offset* is applied relative to the current\n position in the stream.\n \"SEEK_END\": *offset* is applied relative to the end of\n the file (a positive *offset* will seek beyond the\n end of the file, without an error)\n\n Raises\n ------\n ValueError\n If *whence* is not one of the expected strings.\n\n IOError\n If the seek fails (the low-level system error is reported).\n "; +static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_21_bytes_seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + PyObject *__pyx_v_offset = 0; + PyObject *__pyx_v_whence = 0; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; - __Pyx_RefNannySetupContext("offsets", 0); - - /* "MDAnalysis/lib/formats/xdrlib.pyx":274 - * set_offsets - * """ - * if not self._has_offsets: # <<<<<<<<<<<<<< - * self._offsets = self.calc_offsets() - * self._has_offsets = True - */ - __pyx_t_1 = ((!(__pyx_v_self->_has_offsets != 0)) != 0); - if (__pyx_t_1) { - - /* "MDAnalysis/lib/formats/xdrlib.pyx":275 - * """ - * if not self._has_offsets: - * self._offsets = self.calc_offsets() # <<<<<<<<<<<<<< - * self._has_offsets = True - * return self._offsets - */ - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_calc_offsets); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = NULL; - if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_3))) { - __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); - if (likely(__pyx_t_4)) { - PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); - __Pyx_INCREF(__pyx_t_4); - __Pyx_INCREF(function); + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("_bytes_seek (wrapper)", 0); + { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_offset,&__pyx_n_s_whence,0}; + PyObject* values[2] = {0,0}; + values[1] = ((PyObject *)__pyx_n_s_SEEK_SET); + if (unlikely(__pyx_kwds)) { + Py_ssize_t kw_args; + const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); + switch (pos_args) { + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + case 0: break; + default: goto __pyx_L5_argtuple_error; + } + kw_args = PyDict_Size(__pyx_kwds); + switch (pos_args) { + case 0: + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_offset)) != 0)) kw_args--; + else goto __pyx_L5_argtuple_error; + case 1: + if (kw_args > 0) { + PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_whence); + if (value) { values[1] = value; kw_args--; } + } + } + if (unlikely(kw_args > 0)) { + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_bytes_seek") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 273; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + } else { + switch (PyTuple_GET_SIZE(__pyx_args)) { + case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + break; + default: goto __pyx_L5_argtuple_error; + } + } + __pyx_v_offset = values[0]; + __pyx_v_whence = values[1]; + } + goto __pyx_L4_argument_unpacking_done; + __pyx_L5_argtuple_error:; + __Pyx_RaiseArgtupleInvalid("_bytes_seek", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 273; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_L3_error:; + __Pyx_AddTraceback("MDAnalysis.lib.formats.xdrlib._XDRFile._bytes_seek", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_RefNannyFinishContext(); + return NULL; + __pyx_L4_argument_unpacking_done:; + __pyx_r = __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20_bytes_seek(((struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *)__pyx_v_self), __pyx_v_offset, __pyx_v_whence); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20_bytes_seek(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self, PyObject *__pyx_v_offset, PyObject *__pyx_v_whence) { + int __pyx_v_whn; + int64_t __pyx_v_offst; + int __pyx_v_ok; + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + PyObject *__pyx_t_5 = NULL; + int __pyx_t_6; + PyObject *__pyx_t_7 = NULL; + PyObject *__pyx_t_8 = NULL; + PyObject *__pyx_t_9 = NULL; + PyObject *__pyx_t_10 = NULL; + PyObject *__pyx_t_11 = NULL; + PyObject *__pyx_t_12 = NULL; + int64_t __pyx_t_13; + int __pyx_t_14; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("_bytes_seek", 0); + + /* "MDAnalysis/lib/formats/xdrlib.pyx":307 + * cdef int64_t offst + * + * try: # <<<<<<<<<<<<<< + * whn = _whence_vals[whence] + * except KeyError: + */ + { + __Pyx_ExceptionSave(&__pyx_t_1, &__pyx_t_2, &__pyx_t_3); + __Pyx_XGOTREF(__pyx_t_1); + __Pyx_XGOTREF(__pyx_t_2); + __Pyx_XGOTREF(__pyx_t_3); + /*try:*/ { + + /* "MDAnalysis/lib/formats/xdrlib.pyx":308 + * + * try: + * whn = _whence_vals[whence] # <<<<<<<<<<<<<< + * except KeyError: + * raise ValueError("Parameter 'whence' must be " + */ + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_whence_vals); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = PyObject_GetItem(__pyx_t_4, __pyx_v_whence); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L3_error;}; + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_6 = __Pyx_PyInt_As_int(__pyx_t_5); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_v_whn = __pyx_t_6; + + /* "MDAnalysis/lib/formats/xdrlib.pyx":307 + * cdef int64_t offst + * + * try: # <<<<<<<<<<<<<< + * whn = _whence_vals[whence] + * except KeyError: + */ + } + __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; + goto __pyx_L10_try_end; + __pyx_L3_error:; + __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; + + /* "MDAnalysis/lib/formats/xdrlib.pyx":309 + * try: + * whn = _whence_vals[whence] + * except KeyError: # <<<<<<<<<<<<<< + * raise ValueError("Parameter 'whence' must be " + * "one of {}".format(tuple(_whence_vals.keys()))) + */ + __pyx_t_6 = PyErr_ExceptionMatches(__pyx_builtin_KeyError); + if (__pyx_t_6) { + __Pyx_AddTraceback("MDAnalysis.lib.formats.xdrlib._XDRFile._bytes_seek", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_4, &__pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_5); + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GOTREF(__pyx_t_7); + + /* "MDAnalysis/lib/formats/xdrlib.pyx":311 + * except KeyError: + * raise ValueError("Parameter 'whence' must be " + * "one of {}".format(tuple(_whence_vals.keys()))) # <<<<<<<<<<<<<< + * offst = offset + * self.reached_eof = False + */ + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Parameter_whence_must_be_one_of, __pyx_n_s_format); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_11 = __Pyx_GetModuleGlobalName(__pyx_n_s_whence_vals); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_11); + __pyx_t_12 = __Pyx_PyObject_GetAttrStr(__pyx_t_11, __pyx_n_s_keys); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_12); + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + __pyx_t_11 = NULL; + if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_12))) { + __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_12); + if (likely(__pyx_t_11)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_12); + __Pyx_INCREF(__pyx_t_11); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_12, function); + } + } + if (__pyx_t_11) { + __pyx_t_10 = __Pyx_PyObject_CallOneArg(__pyx_t_12, __pyx_t_11); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + } else { + __pyx_t_10 = __Pyx_PyObject_CallNoArg(__pyx_t_12); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + } + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; + __pyx_t_12 = PySequence_Tuple(__pyx_t_10); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_12); + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_10 = NULL; + if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_9))) { + __pyx_t_10 = PyMethod_GET_SELF(__pyx_t_9); + if (likely(__pyx_t_10)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_9); + __Pyx_INCREF(__pyx_t_10); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_9, function); + } + } + if (!__pyx_t_10) { + __pyx_t_8 = __Pyx_PyObject_CallOneArg(__pyx_t_9, __pyx_t_12); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; + __Pyx_GOTREF(__pyx_t_8); + } else { + __pyx_t_11 = PyTuple_New(1+1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_11); + __Pyx_GIVEREF(__pyx_t_10); PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_10); __pyx_t_10 = NULL; + __Pyx_GIVEREF(__pyx_t_12); + PyTuple_SET_ITEM(__pyx_t_11, 0+1, __pyx_t_12); + __pyx_t_12 = 0; + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_9, __pyx_t_11, NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; + } + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + + /* "MDAnalysis/lib/formats/xdrlib.pyx":310 + * whn = _whence_vals[whence] + * except KeyError: + * raise ValueError("Parameter 'whence' must be " # <<<<<<<<<<<<<< + * "one of {}".format(tuple(_whence_vals.keys()))) + * offst = offset + */ + __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 310; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_9); + __Pyx_GIVEREF(__pyx_t_8); + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8); + __pyx_t_8 = 0; + __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_9, NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 310; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_Raise(__pyx_t_8, 0, 0, 0); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 310; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + } + goto __pyx_L5_except_error; + __pyx_L5_except_error:; + + /* "MDAnalysis/lib/formats/xdrlib.pyx":307 + * cdef int64_t offst + * + * try: # <<<<<<<<<<<<<< + * whn = _whence_vals[whence] + * except KeyError: + */ + __Pyx_XGIVEREF(__pyx_t_1); + __Pyx_XGIVEREF(__pyx_t_2); + __Pyx_XGIVEREF(__pyx_t_3); + __Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3); + goto __pyx_L1_error; + __pyx_L10_try_end:; + } + + /* "MDAnalysis/lib/formats/xdrlib.pyx":312 + * raise ValueError("Parameter 'whence' must be " + * "one of {}".format(tuple(_whence_vals.keys()))) + * offst = offset # <<<<<<<<<<<<<< + * self.reached_eof = False + * ok = xdr_seek(self.xfp, offst, whn) + */ + __pyx_t_13 = __Pyx_PyInt_As_int64_t(__pyx_v_offset); if (unlikely((__pyx_t_13 == (int64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_offst = __pyx_t_13; + + /* "MDAnalysis/lib/formats/xdrlib.pyx":313 + * "one of {}".format(tuple(_whence_vals.keys()))) + * offst = offset + * self.reached_eof = False # <<<<<<<<<<<<<< + * ok = xdr_seek(self.xfp, offst, whn) + * if ok != EOK: + */ + __pyx_v_self->reached_eof = 0; + + /* "MDAnalysis/lib/formats/xdrlib.pyx":314 + * offst = offset + * self.reached_eof = False + * ok = xdr_seek(self.xfp, offst, whn) # <<<<<<<<<<<<<< + * if ok != EOK: + * # See the comments to seek() for hints on errno meaning. + */ + __pyx_v_ok = xdr_seek(__pyx_v_self->xfp, __pyx_v_offst, __pyx_v_whn); + + /* "MDAnalysis/lib/formats/xdrlib.pyx":315 + * self.reached_eof = False + * ok = xdr_seek(self.xfp, offst, whn) + * if ok != EOK: # <<<<<<<<<<<<<< + * # See the comments to seek() for hints on errno meaning. + * raise IOError("XDR seek failed with system errno={}".format(ok)) + */ + __pyx_t_14 = ((__pyx_v_ok != __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EOK) != 0); + if (__pyx_t_14) { + + /* "MDAnalysis/lib/formats/xdrlib.pyx":317 + * if ok != EOK: + * # See the comments to seek() for hints on errno meaning. + * raise IOError("XDR seek failed with system errno={}".format(ok)) # <<<<<<<<<<<<<< + * + * @property + */ + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_XDR_seek_failed_with_system_errn, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_ok); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __pyx_t_8 = NULL; + if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_4))) { + __pyx_t_8 = PyMethod_GET_SELF(__pyx_t_4); + if (likely(__pyx_t_8)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4); + __Pyx_INCREF(__pyx_t_8); + __Pyx_INCREF(function); + __Pyx_DECREF_SET(__pyx_t_4, function); + } + } + if (!__pyx_t_8) { + __pyx_t_7 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __Pyx_GOTREF(__pyx_t_7); + } else { + __pyx_t_9 = PyTuple_New(1+1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __Pyx_GIVEREF(__pyx_t_8); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8); __pyx_t_8 = NULL; + __Pyx_GIVEREF(__pyx_t_5); + PyTuple_SET_ITEM(__pyx_t_9, 0+1, __pyx_t_5); + __pyx_t_5 = 0; + __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_9, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + } + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __Pyx_GIVEREF(__pyx_t_7); + PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_7); + __pyx_t_7 = 0; + __pyx_t_7 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_7); + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; + __Pyx_Raise(__pyx_t_7, 0, 0, 0); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "MDAnalysis/lib/formats/xdrlib.pyx":315 + * self.reached_eof = False + * ok = xdr_seek(self.xfp, offst, whn) + * if ok != EOK: # <<<<<<<<<<<<<< + * # See the comments to seek() for hints on errno meaning. + * raise IOError("XDR seek failed with system errno={}".format(ok)) + */ + } + + /* "MDAnalysis/lib/formats/xdrlib.pyx":273 + * self.current_frame = frame + * + * def _bytes_seek(self, offset, whence="SEEK_SET"): # <<<<<<<<<<<<<< + * """Low-level access to the stream repositioning xdr_seek call. + * + */ + + /* function exit code */ + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_8); + __Pyx_XDECREF(__pyx_t_9); + __Pyx_XDECREF(__pyx_t_10); + __Pyx_XDECREF(__pyx_t_11); + __Pyx_XDECREF(__pyx_t_12); + __Pyx_AddTraceback("MDAnalysis.lib.formats.xdrlib._XDRFile._bytes_seek", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "MDAnalysis/lib/formats/xdrlib.pyx":320 + * + * @property + * def offsets(self): # <<<<<<<<<<<<<< + * """get byte offsets from current xdr file + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_23offsets(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22offsets[] = "get byte offsets from current xdr file\n\n See Also\n --------\n set_offsets\n "; +static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_23offsets(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("offsets (wrapper)", 0); + __pyx_r = __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22offsets(((struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22offsets(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + int __pyx_t_1; + PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("offsets", 0); + + /* "MDAnalysis/lib/formats/xdrlib.pyx":327 + * set_offsets + * """ + * if not self._has_offsets: # <<<<<<<<<<<<<< + * self._offsets = self.calc_offsets() + * self._has_offsets = True + */ + __pyx_t_1 = ((!(__pyx_v_self->_has_offsets != 0)) != 0); + if (__pyx_t_1) { + + /* "MDAnalysis/lib/formats/xdrlib.pyx":328 + * """ + * if not self._has_offsets: + * self._offsets = self.calc_offsets() # <<<<<<<<<<<<<< + * self._has_offsets = True + * return self._offsets + */ + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_calc_offsets); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = NULL; + if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_3))) { + __pyx_t_4 = PyMethod_GET_SELF(__pyx_t_3); + if (likely(__pyx_t_4)) { + PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_3); + __Pyx_INCREF(__pyx_t_4); + __Pyx_INCREF(function); __Pyx_DECREF_SET(__pyx_t_3, function); } } if (__pyx_t_4) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; } else { - __pyx_t_2 = __Pyx_PyObject_CallNoArg(__pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallNoArg(__pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GIVEREF(__pyx_t_2); __Pyx_GOTREF(__pyx_v_self->_offsets); __Pyx_DECREF(((PyObject *)__pyx_v_self->_offsets)); __pyx_v_self->_offsets = ((PyArrayObject *)__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":276 + /* "MDAnalysis/lib/formats/xdrlib.pyx":329 * if not self._has_offsets: * self._offsets = self.calc_offsets() * self._has_offsets = True # <<<<<<<<<<<<<< @@ -4310,7 +4702,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20offsets */ __pyx_v_self->_has_offsets = 1; - /* "MDAnalysis/lib/formats/xdrlib.pyx":274 + /* "MDAnalysis/lib/formats/xdrlib.pyx":327 * set_offsets * """ * if not self._has_offsets: # <<<<<<<<<<<<<< @@ -4319,7 +4711,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20offsets */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":277 + /* "MDAnalysis/lib/formats/xdrlib.pyx":330 * self._offsets = self.calc_offsets() * self._has_offsets = True * return self._offsets # <<<<<<<<<<<<<< @@ -4331,7 +4723,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20offsets __pyx_r = ((PyObject *)__pyx_v_self->_offsets); goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":267 + /* "MDAnalysis/lib/formats/xdrlib.pyx":320 * * @property * def offsets(self): # <<<<<<<<<<<<<< @@ -4352,7 +4744,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20offsets return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":279 +/* "MDAnalysis/lib/formats/xdrlib.pyx":332 * return self._offsets * * def set_offsets(self, offsets): # <<<<<<<<<<<<<< @@ -4361,20 +4753,20 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20offsets */ /* Python wrapper */ -static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_23set_offsets(PyObject *__pyx_v_self, PyObject *__pyx_v_offsets); /*proto*/ -static char __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22set_offsets[] = "set frame offsets"; -static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_23set_offsets(PyObject *__pyx_v_self, PyObject *__pyx_v_offsets) { +static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_25set_offsets(PyObject *__pyx_v_self, PyObject *__pyx_v_offsets); /*proto*/ +static char __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_24set_offsets[] = "set frame offsets"; +static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_25set_offsets(PyObject *__pyx_v_self, PyObject *__pyx_v_offsets) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("set_offsets (wrapper)", 0); - __pyx_r = __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22set_offsets(((struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *)__pyx_v_self), ((PyObject *)__pyx_v_offsets)); + __pyx_r = __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_24set_offsets(((struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *)__pyx_v_self), ((PyObject *)__pyx_v_offsets)); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22set_offsets(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self, PyObject *__pyx_v_offsets) { +static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_24set_offsets(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self, PyObject *__pyx_v_offsets) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -4383,14 +4775,14 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22set_off int __pyx_clineno = 0; __Pyx_RefNannySetupContext("set_offsets", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":281 + /* "MDAnalysis/lib/formats/xdrlib.pyx":334 * def set_offsets(self, offsets): * """set frame offsets""" * self._offsets = offsets # <<<<<<<<<<<<<< * self._has_offsets = True * */ - if (!(likely(((__pyx_v_offsets) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_offsets, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_v_offsets) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_offsets, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = __pyx_v_offsets; __Pyx_INCREF(__pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); @@ -4399,7 +4791,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22set_off __pyx_v_self->_offsets = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":282 + /* "MDAnalysis/lib/formats/xdrlib.pyx":335 * """set frame offsets""" * self._offsets = offsets * self._has_offsets = True # <<<<<<<<<<<<<< @@ -4408,7 +4800,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22set_off */ __pyx_v_self->_has_offsets = 1; - /* "MDAnalysis/lib/formats/xdrlib.pyx":279 + /* "MDAnalysis/lib/formats/xdrlib.pyx":332 * return self._offsets * * def set_offsets(self, offsets): # <<<<<<<<<<<<<< @@ -4429,7 +4821,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22set_off return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":284 +/* "MDAnalysis/lib/formats/xdrlib.pyx":337 * self._has_offsets = True * * def tell(self): # <<<<<<<<<<<<<< @@ -4438,20 +4830,20 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22set_off */ /* Python wrapper */ -static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_25tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ -static char __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_24tell[] = "Get current frame"; -static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_25tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { +static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_27tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_26tell[] = "Get current frame"; +static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_27tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("tell (wrapper)", 0); - __pyx_r = __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_24tell(((struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *)__pyx_v_self)); + __pyx_r = __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_26tell(((struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *)__pyx_v_self)); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_24tell(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self) { +static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_26tell(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -4460,21 +4852,21 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_24tell(st int __pyx_clineno = 0; __Pyx_RefNannySetupContext("tell", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":286 + /* "MDAnalysis/lib/formats/xdrlib.pyx":339 * def tell(self): * """Get current frame""" * return self.current_frame # <<<<<<<<<<<<<< * - * + * def _bytes_tell(self): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->current_frame); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 286; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->current_frame); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":284 + /* "MDAnalysis/lib/formats/xdrlib.pyx":337 * self._has_offsets = True * * def tell(self): # <<<<<<<<<<<<<< @@ -4493,7 +4885,71 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_24tell(st return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":119 +/* "MDAnalysis/lib/formats/xdrlib.pyx":341 + * return self.current_frame + * + * def _bytes_tell(self): # <<<<<<<<<<<<<< + * """Low-level call to xdr_tell to get current byte offset.""" + * return xdr_tell(self.xfp) + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_29_bytes_tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_28_bytes_tell[] = "Low-level call to xdr_tell to get current byte offset."; +static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_29_bytes_tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { + PyObject *__pyx_r = 0; + __Pyx_RefNannyDeclarations + __Pyx_RefNannySetupContext("_bytes_tell (wrapper)", 0); + __pyx_r = __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_28_bytes_tell(((struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *)__pyx_v_self)); + + /* function exit code */ + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_28_bytes_tell(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile *__pyx_v_self) { + PyObject *__pyx_r = NULL; + __Pyx_RefNannyDeclarations + PyObject *__pyx_t_1 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("_bytes_tell", 0); + + /* "MDAnalysis/lib/formats/xdrlib.pyx":343 + * def _bytes_tell(self): + * """Low-level call to xdr_tell to get current byte offset.""" + * return xdr_tell(self.xfp) # <<<<<<<<<<<<<< + * + * + */ + __Pyx_XDECREF(__pyx_r); + __pyx_t_1 = __Pyx_PyInt_From_int64_t(xdr_tell(__pyx_v_self->xfp)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = __pyx_t_1; + __pyx_t_1 = 0; + goto __pyx_L0; + + /* "MDAnalysis/lib/formats/xdrlib.pyx":341 + * return self.current_frame + * + * def _bytes_tell(self): # <<<<<<<<<<<<<< + * """Low-level call to xdr_tell to get current byte offset.""" + * return xdr_tell(self.xfp) + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_1); + __Pyx_AddTraceback("MDAnalysis.lib.formats.xdrlib._XDRFile._bytes_tell", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = NULL; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "MDAnalysis/lib/formats/xdrlib.pyx":121 * This class can't be initialized use one of the subclasses XTCFile, TRRFile * """ * cdef readonly int n_atoms # <<<<<<<<<<<<<< @@ -4523,7 +4979,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_7n_atoms_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__get__", 0); __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->n_atoms); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_self->n_atoms); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -4540,7 +4996,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_7n_atoms_ return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":123 +/* "MDAnalysis/lib/formats/xdrlib.pyx":125 * cdef int reached_eof * cdef XDRFILE *xfp * cdef readonly fname # <<<<<<<<<<<<<< @@ -4577,7 +5033,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_5fname___ return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":314 +/* "MDAnalysis/lib/formats/xdrlib.pyx":371 * """ * * def _calc_natoms(self, fname): # <<<<<<<<<<<<<< @@ -4612,17 +5068,17 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile__calc_nato int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_calc_natoms", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":316 + /* "MDAnalysis/lib/formats/xdrlib.pyx":373 * def _calc_natoms(self, fname): * cdef int n_atoms * return_code = read_trr_natoms(fname, &n_atoms) # <<<<<<<<<<<<<< * return return_code, n_atoms * */ - __pyx_t_1 = __Pyx_PyObject_AsString(__pyx_v_fname); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_AsString(__pyx_v_fname); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 373; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_return_code = read_trr_natoms(__pyx_t_1, (&__pyx_v_n_atoms)); - /* "MDAnalysis/lib/formats/xdrlib.pyx":317 + /* "MDAnalysis/lib/formats/xdrlib.pyx":374 * cdef int n_atoms * return_code = read_trr_natoms(fname, &n_atoms) * return return_code, n_atoms # <<<<<<<<<<<<<< @@ -4630,11 +5086,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile__calc_nato * */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_return_code); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_return_code); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_atoms); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_atoms); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); @@ -4646,7 +5102,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile__calc_nato __pyx_t_4 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":314 + /* "MDAnalysis/lib/formats/xdrlib.pyx":371 * """ * * def _calc_natoms(self, fname): # <<<<<<<<<<<<<< @@ -4667,7 +5123,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile__calc_nato return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":320 +/* "MDAnalysis/lib/formats/xdrlib.pyx":377 * * * def calc_offsets(self): # <<<<<<<<<<<<<< @@ -4711,7 +5167,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs int __pyx_clineno = 0; __Pyx_RefNannySetupContext("calc_offsets", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":322 + /* "MDAnalysis/lib/formats/xdrlib.pyx":379 * def calc_offsets(self): * """read byte offsets from TRR file directly""" * if not self.is_open: # <<<<<<<<<<<<<< @@ -4721,7 +5177,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs __pyx_t_1 = ((!(__pyx_v_self->__pyx_base.is_open != 0)) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":323 + /* "MDAnalysis/lib/formats/xdrlib.pyx":380 * """read byte offsets from TRR file directly""" * if not self.is_open: * return np.array([]) # <<<<<<<<<<<<<< @@ -4729,12 +5185,12 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs * cdef int est_nframes = 0 */ __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 380; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_array); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_array); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 380; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 380; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_4))) { @@ -4747,17 +5203,17 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs } } if (!__pyx_t_5) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 380; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_GOTREF(__pyx_t_2); } else { - __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 380; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5); __pyx_t_5 = NULL; __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_6, 0+1, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 380; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } @@ -4766,7 +5222,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs __pyx_t_2 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":322 + /* "MDAnalysis/lib/formats/xdrlib.pyx":379 * def calc_offsets(self): * """read byte offsets from TRR file directly""" * if not self.is_open: # <<<<<<<<<<<<<< @@ -4775,7 +5231,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":324 + /* "MDAnalysis/lib/formats/xdrlib.pyx":381 * if not self.is_open: * return np.array([]) * cdef int n_frames = 0 # <<<<<<<<<<<<<< @@ -4784,7 +5240,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs */ __pyx_v_n_frames = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":325 + /* "MDAnalysis/lib/formats/xdrlib.pyx":382 * return np.array([]) * cdef int n_frames = 0 * cdef int est_nframes = 0 # <<<<<<<<<<<<<< @@ -4793,55 +5249,55 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs */ __pyx_v_est_nframes = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":326 + /* "MDAnalysis/lib/formats/xdrlib.pyx":383 * cdef int n_frames = 0 * cdef int est_nframes = 0 * cdef int64_t* offsets = NULL # <<<<<<<<<<<<<< * ok = read_trr_n_frames(self.fname, &n_frames, &est_nframes, &offsets); - * if ok != 0: + * if ok != EOK: */ __pyx_v_offsets = NULL; - /* "MDAnalysis/lib/formats/xdrlib.pyx":327 + /* "MDAnalysis/lib/formats/xdrlib.pyx":384 * cdef int est_nframes = 0 * cdef int64_t* offsets = NULL * ok = read_trr_n_frames(self.fname, &n_frames, &est_nframes, &offsets); # <<<<<<<<<<<<<< - * if ok != 0: + * if ok != EOK: * raise RuntimeError("TRR couldn't calculate offsets, error={}".format( */ - __pyx_t_7 = __Pyx_PyObject_AsString(__pyx_v_self->__pyx_base.fname); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_AsString(__pyx_v_self->__pyx_base.fname); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 384; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_ok = read_trr_n_frames(__pyx_t_7, (&__pyx_v_n_frames), (&__pyx_v_est_nframes), (&__pyx_v_offsets)); - /* "MDAnalysis/lib/formats/xdrlib.pyx":328 + /* "MDAnalysis/lib/formats/xdrlib.pyx":385 * cdef int64_t* offsets = NULL * ok = read_trr_n_frames(self.fname, &n_frames, &est_nframes, &offsets); - * if ok != 0: # <<<<<<<<<<<<<< + * if ok != EOK: # <<<<<<<<<<<<<< * raise RuntimeError("TRR couldn't calculate offsets, error={}".format( * error_message[ok])) */ - __pyx_t_1 = ((__pyx_v_ok != 0) != 0); + __pyx_t_1 = ((__pyx_v_ok != __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EOK) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":329 + /* "MDAnalysis/lib/formats/xdrlib.pyx":386 * ok = read_trr_n_frames(self.fname, &n_frames, &est_nframes, &offsets); - * if ok != 0: + * if ok != EOK: * raise RuntimeError("TRR couldn't calculate offsets, error={}".format( # <<<<<<<<<<<<<< * error_message[ok])) * # the read_xtc_n_frames allocates memory for the offsets with an */ - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_TRR_couldn_t_calculate_offsets_e, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_TRR_couldn_t_calculate_offsets_e, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - /* "MDAnalysis/lib/formats/xdrlib.pyx":330 - * if ok != 0: + /* "MDAnalysis/lib/formats/xdrlib.pyx":387 + * if ok != EOK: * raise RuntimeError("TRR couldn't calculate offsets, error={}".format( * error_message[ok])) # <<<<<<<<<<<<<< * # the read_xtc_n_frames allocates memory for the offsets with an * # overestimation. This number is saved in est_nframes and we need to */ - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_6, __pyx_v_ok, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_6, __pyx_v_ok, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_6 = NULL; @@ -4855,93 +5311,93 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs } } if (!__pyx_t_6) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_GOTREF(__pyx_t_2); } else { - __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_6); __pyx_t_6 = NULL; __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_5, 0+1, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":329 + /* "MDAnalysis/lib/formats/xdrlib.pyx":386 * ok = read_trr_n_frames(self.fname, &n_frames, &est_nframes, &offsets); - * if ok != 0: + * if ok != EOK: * raise RuntimeError("TRR couldn't calculate offsets, error={}".format( # <<<<<<<<<<<<<< * error_message[ok])) * # the read_xtc_n_frames allocates memory for the offsets with an */ - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":328 + /* "MDAnalysis/lib/formats/xdrlib.pyx":385 * cdef int64_t* offsets = NULL * ok = read_trr_n_frames(self.fname, &n_frames, &est_nframes, &offsets); - * if ok != 0: # <<<<<<<<<<<<<< + * if ok != EOK: # <<<<<<<<<<<<<< * raise RuntimeError("TRR couldn't calculate offsets, error={}".format( * error_message[ok])) */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":335 + /* "MDAnalysis/lib/formats/xdrlib.pyx":392 * # tell the new numpy array about the whole allocated memory to avoid * # memory leaks. * cdef np.ndarray dims = np.array([est_nframes], dtype=np.int64) # <<<<<<<<<<<<<< * # this handles freeing the allocated memory correctly. * cdef np.ndarray nd_offsets = ptr_to_ndarray( offsets, dims, np.NPY_INT64) */ - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_array); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_array); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_est_nframes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_est_nframes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_5 = PyList_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyList_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_2); PyList_SET_ITEM(__pyx_t_5, 0, __pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_int64); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_int64); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_dims = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":337 + /* "MDAnalysis/lib/formats/xdrlib.pyx":394 * cdef np.ndarray dims = np.array([est_nframes], dtype=np.int64) * # this handles freeing the allocated memory correctly. * cdef np.ndarray nd_offsets = ptr_to_ndarray( offsets, dims, np.NPY_INT64) # <<<<<<<<<<<<<< @@ -4949,14 +5405,14 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs * */ __pyx_t_8 = __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_int64_t(((PyObject *)__pyx_v_dims)); - if (unlikely(!__pyx_t_8.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_6 = ((PyObject *)__pyx_f_10MDAnalysis_3lib_7formats_11cython_util_ptr_to_ndarray(((void *)__pyx_v_offsets), __pyx_t_8, NPY_INT64)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_t_8.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = ((PyObject *)__pyx_f_10MDAnalysis_3lib_7formats_11cython_util_ptr_to_ndarray(((void *)__pyx_v_offsets), __pyx_t_8, NPY_INT64)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __PYX_XDEC_MEMVIEW(&__pyx_t_8, 1); __pyx_v_nd_offsets = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":338 + /* "MDAnalysis/lib/formats/xdrlib.pyx":395 * # this handles freeing the allocated memory correctly. * cdef np.ndarray nd_offsets = ptr_to_ndarray( offsets, dims, np.NPY_INT64) * return nd_offsets[:n_frames] # <<<<<<<<<<<<<< @@ -4964,13 +5420,13 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs * def read(self): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_6 = __Pyx_PyObject_GetSlice(((PyObject *)__pyx_v_nd_offsets), 0, __pyx_v_n_frames, NULL, NULL, NULL, 0, 1, 1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetSlice(((PyObject *)__pyx_v_nd_offsets), 0, __pyx_v_n_frames, NULL, NULL, NULL, 0, 1, 1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_r = __pyx_t_6; __pyx_t_6 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":320 + /* "MDAnalysis/lib/formats/xdrlib.pyx":377 * * * def calc_offsets(self): # <<<<<<<<<<<<<< @@ -4996,7 +5452,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":340 +/* "MDAnalysis/lib/formats/xdrlib.pyx":397 * return nd_offsets[:n_frames] * * def read(self): # <<<<<<<<<<<<<< @@ -5019,7 +5475,7 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_5read(PyOb } static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib_TRRFile *__pyx_v_self) { - int __pyx_v_return_code; + long __pyx_v_return_code; int __pyx_v_step; int __pyx_v_has_prop; float __pyx_v_time; @@ -5048,7 +5504,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru int __pyx_clineno = 0; __Pyx_RefNannySetupContext("read", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":358 + /* "MDAnalysis/lib/formats/xdrlib.pyx":415 * Something must have happened reading the file * """ * if self.reached_eof: # <<<<<<<<<<<<<< @@ -5058,20 +5514,20 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru __pyx_t_1 = (__pyx_v_self->__pyx_base.reached_eof != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":359 + /* "MDAnalysis/lib/formats/xdrlib.pyx":416 * """ * if self.reached_eof: * raise RuntimeError('Reached last frame in TRR, seek to 0') # <<<<<<<<<<<<<< * if not self.is_open: * raise RuntimeError('No file opened') */ - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":358 + /* "MDAnalysis/lib/formats/xdrlib.pyx":415 * Something must have happened reading the file * """ * if self.reached_eof: # <<<<<<<<<<<<<< @@ -5080,7 +5536,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":360 + /* "MDAnalysis/lib/formats/xdrlib.pyx":417 * if self.reached_eof: * raise RuntimeError('Reached last frame in TRR, seek to 0') * if not self.is_open: # <<<<<<<<<<<<<< @@ -5090,20 +5546,20 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru __pyx_t_1 = ((!(__pyx_v_self->__pyx_base.is_open != 0)) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":361 + /* "MDAnalysis/lib/formats/xdrlib.pyx":418 * raise RuntimeError('Reached last frame in TRR, seek to 0') * if not self.is_open: * raise RuntimeError('No file opened') # <<<<<<<<<<<<<< * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. Reading only allow ' */ - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":360 + /* "MDAnalysis/lib/formats/xdrlib.pyx":417 * if self.reached_eof: * raise RuntimeError('Reached last frame in TRR, seek to 0') * if not self.is_open: # <<<<<<<<<<<<<< @@ -5112,50 +5568,50 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":362 + /* "MDAnalysis/lib/formats/xdrlib.pyx":419 * if not self.is_open: * raise RuntimeError('No file opened') * if self.mode != 'r': # <<<<<<<<<<<<<< * raise RuntimeError('File opened in mode: {}. Reading only allow ' * 'in mode "r"'.format('self.mode')) */ - __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_self->__pyx_base.mode, __pyx_n_s_r, Py_NE)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_self->__pyx_base.mode, __pyx_n_s_r, Py_NE)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = (__pyx_t_1 != 0); if (__pyx_t_3) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":364 + /* "MDAnalysis/lib/formats/xdrlib.pyx":421 * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. Reading only allow ' * 'in mode "r"'.format('self.mode')) # <<<<<<<<<<<<<< * - * cdef int return_code = 1 + * return_code = 1 */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_opened_in_mode_Reading_only, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_opened_in_mode_Reading_only, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":363 + /* "MDAnalysis/lib/formats/xdrlib.pyx":420 * raise RuntimeError('No file opened') * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. Reading only allow ' # <<<<<<<<<<<<<< * 'in mode "r"'.format('self.mode')) * */ - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":362 + /* "MDAnalysis/lib/formats/xdrlib.pyx":419 * if not self.is_open: * raise RuntimeError('No file opened') * if self.mode != 'r': # <<<<<<<<<<<<<< @@ -5164,26 +5620,26 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":366 + /* "MDAnalysis/lib/formats/xdrlib.pyx":423 * 'in mode "r"'.format('self.mode')) * - * cdef int return_code = 1 # <<<<<<<<<<<<<< + * return_code = 1 # <<<<<<<<<<<<<< * cdef int step = 0 * cdef int has_prop = 0 */ __pyx_v_return_code = 1; - /* "MDAnalysis/lib/formats/xdrlib.pyx":367 + /* "MDAnalysis/lib/formats/xdrlib.pyx":424 * - * cdef int return_code = 1 + * return_code = 1 * cdef int step = 0 # <<<<<<<<<<<<<< * cdef int has_prop = 0 * cdef float time = 0 */ __pyx_v_step = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":368 - * cdef int return_code = 1 + /* "MDAnalysis/lib/formats/xdrlib.pyx":425 + * return_code = 1 * cdef int step = 0 * cdef int has_prop = 0 # <<<<<<<<<<<<<< * cdef float time = 0 @@ -5191,7 +5647,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ __pyx_v_has_prop = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":369 + /* "MDAnalysis/lib/formats/xdrlib.pyx":426 * cdef int step = 0 * cdef int has_prop = 0 * cdef float time = 0 # <<<<<<<<<<<<<< @@ -5200,7 +5656,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ __pyx_v_time = 0.0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":370 + /* "MDAnalysis/lib/formats/xdrlib.pyx":427 * cdef int has_prop = 0 * cdef float time = 0 * cdef float lmbda = 0 # <<<<<<<<<<<<<< @@ -5209,23 +5665,23 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ __pyx_v_lmbda = 0.0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":374 + /* "MDAnalysis/lib/formats/xdrlib.pyx":431 * # Use this instead of memviews here to make sure that references are * # counted correctly * cdef np.ndarray xyz = np.empty((self.n_atoms, DIMS), dtype=DTYPE) # <<<<<<<<<<<<<< * cdef np.ndarray velocity = np.empty((self.n_atoms, DIMS), dtype=DTYPE) * cdef np.ndarray forces = np.empty((self.n_atoms, DIMS), dtype=DTYPE) */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_empty); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_empty); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_4); @@ -5233,43 +5689,43 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5); __pyx_t_4 = 0; __pyx_t_5 = 0; - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_xyz = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":375 + /* "MDAnalysis/lib/formats/xdrlib.pyx":432 * # counted correctly * cdef np.ndarray xyz = np.empty((self.n_atoms, DIMS), dtype=DTYPE) * cdef np.ndarray velocity = np.empty((self.n_atoms, DIMS), dtype=DTYPE) # <<<<<<<<<<<<<< * cdef np.ndarray forces = np.empty((self.n_atoms, DIMS), dtype=DTYPE) * cdef np.ndarray box = np.empty((DIMS, DIMS), dtype=DTYPE) */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_empty); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_empty); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4); @@ -5277,43 +5733,43 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_5); __pyx_t_4 = 0; __pyx_t_5 = 0; - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_velocity = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":376 + /* "MDAnalysis/lib/formats/xdrlib.pyx":433 * cdef np.ndarray xyz = np.empty((self.n_atoms, DIMS), dtype=DTYPE) * cdef np.ndarray velocity = np.empty((self.n_atoms, DIMS), dtype=DTYPE) * cdef np.ndarray forces = np.empty((self.n_atoms, DIMS), dtype=DTYPE) # <<<<<<<<<<<<<< * cdef np.ndarray box = np.empty((DIMS, DIMS), dtype=DTYPE) * */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_empty); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_empty); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_4); @@ -5321,43 +5777,43 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5); __pyx_t_4 = 0; __pyx_t_5 = 0; - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_forces = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":377 + /* "MDAnalysis/lib/formats/xdrlib.pyx":434 * cdef np.ndarray velocity = np.empty((self.n_atoms, DIMS), dtype=DTYPE) * cdef np.ndarray forces = np.empty((self.n_atoms, DIMS), dtype=DTYPE) * cdef np.ndarray box = np.empty((DIMS, DIMS), dtype=DTYPE) # <<<<<<<<<<<<<< * * return_code = read_trr(self.xfp, self.n_atoms, &step, */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_empty); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_empty); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4); @@ -5365,27 +5821,27 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_5); __pyx_t_4 = 0; __pyx_t_5 = 0; - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_box = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":379 + /* "MDAnalysis/lib/formats/xdrlib.pyx":436 * cdef np.ndarray box = np.empty((DIMS, DIMS), dtype=DTYPE) * * return_code = read_trr(self.xfp, self.n_atoms, &step, # <<<<<<<<<<<<<< @@ -5394,7 +5850,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ __pyx_v_return_code = read_trr(__pyx_v_self->__pyx_base.xfp, __pyx_v_self->__pyx_base.n_atoms, ((int *)(&__pyx_v_step)), (&__pyx_v_time), (&__pyx_v_lmbda), ((float (*)[3])__pyx_v_box->data), ((rvec *)__pyx_v_xyz->data), ((rvec *)__pyx_v_velocity->data), ((rvec *)__pyx_v_forces->data), ((int *)(&__pyx_v_has_prop))); - /* "MDAnalysis/lib/formats/xdrlib.pyx":388 + /* "MDAnalysis/lib/formats/xdrlib.pyx":445 * # results in an integer error while reading. I tried it also with trr * # produced by different codes (Gromacs, ...). * if return_code != EOK and return_code != EENDOFFILE \ # <<<<<<<<<<<<<< @@ -5404,7 +5860,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru switch (__pyx_v_return_code) { case __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EOK: - /* "MDAnalysis/lib/formats/xdrlib.pyx":389 + /* "MDAnalysis/lib/formats/xdrlib.pyx":446 * # produced by different codes (Gromacs, ...). * if return_code != EOK and return_code != EENDOFFILE \ * and return_code != EINTEGER: # <<<<<<<<<<<<<< @@ -5414,7 +5870,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru case __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EENDOFFILE: case __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EINTEGER: - /* "MDAnalysis/lib/formats/xdrlib.pyx":388 + /* "MDAnalysis/lib/formats/xdrlib.pyx":445 * # results in an integer error while reading. I tried it also with trr * # produced by different codes (Gromacs, ...). * if return_code != EOK and return_code != EENDOFFILE \ # <<<<<<<<<<<<<< @@ -5429,26 +5885,26 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru } if (__pyx_t_3) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":390 + /* "MDAnalysis/lib/formats/xdrlib.pyx":447 * if return_code != EOK and return_code != EENDOFFILE \ * and return_code != EINTEGER: * raise RuntimeError('TRR Read Error occured: {}'.format( # <<<<<<<<<<<<<< * error_message[return_code])) * */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_TRR_Read_Error_occured, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_TRR_Read_Error_occured, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - /* "MDAnalysis/lib/formats/xdrlib.pyx":391 + /* "MDAnalysis/lib/formats/xdrlib.pyx":448 * and return_code != EINTEGER: * raise RuntimeError('TRR Read Error occured: {}'.format( * error_message[return_code])) # <<<<<<<<<<<<<< * * # In a trr the integer error seems to indicate that the file is ending. */ - __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_5, __pyx_v_return_code, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_5, __pyx_v_return_code, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_5 = NULL; @@ -5462,42 +5918,42 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru } } if (!__pyx_t_5) { - __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_GOTREF(__pyx_t_4); } else { - __pyx_t_7 = PyTuple_New(1+1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(1+1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5); __pyx_t_5 = NULL; __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_7, 0+1, __pyx_t_6); __pyx_t_6 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_7, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_7, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":390 + /* "MDAnalysis/lib/formats/xdrlib.pyx":447 * if return_code != EOK and return_code != EENDOFFILE \ * and return_code != EINTEGER: * raise RuntimeError('TRR Read Error occured: {}'.format( # <<<<<<<<<<<<<< * error_message[return_code])) * */ - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":388 + /* "MDAnalysis/lib/formats/xdrlib.pyx":445 * # results in an integer error while reading. I tried it also with trr * # produced by different codes (Gromacs, ...). * if return_code != EOK and return_code != EENDOFFILE \ # <<<<<<<<<<<<<< @@ -5506,9 +5962,9 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":396 + /* "MDAnalysis/lib/formats/xdrlib.pyx":453 * # There might be corrupted files where this is a legitimate error. But - * # then we just can't read it and stop there which is not to bad. + * # then we just can't read it and stop there which is not too bad. * if return_code == EENDOFFILE or return_code == EINTEGER: # <<<<<<<<<<<<<< * self.reached_eof = True * raise StopIteration @@ -5517,8 +5973,8 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru case __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EENDOFFILE: case __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EINTEGER: - /* "MDAnalysis/lib/formats/xdrlib.pyx":397 - * # then we just can't read it and stop there which is not to bad. + /* "MDAnalysis/lib/formats/xdrlib.pyx":454 + * # then we just can't read it and stop there which is not too bad. * if return_code == EENDOFFILE or return_code == EINTEGER: * self.reached_eof = True # <<<<<<<<<<<<<< * raise StopIteration @@ -5526,7 +5982,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ __pyx_v_self->__pyx_base.reached_eof = 1; - /* "MDAnalysis/lib/formats/xdrlib.pyx":398 + /* "MDAnalysis/lib/formats/xdrlib.pyx":455 * if return_code == EENDOFFILE or return_code == EINTEGER: * self.reached_eof = True * raise StopIteration # <<<<<<<<<<<<<< @@ -5534,11 +5990,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru * if return_code == EOK: */ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":396 + /* "MDAnalysis/lib/formats/xdrlib.pyx":453 * # There might be corrupted files where this is a legitimate error. But - * # then we just can't read it and stop there which is not to bad. + * # then we just can't read it and stop there which is not too bad. * if return_code == EENDOFFILE or return_code == EINTEGER: # <<<<<<<<<<<<<< * self.reached_eof = True * raise StopIteration @@ -5547,7 +6003,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru default: break; } - /* "MDAnalysis/lib/formats/xdrlib.pyx":400 + /* "MDAnalysis/lib/formats/xdrlib.pyx":457 * raise StopIteration * * if return_code == EOK: # <<<<<<<<<<<<<< @@ -5557,7 +6013,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru __pyx_t_3 = ((__pyx_v_return_code == __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EOK) != 0); if (__pyx_t_3) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":401 + /* "MDAnalysis/lib/formats/xdrlib.pyx":458 * * if return_code == EOK: * self.current_frame += 1 # <<<<<<<<<<<<<< @@ -5566,7 +6022,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ __pyx_v_self->__pyx_base.current_frame = (__pyx_v_self->__pyx_base.current_frame + 1); - /* "MDAnalysis/lib/formats/xdrlib.pyx":400 + /* "MDAnalysis/lib/formats/xdrlib.pyx":457 * raise StopIteration * * if return_code == EOK: # <<<<<<<<<<<<<< @@ -5575,55 +6031,55 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":403 + /* "MDAnalysis/lib/formats/xdrlib.pyx":460 * self.current_frame += 1 * * has_x = bool(has_prop & HASX) # <<<<<<<<<<<<<< * has_v = bool(has_prop & HASV) * has_f = bool(has_prop & HASF) */ - __pyx_t_4 = __Pyx_PyInt_From_int((__pyx_v_has_prop & __pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_HASX)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int((__pyx_v_has_prop & __pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_HASX)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyBool_FromLong((!(!__pyx_t_3))); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyBool_FromLong((!(!__pyx_t_3))); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_v_has_x = __pyx_t_4; __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":404 + /* "MDAnalysis/lib/formats/xdrlib.pyx":461 * * has_x = bool(has_prop & HASX) * has_v = bool(has_prop & HASV) # <<<<<<<<<<<<<< * has_f = bool(has_prop & HASF) * return TRRFrame(xyz, velocity, forces, box, step, time, lmbda, */ - __pyx_t_4 = __Pyx_PyInt_From_int((__pyx_v_has_prop & __pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_HASV)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int((__pyx_v_has_prop & __pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_HASV)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyBool_FromLong((!(!__pyx_t_3))); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyBool_FromLong((!(!__pyx_t_3))); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_v_has_v = __pyx_t_4; __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":405 + /* "MDAnalysis/lib/formats/xdrlib.pyx":462 * has_x = bool(has_prop & HASX) * has_v = bool(has_prop & HASV) * has_f = bool(has_prop & HASF) # <<<<<<<<<<<<<< * return TRRFrame(xyz, velocity, forces, box, step, time, lmbda, * has_x, has_v, has_f) */ - __pyx_t_4 = __Pyx_PyInt_From_int((__pyx_v_has_prop & __pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_HASF)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int((__pyx_v_has_prop & __pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_HASF)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyBool_FromLong((!(!__pyx_t_3))); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyBool_FromLong((!(!__pyx_t_3))); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_v_has_f = __pyx_t_4; __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":406 + /* "MDAnalysis/lib/formats/xdrlib.pyx":463 * has_v = bool(has_prop & HASV) * has_f = bool(has_prop & HASF) * return TRRFrame(xyz, velocity, forces, box, step, time, lmbda, # <<<<<<<<<<<<<< @@ -5631,16 +6087,16 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru * */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_TRRFrame); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 406; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_TRRFrame); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_step); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 406; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_step); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_6 = PyFloat_FromDouble(__pyx_v_time); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 406; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_v_time); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_5 = PyFloat_FromDouble(__pyx_v_lmbda); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 406; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyFloat_FromDouble(__pyx_v_lmbda); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "MDAnalysis/lib/formats/xdrlib.pyx":407 + /* "MDAnalysis/lib/formats/xdrlib.pyx":464 * has_f = bool(has_prop & HASF) * return TRRFrame(xyz, velocity, forces, box, step, time, lmbda, * has_x, has_v, has_f) # <<<<<<<<<<<<<< @@ -5659,7 +6115,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru __pyx_t_9 = 1; } } - __pyx_t_10 = PyTuple_New(10+__pyx_t_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 406; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyTuple_New(10+__pyx_t_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); if (__pyx_t_8) { __Pyx_GIVEREF(__pyx_t_8); PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_8); __pyx_t_8 = NULL; @@ -5694,7 +6150,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru __pyx_t_7 = 0; __pyx_t_6 = 0; __pyx_t_5 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_10, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 406; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_10, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -5702,7 +6158,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru __pyx_t_4 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":340 + /* "MDAnalysis/lib/formats/xdrlib.pyx":397 * return nd_offsets[:n_frames] * * def read(self): # <<<<<<<<<<<<<< @@ -5734,7 +6190,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":409 +/* "MDAnalysis/lib/formats/xdrlib.pyx":466 * has_x, has_v, has_f) * * def write(self, xyz, velocity, forces, box, int step, float time, # <<<<<<<<<<<<<< @@ -5786,41 +6242,41 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_7write(PyO case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_velocity)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_forces)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_box)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_step)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_time)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 6: if (likely((values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_lambda)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 7: if (likely((values[7] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_natoms)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 7); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 7); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "write") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "write") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 8) { goto __pyx_L5_argtuple_error; @@ -5838,14 +6294,14 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_7write(PyO __pyx_v_velocity = values[1]; __pyx_v_forces = values[2]; __pyx_v_box = values[3]; - __pyx_v_step = __Pyx_PyInt_As_int(values[4]); if (unlikely((__pyx_v_step == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_time = __pyx_PyFloat_AsFloat(values[5]); if (unlikely((__pyx_v_time == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v__lambda = __pyx_PyFloat_AsFloat(values[6]); if (unlikely((__pyx_v__lambda == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_natoms = __Pyx_PyInt_As_int(values[7]); if (unlikely((__pyx_v_natoms == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_step = __Pyx_PyInt_As_int(values[4]); if (unlikely((__pyx_v_step == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_time = __pyx_PyFloat_AsFloat(values[5]); if (unlikely((__pyx_v_time == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v__lambda = __pyx_PyFloat_AsFloat(values[6]); if (unlikely((__pyx_v__lambda == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_natoms = __Pyx_PyInt_As_int(values[7]); if (unlikely((__pyx_v_natoms == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MDAnalysis.lib.formats.xdrlib.TRRFile.write", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); @@ -5885,50 +6341,50 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str int __pyx_clineno = 0; __Pyx_RefNannySetupContext("write", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":435 + /* "MDAnalysis/lib/formats/xdrlib.pyx":492 * The arguments do not match with previous saved frames. * """ * if self.mode != 'w' : # <<<<<<<<<<<<<< * raise RuntimeError('File opened in mode: {}. Writing only allow ' * 'in mode "w"'.format('self.mode')) */ - __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_self->__pyx_base.mode, __pyx_n_s_w, Py_NE)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 435; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_self->__pyx_base.mode, __pyx_n_s_w, Py_NE)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":437 + /* "MDAnalysis/lib/formats/xdrlib.pyx":494 * if self.mode != 'w' : * raise RuntimeError('File opened in mode: {}. Writing only allow ' * 'in mode "w"'.format('self.mode')) # <<<<<<<<<<<<<< * * cdef float* xyz_ptr = NULL */ - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_opened_in_mode_Writing_only, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_opened_in_mode_Writing_only, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":436 + /* "MDAnalysis/lib/formats/xdrlib.pyx":493 * """ * if self.mode != 'w' : * raise RuntimeError('File opened in mode: {}. Writing only allow ' # <<<<<<<<<<<<<< * 'in mode "w"'.format('self.mode')) * */ - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":435 + /* "MDAnalysis/lib/formats/xdrlib.pyx":492 * The arguments do not match with previous saved frames. * """ * if self.mode != 'w' : # <<<<<<<<<<<<<< @@ -5937,7 +6393,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":439 + /* "MDAnalysis/lib/formats/xdrlib.pyx":496 * 'in mode "w"'.format('self.mode')) * * cdef float* xyz_ptr = NULL # <<<<<<<<<<<<<< @@ -5946,7 +6402,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ __pyx_v_xyz_ptr = NULL; - /* "MDAnalysis/lib/formats/xdrlib.pyx":440 + /* "MDAnalysis/lib/formats/xdrlib.pyx":497 * * cdef float* xyz_ptr = NULL * cdef float* velocity_ptr = NULL # <<<<<<<<<<<<<< @@ -5955,7 +6411,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ __pyx_v_velocity_ptr = NULL; - /* "MDAnalysis/lib/formats/xdrlib.pyx":441 + /* "MDAnalysis/lib/formats/xdrlib.pyx":498 * cdef float* xyz_ptr = NULL * cdef float* velocity_ptr = NULL * cdef float* forces_ptr = NULL # <<<<<<<<<<<<<< @@ -5964,7 +6420,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ __pyx_v_forces_ptr = NULL; - /* "MDAnalysis/lib/formats/xdrlib.pyx":451 + /* "MDAnalysis/lib/formats/xdrlib.pyx":508 * cdef np.ndarray forces_helper * * if xyz is not None: # <<<<<<<<<<<<<< @@ -5975,39 +6431,39 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_1 = (__pyx_t_2 != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":452 + /* "MDAnalysis/lib/formats/xdrlib.pyx":509 * * if xyz is not None: * xyz_helper = np.ascontiguousarray(xyz, dtype=DTYPE) # <<<<<<<<<<<<<< * xyz_ptr = xyz_helper.data * if velocity is not None: */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_ascontiguousarray); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_ascontiguousarray); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_INCREF(__pyx_v_xyz); __Pyx_GIVEREF(__pyx_v_xyz); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_xyz); - __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_xyz_helper = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":453 + /* "MDAnalysis/lib/formats/xdrlib.pyx":510 * if xyz is not None: * xyz_helper = np.ascontiguousarray(xyz, dtype=DTYPE) * xyz_ptr = xyz_helper.data # <<<<<<<<<<<<<< @@ -6016,7 +6472,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ __pyx_v_xyz_ptr = ((float *)__pyx_v_xyz_helper->data); - /* "MDAnalysis/lib/formats/xdrlib.pyx":451 + /* "MDAnalysis/lib/formats/xdrlib.pyx":508 * cdef np.ndarray forces_helper * * if xyz is not None: # <<<<<<<<<<<<<< @@ -6025,7 +6481,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":454 + /* "MDAnalysis/lib/formats/xdrlib.pyx":511 * xyz_helper = np.ascontiguousarray(xyz, dtype=DTYPE) * xyz_ptr = xyz_helper.data * if velocity is not None: # <<<<<<<<<<<<<< @@ -6036,39 +6492,39 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":455 + /* "MDAnalysis/lib/formats/xdrlib.pyx":512 * xyz_ptr = xyz_helper.data * if velocity is not None: * velocity_helper = np.ascontiguousarray(velocity, dtype=DTYPE) # <<<<<<<<<<<<<< * velocity_ptr = velocity_helper.data * if forces is not None: */ - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_ascontiguousarray); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_ascontiguousarray); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_INCREF(__pyx_v_velocity); __Pyx_GIVEREF(__pyx_v_velocity); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_velocity); - __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_dtype, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_dtype, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_6, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_6, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_velocity_helper = ((PyArrayObject *)__pyx_t_3); __pyx_t_3 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":456 + /* "MDAnalysis/lib/formats/xdrlib.pyx":513 * if velocity is not None: * velocity_helper = np.ascontiguousarray(velocity, dtype=DTYPE) * velocity_ptr = velocity_helper.data # <<<<<<<<<<<<<< @@ -6077,7 +6533,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ __pyx_v_velocity_ptr = ((float *)__pyx_v_velocity_helper->data); - /* "MDAnalysis/lib/formats/xdrlib.pyx":454 + /* "MDAnalysis/lib/formats/xdrlib.pyx":511 * xyz_helper = np.ascontiguousarray(xyz, dtype=DTYPE) * xyz_ptr = xyz_helper.data * if velocity is not None: # <<<<<<<<<<<<<< @@ -6086,7 +6542,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":457 + /* "MDAnalysis/lib/formats/xdrlib.pyx":514 * velocity_helper = np.ascontiguousarray(velocity, dtype=DTYPE) * velocity_ptr = velocity_helper.data * if forces is not None: # <<<<<<<<<<<<<< @@ -6097,39 +6553,39 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_1 = (__pyx_t_2 != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":458 + /* "MDAnalysis/lib/formats/xdrlib.pyx":515 * velocity_ptr = velocity_helper.data * if forces is not None: * forces_helper = np.ascontiguousarray(forces, dtype=DTYPE) # <<<<<<<<<<<<<< * forces_ptr = forces_helper.data * */ - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_ascontiguousarray); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_ascontiguousarray); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_v_forces); __Pyx_GIVEREF(__pyx_v_forces); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_forces); - __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_3, __pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_3, __pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_forces_helper = ((PyArrayObject *)__pyx_t_5); __pyx_t_5 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":459 + /* "MDAnalysis/lib/formats/xdrlib.pyx":516 * if forces is not None: * forces_helper = np.ascontiguousarray(forces, dtype=DTYPE) * forces_ptr = forces_helper.data # <<<<<<<<<<<<<< @@ -6138,7 +6594,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ __pyx_v_forces_ptr = ((float *)__pyx_v_forces_helper->data); - /* "MDAnalysis/lib/formats/xdrlib.pyx":457 + /* "MDAnalysis/lib/formats/xdrlib.pyx":514 * velocity_helper = np.ascontiguousarray(velocity, dtype=DTYPE) * velocity_ptr = velocity_helper.data * if forces is not None: # <<<<<<<<<<<<<< @@ -6147,39 +6603,39 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":461 + /* "MDAnalysis/lib/formats/xdrlib.pyx":518 * forces_ptr = forces_helper.data * * cdef np.ndarray box_helper = np.ascontiguousarray(box, dtype=DTYPE) # <<<<<<<<<<<<<< * cdef float* box_ptr = box_helper.data * */ - __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_ascontiguousarray); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_ascontiguousarray); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_INCREF(__pyx_v_box); __Pyx_GIVEREF(__pyx_v_box); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_box); - __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_box_helper = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":462 + /* "MDAnalysis/lib/formats/xdrlib.pyx":519 * * cdef np.ndarray box_helper = np.ascontiguousarray(box, dtype=DTYPE) * cdef float* box_ptr = box_helper.data # <<<<<<<<<<<<<< @@ -6188,7 +6644,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ __pyx_v_box_ptr = ((float *)__pyx_v_box_helper->data); - /* "MDAnalysis/lib/formats/xdrlib.pyx":464 + /* "MDAnalysis/lib/formats/xdrlib.pyx":521 * cdef float* box_ptr = box_helper.data * * if self.current_frame == 0: # <<<<<<<<<<<<<< @@ -6198,14 +6654,14 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_1 = ((__pyx_v_self->__pyx_base.current_frame == 0) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":465 + /* "MDAnalysis/lib/formats/xdrlib.pyx":522 * * if self.current_frame == 0: * self.box = box # <<<<<<<<<<<<<< * self.n_atoms = natoms * else: */ - if (!(likely(((__pyx_v_box) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_box, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_v_box) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_box, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = __pyx_v_box; __Pyx_INCREF(__pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); @@ -6214,7 +6670,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_v_self->__pyx_base.box = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":466 + /* "MDAnalysis/lib/formats/xdrlib.pyx":523 * if self.current_frame == 0: * self.box = box * self.n_atoms = natoms # <<<<<<<<<<<<<< @@ -6223,7 +6679,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ __pyx_v_self->__pyx_base.n_atoms = __pyx_v_natoms; - /* "MDAnalysis/lib/formats/xdrlib.pyx":464 + /* "MDAnalysis/lib/formats/xdrlib.pyx":521 * cdef float* box_ptr = box_helper.data * * if self.current_frame == 0: # <<<<<<<<<<<<<< @@ -6233,7 +6689,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str goto __pyx_L7; } - /* "MDAnalysis/lib/formats/xdrlib.pyx":468 + /* "MDAnalysis/lib/formats/xdrlib.pyx":525 * self.n_atoms = natoms * else: * if self.n_atoms != natoms: # <<<<<<<<<<<<<< @@ -6244,26 +6700,26 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_1 = ((__pyx_v_self->__pyx_base.n_atoms != __pyx_v_natoms) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":470 + /* "MDAnalysis/lib/formats/xdrlib.pyx":527 * if self.n_atoms != natoms: * raise ValueError('Previous frames contained {} atoms. You ' * 'are trying to write {} atoms.'.format( # <<<<<<<<<<<<<< * self.n_atoms, natoms)) * if xyz is not None and self.n_atoms != xyz.shape[0]: */ - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_contained_atoms, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_contained_atoms, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 527; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - /* "MDAnalysis/lib/formats/xdrlib.pyx":471 + /* "MDAnalysis/lib/formats/xdrlib.pyx":528 * raise ValueError('Previous frames contained {} atoms. You ' * 'are trying to write {} atoms.'.format( * self.n_atoms, natoms)) # <<<<<<<<<<<<<< * if xyz is not None and self.n_atoms != xyz.shape[0]: * raise ValueError('Previous frames xyz contained {} atoms. You ' */ - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 528; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_natoms); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_natoms); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 528; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_t_7 = NULL; __pyx_t_8 = 0; @@ -6277,7 +6733,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_8 = 1; } } - __pyx_t_9 = PyTuple_New(2+__pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyTuple_New(2+__pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 527; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); if (__pyx_t_7) { __Pyx_GIVEREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_7); __pyx_t_7 = NULL; @@ -6288,31 +6744,31 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str PyTuple_SET_ITEM(__pyx_t_9, 1+__pyx_t_8, __pyx_t_6); __pyx_t_5 = 0; __pyx_t_6 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_9, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_9, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 527; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":469 + /* "MDAnalysis/lib/formats/xdrlib.pyx":526 * else: * if self.n_atoms != natoms: * raise ValueError('Previous frames contained {} atoms. You ' # <<<<<<<<<<<<<< * 'are trying to write {} atoms.'.format( * self.n_atoms, natoms)) */ - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":468 + /* "MDAnalysis/lib/formats/xdrlib.pyx":525 * self.n_atoms = natoms * else: * if self.n_atoms != natoms: # <<<<<<<<<<<<<< @@ -6321,7 +6777,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":472 + /* "MDAnalysis/lib/formats/xdrlib.pyx":529 * 'are trying to write {} atoms.'.format( * self.n_atoms, natoms)) * if xyz is not None and self.n_atoms != xyz.shape[0]: # <<<<<<<<<<<<<< @@ -6335,44 +6791,44 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_1 = __pyx_t_10; goto __pyx_L10_bool_binop_done; } - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 529; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_xyz, __pyx_n_s_shape); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_xyz, __pyx_n_s_shape); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 529; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_9 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_9 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 529; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyObject_RichCompare(__pyx_t_4, __pyx_t_9, Py_NE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_RichCompare(__pyx_t_4, __pyx_t_9, Py_NE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 529; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 529; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_1 = __pyx_t_10; __pyx_L10_bool_binop_done:; if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":474 + /* "MDAnalysis/lib/formats/xdrlib.pyx":531 * if xyz is not None and self.n_atoms != xyz.shape[0]: * raise ValueError('Previous frames xyz contained {} atoms. You ' * 'are trying to write {} atoms.'.format( # <<<<<<<<<<<<<< * self.n_atoms, xyz.shape[0])) * if velocity is not None and self.n_atoms != velocity.shape[0]: */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_xyz_contained_at, __pyx_n_s_format); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_xyz_contained_at, __pyx_n_s_format); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - /* "MDAnalysis/lib/formats/xdrlib.pyx":475 + /* "MDAnalysis/lib/formats/xdrlib.pyx":532 * raise ValueError('Previous frames xyz contained {} atoms. You ' * 'are trying to write {} atoms.'.format( * self.n_atoms, xyz.shape[0])) # <<<<<<<<<<<<<< * if velocity is not None and self.n_atoms != velocity.shape[0]: * raise ValueError('Previous frames velocity contained {} atoms. You ' */ - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 475; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 532; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_xyz, __pyx_n_s_shape); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 475; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_xyz, __pyx_n_s_shape); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 532; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_6, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 475; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_6, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 532; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_6 = NULL; @@ -6387,7 +6843,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_8 = 1; } } - __pyx_t_7 = PyTuple_New(2+__pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(2+__pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (__pyx_t_6) { __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_6); __pyx_t_6 = NULL; @@ -6398,31 +6854,31 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str PyTuple_SET_ITEM(__pyx_t_7, 1+__pyx_t_8, __pyx_t_5); __pyx_t_4 = 0; __pyx_t_5 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_9, __pyx_t_7, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_9, __pyx_t_7, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":473 + /* "MDAnalysis/lib/formats/xdrlib.pyx":530 * self.n_atoms, natoms)) * if xyz is not None and self.n_atoms != xyz.shape[0]: * raise ValueError('Previous frames xyz contained {} atoms. You ' # <<<<<<<<<<<<<< * 'are trying to write {} atoms.'.format( * self.n_atoms, xyz.shape[0])) */ - __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 530; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_9, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_9, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 530; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 530; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":472 + /* "MDAnalysis/lib/formats/xdrlib.pyx":529 * 'are trying to write {} atoms.'.format( * self.n_atoms, natoms)) * if xyz is not None and self.n_atoms != xyz.shape[0]: # <<<<<<<<<<<<<< @@ -6431,7 +6887,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":476 + /* "MDAnalysis/lib/formats/xdrlib.pyx":533 * 'are trying to write {} atoms.'.format( * self.n_atoms, xyz.shape[0])) * if velocity is not None and self.n_atoms != velocity.shape[0]: # <<<<<<<<<<<<<< @@ -6445,44 +6901,44 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_1 = __pyx_t_2; goto __pyx_L13_bool_binop_done; } - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 533; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_velocity, __pyx_n_s_shape); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_velocity, __pyx_n_s_shape); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 533; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_9, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_9, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_9 = PyObject_RichCompare(__pyx_t_3, __pyx_t_7, Py_NE); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyObject_RichCompare(__pyx_t_3, __pyx_t_7, Py_NE); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 533; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 533; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_t_1 = __pyx_t_2; __pyx_L13_bool_binop_done:; if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":478 + /* "MDAnalysis/lib/formats/xdrlib.pyx":535 * if velocity is not None and self.n_atoms != velocity.shape[0]: * raise ValueError('Previous frames velocity contained {} atoms. You ' * 'are trying to write {} atoms.'.format( # <<<<<<<<<<<<<< * self.n_atoms, velocity.shape[0])) * if forces is not None and self.n_atoms != forces.shape[0]: */ - __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_velocity_contain, __pyx_n_s_format); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 478; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_velocity_contain, __pyx_n_s_format); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - /* "MDAnalysis/lib/formats/xdrlib.pyx":479 + /* "MDAnalysis/lib/formats/xdrlib.pyx":536 * raise ValueError('Previous frames velocity contained {} atoms. You ' * 'are trying to write {} atoms.'.format( * self.n_atoms, velocity.shape[0])) # <<<<<<<<<<<<<< * if forces is not None and self.n_atoms != forces.shape[0]: * raise ValueError('Previous frames forces contained {} atoms. You ' */ - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_velocity, __pyx_n_s_shape); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_velocity, __pyx_n_s_shape); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_5, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_5, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_5 = NULL; @@ -6497,7 +6953,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_8 = 1; } } - __pyx_t_6 = PyTuple_New(2+__pyx_t_8); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 478; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(2+__pyx_t_8); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); if (__pyx_t_5) { __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5); __pyx_t_5 = NULL; @@ -6508,31 +6964,31 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str PyTuple_SET_ITEM(__pyx_t_6, 1+__pyx_t_8, __pyx_t_4); __pyx_t_3 = 0; __pyx_t_4 = 0; - __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_7, __pyx_t_6, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 478; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_7, __pyx_t_6, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":477 + /* "MDAnalysis/lib/formats/xdrlib.pyx":534 * self.n_atoms, xyz.shape[0])) * if velocity is not None and self.n_atoms != velocity.shape[0]: * raise ValueError('Previous frames velocity contained {} atoms. You ' # <<<<<<<<<<<<<< * 'are trying to write {} atoms.'.format( * self.n_atoms, velocity.shape[0])) */ - __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 534; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_GIVEREF(__pyx_t_9); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_9); __pyx_t_9 = 0; - __pyx_t_9 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_7, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_7, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 534; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_Raise(__pyx_t_9, 0, 0, 0); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 534; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":476 + /* "MDAnalysis/lib/formats/xdrlib.pyx":533 * 'are trying to write {} atoms.'.format( * self.n_atoms, xyz.shape[0])) * if velocity is not None and self.n_atoms != velocity.shape[0]: # <<<<<<<<<<<<<< @@ -6541,7 +6997,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":480 + /* "MDAnalysis/lib/formats/xdrlib.pyx":537 * 'are trying to write {} atoms.'.format( * self.n_atoms, velocity.shape[0])) * if forces is not None and self.n_atoms != forces.shape[0]: # <<<<<<<<<<<<<< @@ -6555,44 +7011,44 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_1 = __pyx_t_10; goto __pyx_L16_bool_binop_done; } - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_forces, __pyx_n_s_shape); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_forces, __pyx_n_s_shape); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_7, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_7, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - __pyx_t_7 = PyObject_RichCompare(__pyx_t_9, __pyx_t_6, Py_NE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyObject_RichCompare(__pyx_t_9, __pyx_t_6, Py_NE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_1 = __pyx_t_10; __pyx_L16_bool_binop_done:; if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":482 + /* "MDAnalysis/lib/formats/xdrlib.pyx":539 * if forces is not None and self.n_atoms != forces.shape[0]: * raise ValueError('Previous frames forces contained {} atoms. You ' * 'are trying to write {} atoms.'.format( # <<<<<<<<<<<<<< * self.n_atoms, forces.shape[0])) * if not np.allclose(self.box, box, rtol=0, atol=1e-2): */ - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_forces_contained, __pyx_n_s_format); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_forces_contained, __pyx_n_s_format); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - /* "MDAnalysis/lib/formats/xdrlib.pyx":483 + /* "MDAnalysis/lib/formats/xdrlib.pyx":540 * raise ValueError('Previous frames forces contained {} atoms. You ' * 'are trying to write {} atoms.'.format( * self.n_atoms, forces.shape[0])) # <<<<<<<<<<<<<< * if not np.allclose(self.box, box, rtol=0, atol=1e-2): * raise ValueError('Previous frames contained {} box. You ' */ - __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 540; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_forces, __pyx_n_s_shape); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_forces, __pyx_n_s_shape); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 540; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_4, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_4, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_4 = NULL; @@ -6607,7 +7063,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_8 = 1; } } - __pyx_t_5 = PyTuple_New(2+__pyx_t_8); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(2+__pyx_t_8); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); if (__pyx_t_4) { __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4); __pyx_t_4 = NULL; @@ -6618,31 +7074,31 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str PyTuple_SET_ITEM(__pyx_t_5, 1+__pyx_t_8, __pyx_t_3); __pyx_t_9 = 0; __pyx_t_3 = 0; - __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":481 + /* "MDAnalysis/lib/formats/xdrlib.pyx":538 * self.n_atoms, velocity.shape[0])) * if forces is not None and self.n_atoms != forces.shape[0]: * raise ValueError('Previous frames forces contained {} atoms. You ' # <<<<<<<<<<<<<< * 'are trying to write {} atoms.'.format( * self.n_atoms, forces.shape[0])) */ - __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_7); __pyx_t_7 = 0; - __pyx_t_7 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_Raise(__pyx_t_7, 0, 0, 0); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":480 + /* "MDAnalysis/lib/formats/xdrlib.pyx":537 * 'are trying to write {} atoms.'.format( * self.n_atoms, velocity.shape[0])) * if forces is not None and self.n_atoms != forces.shape[0]: # <<<<<<<<<<<<<< @@ -6651,19 +7107,19 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":484 + /* "MDAnalysis/lib/formats/xdrlib.pyx":541 * 'are trying to write {} atoms.'.format( * self.n_atoms, forces.shape[0])) * if not np.allclose(self.box, box, rtol=0, atol=1e-2): # <<<<<<<<<<<<<< * raise ValueError('Previous frames contained {} box. You ' * 'are trying to write {} box.'.format( */ - __pyx_t_7 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 541; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_allclose); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_allclose); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 541; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 541; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_INCREF(((PyObject *)__pyx_v_self->__pyx_base.box)); __Pyx_GIVEREF(((PyObject *)__pyx_v_self->__pyx_base.box)); @@ -6671,36 +7127,36 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __Pyx_INCREF(__pyx_v_box); __Pyx_GIVEREF(__pyx_v_box); PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_v_box); - __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 541; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_rtol, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_atol, __pyx_float_1eneg_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_7, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_rtol, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 541; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_atol, __pyx_float_1eneg_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 541; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_7, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 541; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 541; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_10 = ((!__pyx_t_1) != 0); if (__pyx_t_10) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":486 + /* "MDAnalysis/lib/formats/xdrlib.pyx":543 * if not np.allclose(self.box, box, rtol=0, atol=1e-2): * raise ValueError('Previous frames contained {} box. You ' * 'are trying to write {} box.'.format( # <<<<<<<<<<<<<< * self.box, box)) * */ - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_contained_box_Yo, __pyx_n_s_format); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 486; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_contained_box_Yo, __pyx_n_s_format); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "MDAnalysis/lib/formats/xdrlib.pyx":487 + /* "MDAnalysis/lib/formats/xdrlib.pyx":544 * raise ValueError('Previous frames contained {} box. You ' * 'are trying to write {} box.'.format( * self.box, box)) # <<<<<<<<<<<<<< * - * cdef int return_code + * return_code = write_trr(self.xfp, self.n_atoms, step, time, */ __pyx_t_7 = NULL; __pyx_t_8 = 0; @@ -6714,7 +7170,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_8 = 1; } } - __pyx_t_6 = PyTuple_New(2+__pyx_t_8); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 486; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(2+__pyx_t_8); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); if (__pyx_t_7) { __Pyx_GIVEREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_7); __pyx_t_7 = NULL; @@ -6725,31 +7181,31 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __Pyx_INCREF(__pyx_v_box); __Pyx_GIVEREF(__pyx_v_box); PyTuple_SET_ITEM(__pyx_t_6, 1+__pyx_t_8, __pyx_v_box); - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_6, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 486; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_6, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":485 + /* "MDAnalysis/lib/formats/xdrlib.pyx":542 * self.n_atoms, forces.shape[0])) * if not np.allclose(self.box, box, rtol=0, atol=1e-2): * raise ValueError('Previous frames contained {} box. You ' # <<<<<<<<<<<<<< * 'are trying to write {} box.'.format( * self.box, box)) */ - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 485; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 542; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 485; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 542; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 485; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 542; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":484 + /* "MDAnalysis/lib/formats/xdrlib.pyx":541 * 'are trying to write {} atoms.'.format( * self.n_atoms, forces.shape[0])) * if not np.allclose(self.box, box, rtol=0, atol=1e-2): # <<<<<<<<<<<<<< @@ -6760,16 +7216,16 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str } __pyx_L7:; - /* "MDAnalysis/lib/formats/xdrlib.pyx":490 + /* "MDAnalysis/lib/formats/xdrlib.pyx":546 + * self.box, box)) * - * cdef int return_code * return_code = write_trr(self.xfp, self.n_atoms, step, time, # <<<<<<<<<<<<<< * _lambda, box_ptr, * xyz_ptr, */ __pyx_v_return_code = write_trr(__pyx_v_self->__pyx_base.xfp, __pyx_v_self->__pyx_base.n_atoms, __pyx_v_step, __pyx_v_time, __pyx_v__lambda, ((float (*)[3])__pyx_v_box_ptr), ((rvec *)__pyx_v_xyz_ptr), ((rvec *)__pyx_v_velocity_ptr), ((rvec *)__pyx_v_forces_ptr)); - /* "MDAnalysis/lib/formats/xdrlib.pyx":495 + /* "MDAnalysis/lib/formats/xdrlib.pyx":551 * velocity_ptr, * forces_ptr) * if return_code != EOK: # <<<<<<<<<<<<<< @@ -6779,26 +7235,26 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str __pyx_t_10 = ((__pyx_v_return_code != __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EOK) != 0); if (__pyx_t_10) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":496 + /* "MDAnalysis/lib/formats/xdrlib.pyx":552 * forces_ptr) * if return_code != EOK: * raise RuntimeError('TRR write error: {}'.format( # <<<<<<<<<<<<<< * error_message[return_code])) * */ - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_TRR_write_error, __pyx_n_s_format); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_TRR_write_error, __pyx_n_s_format); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "MDAnalysis/lib/formats/xdrlib.pyx":497 + /* "MDAnalysis/lib/formats/xdrlib.pyx":553 * if return_code != EOK: * raise RuntimeError('TRR write error: {}'.format( * error_message[return_code])) # <<<<<<<<<<<<<< * * self.current_frame += 1 */ - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 497; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_6, __pyx_v_return_code, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 497; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_6, __pyx_v_return_code, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_6 = NULL; @@ -6812,42 +7268,42 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str } } if (!__pyx_t_6) { - __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_7); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_7); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_GOTREF(__pyx_t_3); } else { - __pyx_t_9 = PyTuple_New(1+1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyTuple_New(1+1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_6); __pyx_t_6 = NULL; __Pyx_GIVEREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_9, 0+1, __pyx_t_7); __pyx_t_7 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_9, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_9, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":496 + /* "MDAnalysis/lib/formats/xdrlib.pyx":552 * forces_ptr) * if return_code != EOK: * raise RuntimeError('TRR write error: {}'.format( # <<<<<<<<<<<<<< * error_message[return_code])) * */ - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_5, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":495 + /* "MDAnalysis/lib/formats/xdrlib.pyx":551 * velocity_ptr, * forces_ptr) * if return_code != EOK: # <<<<<<<<<<<<<< @@ -6856,7 +7312,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":499 + /* "MDAnalysis/lib/formats/xdrlib.pyx":555 * error_message[return_code])) * * self.current_frame += 1 # <<<<<<<<<<<<<< @@ -6865,7 +7321,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ __pyx_v_self->__pyx_base.current_frame = (__pyx_v_self->__pyx_base.current_frame + 1); - /* "MDAnalysis/lib/formats/xdrlib.pyx":409 + /* "MDAnalysis/lib/formats/xdrlib.pyx":466 * has_x, has_v, has_f) * * def write(self, xyz, velocity, forces, box, int step, float time, # <<<<<<<<<<<<<< @@ -6895,7 +7351,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":528 +/* "MDAnalysis/lib/formats/xdrlib.pyx":584 * cdef float precision * * def _calc_natoms(self, fname): # <<<<<<<<<<<<<< @@ -6930,17 +7386,17 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile__calc_nato int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_calc_natoms", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":530 + /* "MDAnalysis/lib/formats/xdrlib.pyx":586 * def _calc_natoms(self, fname): * cdef int n_atoms * return_code = read_xtc_natoms(fname, &n_atoms) # <<<<<<<<<<<<<< * return return_code, n_atoms * */ - __pyx_t_1 = __Pyx_PyObject_AsString(__pyx_v_fname); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 530; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_AsString(__pyx_v_fname); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 586; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_return_code = read_xtc_natoms(__pyx_t_1, (&__pyx_v_n_atoms)); - /* "MDAnalysis/lib/formats/xdrlib.pyx":531 + /* "MDAnalysis/lib/formats/xdrlib.pyx":587 * cdef int n_atoms * return_code = read_xtc_natoms(fname, &n_atoms) * return return_code, n_atoms # <<<<<<<<<<<<<< @@ -6948,11 +7404,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile__calc_nato * */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_return_code); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_return_code); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_atoms); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_atoms); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); @@ -6964,7 +7420,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile__calc_nato __pyx_t_4 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":528 + /* "MDAnalysis/lib/formats/xdrlib.pyx":584 * cdef float precision * * def _calc_natoms(self, fname): # <<<<<<<<<<<<<< @@ -6985,7 +7441,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile__calc_nato return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":534 +/* "MDAnalysis/lib/formats/xdrlib.pyx":590 * * * def calc_offsets(self): # <<<<<<<<<<<<<< @@ -7029,7 +7485,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs int __pyx_clineno = 0; __Pyx_RefNannySetupContext("calc_offsets", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":536 + /* "MDAnalysis/lib/formats/xdrlib.pyx":592 * def calc_offsets(self): * """Calculate offsets from XTC file directly""" * if not self.is_open: # <<<<<<<<<<<<<< @@ -7039,7 +7495,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs __pyx_t_1 = ((!(__pyx_v_self->__pyx_base.is_open != 0)) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":537 + /* "MDAnalysis/lib/formats/xdrlib.pyx":593 * """Calculate offsets from XTC file directly""" * if not self.is_open: * return np.array([]) # <<<<<<<<<<<<<< @@ -7047,12 +7503,12 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs * cdef int est_nframes = 0 */ __Pyx_XDECREF(__pyx_r); - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_array); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_array); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_4))) { @@ -7065,17 +7521,17 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs } } if (!__pyx_t_5) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_GOTREF(__pyx_t_2); } else { - __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5); __pyx_t_5 = NULL; __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_6, 0+1, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } @@ -7084,7 +7540,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs __pyx_t_2 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":536 + /* "MDAnalysis/lib/formats/xdrlib.pyx":592 * def calc_offsets(self): * """Calculate offsets from XTC file directly""" * if not self.is_open: # <<<<<<<<<<<<<< @@ -7093,7 +7549,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":538 + /* "MDAnalysis/lib/formats/xdrlib.pyx":594 * if not self.is_open: * return np.array([]) * cdef int n_frames = 0 # <<<<<<<<<<<<<< @@ -7102,7 +7558,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs */ __pyx_v_n_frames = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":539 + /* "MDAnalysis/lib/formats/xdrlib.pyx":595 * return np.array([]) * cdef int n_frames = 0 * cdef int est_nframes = 0 # <<<<<<<<<<<<<< @@ -7111,55 +7567,55 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs */ __pyx_v_est_nframes = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":540 + /* "MDAnalysis/lib/formats/xdrlib.pyx":596 * cdef int n_frames = 0 * cdef int est_nframes = 0 * cdef int64_t* offsets = NULL # <<<<<<<<<<<<<< * ok = read_xtc_n_frames(self.fname, &n_frames, &est_nframes, &offsets); - * if ok != 0: + * if ok != EOK: */ __pyx_v_offsets = NULL; - /* "MDAnalysis/lib/formats/xdrlib.pyx":541 + /* "MDAnalysis/lib/formats/xdrlib.pyx":597 * cdef int est_nframes = 0 * cdef int64_t* offsets = NULL * ok = read_xtc_n_frames(self.fname, &n_frames, &est_nframes, &offsets); # <<<<<<<<<<<<<< - * if ok != 0: + * if ok != EOK: * raise RuntimeError("XTC couldn't calculate offsets, error={}".format( */ - __pyx_t_7 = __Pyx_PyObject_AsString(__pyx_v_self->__pyx_base.fname); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 541; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_AsString(__pyx_v_self->__pyx_base.fname); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_ok = read_xtc_n_frames(__pyx_t_7, (&__pyx_v_n_frames), (&__pyx_v_est_nframes), (&__pyx_v_offsets)); - /* "MDAnalysis/lib/formats/xdrlib.pyx":542 + /* "MDAnalysis/lib/formats/xdrlib.pyx":598 * cdef int64_t* offsets = NULL * ok = read_xtc_n_frames(self.fname, &n_frames, &est_nframes, &offsets); - * if ok != 0: # <<<<<<<<<<<<<< + * if ok != EOK: # <<<<<<<<<<<<<< * raise RuntimeError("XTC couldn't calculate offsets, error={}".format( * error_message[ok])) */ - __pyx_t_1 = ((__pyx_v_ok != 0) != 0); + __pyx_t_1 = ((__pyx_v_ok != __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EOK) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":543 + /* "MDAnalysis/lib/formats/xdrlib.pyx":599 * ok = read_xtc_n_frames(self.fname, &n_frames, &est_nframes, &offsets); - * if ok != 0: + * if ok != EOK: * raise RuntimeError("XTC couldn't calculate offsets, error={}".format( # <<<<<<<<<<<<<< * error_message[ok])) * # the read_xtc_n_frames allocates memory for the offsets with an */ - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_XTC_couldn_t_calculate_offsets_e, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_XTC_couldn_t_calculate_offsets_e, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - /* "MDAnalysis/lib/formats/xdrlib.pyx":544 - * if ok != 0: + /* "MDAnalysis/lib/formats/xdrlib.pyx":600 + * if ok != EOK: * raise RuntimeError("XTC couldn't calculate offsets, error={}".format( * error_message[ok])) # <<<<<<<<<<<<<< * # the read_xtc_n_frames allocates memory for the offsets with an * # overestimation. This number is saved in est_nframes and we need to */ - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 544; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_6, __pyx_v_ok, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_6, __pyx_v_ok, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_6 = NULL; @@ -7173,93 +7629,93 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs } } if (!__pyx_t_6) { - __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_GOTREF(__pyx_t_2); } else { - __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_6); __pyx_t_6 = NULL; __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_5, 0+1, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":543 + /* "MDAnalysis/lib/formats/xdrlib.pyx":599 * ok = read_xtc_n_frames(self.fname, &n_frames, &est_nframes, &offsets); - * if ok != 0: + * if ok != EOK: * raise RuntimeError("XTC couldn't calculate offsets, error={}".format( # <<<<<<<<<<<<<< * error_message[ok])) * # the read_xtc_n_frames allocates memory for the offsets with an */ - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":542 + /* "MDAnalysis/lib/formats/xdrlib.pyx":598 * cdef int64_t* offsets = NULL * ok = read_xtc_n_frames(self.fname, &n_frames, &est_nframes, &offsets); - * if ok != 0: # <<<<<<<<<<<<<< + * if ok != EOK: # <<<<<<<<<<<<<< * raise RuntimeError("XTC couldn't calculate offsets, error={}".format( * error_message[ok])) */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":549 + /* "MDAnalysis/lib/formats/xdrlib.pyx":605 * # tell the new numpy array about the whole allocated memory to avoid * # memory leaks. * cdef np.ndarray dims = np.array([est_nframes], dtype=np.int64) # <<<<<<<<<<<<<< * # this handles freeing the allocated memory correctly. * cdef np.ndarray nd_offsets = ptr_to_ndarray( offsets, dims, np.NPY_INT64) */ - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_array); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_array); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_est_nframes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_est_nframes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_5 = PyList_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyList_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_2); PyList_SET_ITEM(__pyx_t_5, 0, __pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_int64); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_int64); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_dims = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":551 + /* "MDAnalysis/lib/formats/xdrlib.pyx":607 * cdef np.ndarray dims = np.array([est_nframes], dtype=np.int64) * # this handles freeing the allocated memory correctly. * cdef np.ndarray nd_offsets = ptr_to_ndarray( offsets, dims, np.NPY_INT64) # <<<<<<<<<<<<<< @@ -7267,14 +7723,14 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs * */ __pyx_t_8 = __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_int64_t(((PyObject *)__pyx_v_dims)); - if (unlikely(!__pyx_t_8.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_6 = ((PyObject *)__pyx_f_10MDAnalysis_3lib_7formats_11cython_util_ptr_to_ndarray(((void *)__pyx_v_offsets), __pyx_t_8, NPY_INT64)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_t_8.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 607; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = ((PyObject *)__pyx_f_10MDAnalysis_3lib_7formats_11cython_util_ptr_to_ndarray(((void *)__pyx_v_offsets), __pyx_t_8, NPY_INT64)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 607; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __PYX_XDEC_MEMVIEW(&__pyx_t_8, 1); __pyx_v_nd_offsets = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":552 + /* "MDAnalysis/lib/formats/xdrlib.pyx":608 * # this handles freeing the allocated memory correctly. * cdef np.ndarray nd_offsets = ptr_to_ndarray( offsets, dims, np.NPY_INT64) * return nd_offsets[:n_frames] # <<<<<<<<<<<<<< @@ -7282,13 +7738,13 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs * def read(self): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_6 = __Pyx_PyObject_GetSlice(((PyObject *)__pyx_v_nd_offsets), 0, __pyx_v_n_frames, NULL, NULL, NULL, 0, 1, 1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetSlice(((PyObject *)__pyx_v_nd_offsets), 0, __pyx_v_n_frames, NULL, NULL, NULL, 0, 1, 1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_r = __pyx_t_6; __pyx_t_6 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":534 + /* "MDAnalysis/lib/formats/xdrlib.pyx":590 * * * def calc_offsets(self): # <<<<<<<<<<<<<< @@ -7314,7 +7770,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":554 +/* "MDAnalysis/lib/formats/xdrlib.pyx":610 * return nd_offsets[:n_frames] * * def read(self): # <<<<<<<<<<<<<< @@ -7337,7 +7793,7 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_5read(PyOb } static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib_XTCFile *__pyx_v_self) { - int __pyx_v_return_code; + long __pyx_v_return_code; int __pyx_v_step; float __pyx_v_time; float __pyx_v_prec; @@ -7360,7 +7816,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru int __pyx_clineno = 0; __Pyx_RefNannySetupContext("read", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":572 + /* "MDAnalysis/lib/formats/xdrlib.pyx":628 * Something must have happened reading the file * """ * if self.reached_eof: # <<<<<<<<<<<<<< @@ -7370,20 +7826,20 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru __pyx_t_1 = (__pyx_v_self->__pyx_base.reached_eof != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":573 + /* "MDAnalysis/lib/formats/xdrlib.pyx":629 * """ * if self.reached_eof: * raise RuntimeError('Reached last frame in XTC, seek to 0') # <<<<<<<<<<<<<< * if not self.is_open: * raise RuntimeError('No file opened') */ - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 629; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 629; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":572 + /* "MDAnalysis/lib/formats/xdrlib.pyx":628 * Something must have happened reading the file * """ * if self.reached_eof: # <<<<<<<<<<<<<< @@ -7392,7 +7848,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":574 + /* "MDAnalysis/lib/formats/xdrlib.pyx":630 * if self.reached_eof: * raise RuntimeError('Reached last frame in XTC, seek to 0') * if not self.is_open: # <<<<<<<<<<<<<< @@ -7402,20 +7858,20 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru __pyx_t_1 = ((!(__pyx_v_self->__pyx_base.is_open != 0)) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":575 + /* "MDAnalysis/lib/formats/xdrlib.pyx":631 * raise RuntimeError('Reached last frame in XTC, seek to 0') * if not self.is_open: * raise RuntimeError('No file opened') # <<<<<<<<<<<<<< * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. Reading only allow ' */ - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__8, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 575; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__8, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 575; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":574 + /* "MDAnalysis/lib/formats/xdrlib.pyx":630 * if self.reached_eof: * raise RuntimeError('Reached last frame in XTC, seek to 0') * if not self.is_open: # <<<<<<<<<<<<<< @@ -7424,50 +7880,50 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":576 + /* "MDAnalysis/lib/formats/xdrlib.pyx":632 * if not self.is_open: * raise RuntimeError('No file opened') * if self.mode != 'r': # <<<<<<<<<<<<<< * raise RuntimeError('File opened in mode: {}. Reading only allow ' * 'in mode "r"'.format('self.mode')) */ - __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_self->__pyx_base.mode, __pyx_n_s_r, Py_NE)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_self->__pyx_base.mode, __pyx_n_s_r, Py_NE)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = (__pyx_t_1 != 0); if (__pyx_t_3) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":578 + /* "MDAnalysis/lib/formats/xdrlib.pyx":634 * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. Reading only allow ' * 'in mode "r"'.format('self.mode')) # <<<<<<<<<<<<<< * - * cdef int return_code = 1 + * return_code = 1 */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_opened_in_mode_Reading_only, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_opened_in_mode_Reading_only, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__9, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__9, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":577 + /* "MDAnalysis/lib/formats/xdrlib.pyx":633 * raise RuntimeError('No file opened') * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. Reading only allow ' # <<<<<<<<<<<<<< * 'in mode "r"'.format('self.mode')) * */ - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 577; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 577; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 577; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":576 + /* "MDAnalysis/lib/formats/xdrlib.pyx":632 * if not self.is_open: * raise RuntimeError('No file opened') * if self.mode != 'r': # <<<<<<<<<<<<<< @@ -7476,32 +7932,32 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":580 + /* "MDAnalysis/lib/formats/xdrlib.pyx":636 * 'in mode "r"'.format('self.mode')) * - * cdef int return_code = 1 # <<<<<<<<<<<<<< + * return_code = 1 # <<<<<<<<<<<<<< * cdef int step * cdef float time, prec */ __pyx_v_return_code = 1; - /* "MDAnalysis/lib/formats/xdrlib.pyx":584 + /* "MDAnalysis/lib/formats/xdrlib.pyx":640 * cdef float time, prec * * cdef np.ndarray xyz = np.empty((self.n_atoms, DIMS), dtype=DTYPE) # <<<<<<<<<<<<<< * cdef np.ndarray box = np.empty((DIMS, DIMS), dtype=DTYPE) * */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_empty); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_empty); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_4); @@ -7509,43 +7965,43 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5); __pyx_t_4 = 0; __pyx_t_5 = 0; - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_xyz = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":585 + /* "MDAnalysis/lib/formats/xdrlib.pyx":641 * * cdef np.ndarray xyz = np.empty((self.n_atoms, DIMS), dtype=DTYPE) * cdef np.ndarray box = np.empty((DIMS, DIMS), dtype=DTYPE) # <<<<<<<<<<<<<< * * return_code = read_xtc(self.xfp, self.n_atoms, &step, */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_empty); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_empty); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4); @@ -7553,27 +8009,27 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_5); __pyx_t_4 = 0; __pyx_t_5 = 0; - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_box = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":587 + /* "MDAnalysis/lib/formats/xdrlib.pyx":643 * cdef np.ndarray box = np.empty((DIMS, DIMS), dtype=DTYPE) * * return_code = read_xtc(self.xfp, self.n_atoms, &step, # <<<<<<<<<<<<<< @@ -7582,7 +8038,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ __pyx_v_return_code = read_xtc(__pyx_v_self->__pyx_base.xfp, __pyx_v_self->__pyx_base.n_atoms, ((int *)(&__pyx_v_step)), (&__pyx_v_time), ((float (*)[3])__pyx_v_box->data), ((rvec *)__pyx_v_xyz->data), ((float *)(&__pyx_v_prec))); - /* "MDAnalysis/lib/formats/xdrlib.pyx":590 + /* "MDAnalysis/lib/formats/xdrlib.pyx":646 * &time, box.data, * xyz.data, &prec) * if return_code != EOK and return_code != EENDOFFILE: # <<<<<<<<<<<<<< @@ -7600,26 +8056,26 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru } if (__pyx_t_3) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":591 + /* "MDAnalysis/lib/formats/xdrlib.pyx":647 * xyz.data, &prec) * if return_code != EOK and return_code != EENDOFFILE: * raise RuntimeError('XTC Read Error occured: {}'.format( # <<<<<<<<<<<<<< * error_message[return_code])) * */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_XTC_Read_Error_occured, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_XTC_Read_Error_occured, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - /* "MDAnalysis/lib/formats/xdrlib.pyx":592 + /* "MDAnalysis/lib/formats/xdrlib.pyx":648 * if return_code != EOK and return_code != EENDOFFILE: * raise RuntimeError('XTC Read Error occured: {}'.format( * error_message[return_code])) # <<<<<<<<<<<<<< * * if return_code == EENDOFFILE: */ - __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 648; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_5, __pyx_v_return_code, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_5, __pyx_v_return_code, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_5 = NULL; @@ -7633,42 +8089,42 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru } } if (!__pyx_t_5) { - __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_GOTREF(__pyx_t_4); } else { - __pyx_t_7 = PyTuple_New(1+1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(1+1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5); __pyx_t_5 = NULL; __Pyx_GIVEREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_7, 0+1, __pyx_t_6); __pyx_t_6 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_7, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_7, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":591 + /* "MDAnalysis/lib/formats/xdrlib.pyx":647 * xyz.data, &prec) * if return_code != EOK and return_code != EENDOFFILE: * raise RuntimeError('XTC Read Error occured: {}'.format( # <<<<<<<<<<<<<< * error_message[return_code])) * */ - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":590 + /* "MDAnalysis/lib/formats/xdrlib.pyx":646 * &time, box.data, * xyz.data, &prec) * if return_code != EOK and return_code != EENDOFFILE: # <<<<<<<<<<<<<< @@ -7677,7 +8133,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":594 + /* "MDAnalysis/lib/formats/xdrlib.pyx":650 * error_message[return_code])) * * if return_code == EENDOFFILE: # <<<<<<<<<<<<<< @@ -7687,7 +8143,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru __pyx_t_3 = ((__pyx_v_return_code == __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EENDOFFILE) != 0); if (__pyx_t_3) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":595 + /* "MDAnalysis/lib/formats/xdrlib.pyx":651 * * if return_code == EENDOFFILE: * self.reached_eof = True # <<<<<<<<<<<<<< @@ -7696,7 +8152,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ __pyx_v_self->__pyx_base.reached_eof = 1; - /* "MDAnalysis/lib/formats/xdrlib.pyx":596 + /* "MDAnalysis/lib/formats/xdrlib.pyx":652 * if return_code == EENDOFFILE: * self.reached_eof = True * raise StopIteration # <<<<<<<<<<<<<< @@ -7704,9 +8160,9 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru * if return_code == EOK: */ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 652; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":594 + /* "MDAnalysis/lib/formats/xdrlib.pyx":650 * error_message[return_code])) * * if return_code == EENDOFFILE: # <<<<<<<<<<<<<< @@ -7715,7 +8171,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":598 + /* "MDAnalysis/lib/formats/xdrlib.pyx":654 * raise StopIteration * * if return_code == EOK: # <<<<<<<<<<<<<< @@ -7725,7 +8181,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru __pyx_t_3 = ((__pyx_v_return_code == __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EOK) != 0); if (__pyx_t_3) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":599 + /* "MDAnalysis/lib/formats/xdrlib.pyx":655 * * if return_code == EOK: * self.current_frame += 1 # <<<<<<<<<<<<<< @@ -7734,7 +8190,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ __pyx_v_self->__pyx_base.current_frame = (__pyx_v_self->__pyx_base.current_frame + 1); - /* "MDAnalysis/lib/formats/xdrlib.pyx":598 + /* "MDAnalysis/lib/formats/xdrlib.pyx":654 * raise StopIteration * * if return_code == EOK: # <<<<<<<<<<<<<< @@ -7743,7 +8199,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":600 + /* "MDAnalysis/lib/formats/xdrlib.pyx":656 * if return_code == EOK: * self.current_frame += 1 * return XTCFrame(xyz, box, step, time, prec) # <<<<<<<<<<<<<< @@ -7751,13 +8207,13 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru * def write(self, xyz, box, int step, float time, float precision=1000): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_XTCFrame); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_XTCFrame); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_step); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_step); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_6 = PyFloat_FromDouble(__pyx_v_time); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_v_time); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_5 = PyFloat_FromDouble(__pyx_v_prec); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyFloat_FromDouble(__pyx_v_prec); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_8 = NULL; __pyx_t_9 = 0; @@ -7771,7 +8227,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru __pyx_t_9 = 1; } } - __pyx_t_10 = PyTuple_New(5+__pyx_t_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyTuple_New(5+__pyx_t_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); if (__pyx_t_8) { __Pyx_GIVEREF(__pyx_t_8); PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_8); __pyx_t_8 = NULL; @@ -7791,7 +8247,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru __pyx_t_7 = 0; __pyx_t_6 = 0; __pyx_t_5 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_10, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_10, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -7799,7 +8255,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru __pyx_t_4 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":554 + /* "MDAnalysis/lib/formats/xdrlib.pyx":610 * return nd_offsets[:n_frames] * * def read(self): # <<<<<<<<<<<<<< @@ -7826,7 +8282,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":602 +/* "MDAnalysis/lib/formats/xdrlib.pyx":658 * return XTCFrame(xyz, box, step, time, prec) * * def write(self, xyz, box, int step, float time, float precision=1000): # <<<<<<<<<<<<<< @@ -7872,17 +8328,17 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_7write(PyO case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_box)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("write", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_step)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("write", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_time)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("write", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (kw_args > 0) { @@ -7891,7 +8347,7 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_7write(PyO } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "write") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "write") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -7906,17 +8362,17 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_7write(PyO } __pyx_v_xyz = values[0]; __pyx_v_box = values[1]; - __pyx_v_step = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_step == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_time = __pyx_PyFloat_AsFloat(values[3]); if (unlikely((__pyx_v_time == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_step = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_step == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_time = __pyx_PyFloat_AsFloat(values[3]); if (unlikely((__pyx_v_time == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L3_error;} if (values[4]) { - __pyx_v_precision = __pyx_PyFloat_AsFloat(values[4]); if (unlikely((__pyx_v_precision == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_precision = __pyx_PyFloat_AsFloat(values[4]); if (unlikely((__pyx_v_precision == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { __pyx_v_precision = ((float)1000.0); } } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("write", 0, 4, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 0, 4, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MDAnalysis.lib.formats.xdrlib.XTCFile.write", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); @@ -7955,50 +8411,50 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str int __pyx_clineno = 0; __Pyx_RefNannySetupContext("write", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":633 + /* "MDAnalysis/lib/formats/xdrlib.pyx":689 * * """ * if self.mode != 'w': # <<<<<<<<<<<<<< * raise RuntimeError('File opened in mode: {}. Writing only allow ' * 'in mode "w"'.format('self.mode')) */ - __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_self->__pyx_base.mode, __pyx_n_s_w, Py_NE)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = (__Pyx_PyString_Equals(__pyx_v_self->__pyx_base.mode, __pyx_n_s_w, Py_NE)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":635 + /* "MDAnalysis/lib/formats/xdrlib.pyx":691 * if self.mode != 'w': * raise RuntimeError('File opened in mode: {}. Writing only allow ' * 'in mode "w"'.format('self.mode')) # <<<<<<<<<<<<<< * * cdef DTYPE_T[:, ::1] xyz_view = np.ascontiguousarray(xyz, dtype=DTYPE) */ - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_opened_in_mode_Writing_only, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_opened_in_mode_Writing_only, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__10, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__10, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":634 + /* "MDAnalysis/lib/formats/xdrlib.pyx":690 * """ * if self.mode != 'w': * raise RuntimeError('File opened in mode: {}. Writing only allow ' # <<<<<<<<<<<<<< * 'in mode "w"'.format('self.mode')) * */ - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":633 + /* "MDAnalysis/lib/formats/xdrlib.pyx":689 * * """ * if self.mode != 'w': # <<<<<<<<<<<<<< @@ -8007,77 +8463,77 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":637 + /* "MDAnalysis/lib/formats/xdrlib.pyx":693 * 'in mode "w"'.format('self.mode')) * * cdef DTYPE_T[:, ::1] xyz_view = np.ascontiguousarray(xyz, dtype=DTYPE) # <<<<<<<<<<<<<< * cdef DTYPE_T[:, ::1] box_view = np.ascontiguousarray(box, dtype=DTYPE) * */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_ascontiguousarray); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_ascontiguousarray); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_INCREF(__pyx_v_xyz); __Pyx_GIVEREF(__pyx_v_xyz); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_xyz); - __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_7 = __Pyx_PyObject_to_MemoryviewSlice_d_dc_nn___pyx_t_10MDAnalysis_3lib_7formats_6xdrlib_DTYPE_T(__pyx_t_6); - if (unlikely(!__pyx_t_7.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_t_7.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_v_xyz_view = __pyx_t_7; __pyx_t_7.memview = NULL; __pyx_t_7.data = NULL; - /* "MDAnalysis/lib/formats/xdrlib.pyx":638 + /* "MDAnalysis/lib/formats/xdrlib.pyx":694 * * cdef DTYPE_T[:, ::1] xyz_view = np.ascontiguousarray(xyz, dtype=DTYPE) * cdef DTYPE_T[:, ::1] box_view = np.ascontiguousarray(box, dtype=DTYPE) # <<<<<<<<<<<<<< * * if self.current_frame == 0: */ - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_ascontiguousarray); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_ascontiguousarray); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_INCREF(__pyx_v_box); __Pyx_GIVEREF(__pyx_v_box); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_box); - __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_dtype, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_dtype, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_6, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_6, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_7 = __Pyx_PyObject_to_MemoryviewSlice_d_dc_nn___pyx_t_10MDAnalysis_3lib_7formats_6xdrlib_DTYPE_T(__pyx_t_3); - if (unlikely(!__pyx_t_7.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_t_7.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_v_box_view = __pyx_t_7; __pyx_t_7.memview = NULL; __pyx_t_7.data = NULL; - /* "MDAnalysis/lib/formats/xdrlib.pyx":640 + /* "MDAnalysis/lib/formats/xdrlib.pyx":696 * cdef DTYPE_T[:, ::1] box_view = np.ascontiguousarray(box, dtype=DTYPE) * * if self.current_frame == 0: # <<<<<<<<<<<<<< @@ -8087,30 +8543,30 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str __pyx_t_2 = ((__pyx_v_self->__pyx_base.current_frame == 0) != 0); if (__pyx_t_2) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":641 + /* "MDAnalysis/lib/formats/xdrlib.pyx":697 * * if self.current_frame == 0: * self.n_atoms = xyz.shape[0] # <<<<<<<<<<<<<< * self.box = box * self.precision = precision */ - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_xyz, __pyx_n_s_shape); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_xyz, __pyx_n_s_shape); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_8 = __Pyx_PyInt_As_int(__pyx_t_4); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_PyInt_As_int(__pyx_t_4); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_v_self->__pyx_base.n_atoms = __pyx_t_8; - /* "MDAnalysis/lib/formats/xdrlib.pyx":642 + /* "MDAnalysis/lib/formats/xdrlib.pyx":698 * if self.current_frame == 0: * self.n_atoms = xyz.shape[0] * self.box = box # <<<<<<<<<<<<<< * self.precision = precision * else: */ - if (!(likely(((__pyx_v_box) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_box, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_v_box) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_box, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = __pyx_v_box; __Pyx_INCREF(__pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); @@ -8119,7 +8575,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str __pyx_v_self->__pyx_base.box = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":643 + /* "MDAnalysis/lib/formats/xdrlib.pyx":699 * self.n_atoms = xyz.shape[0] * self.box = box * self.precision = precision # <<<<<<<<<<<<<< @@ -8128,7 +8584,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str */ __pyx_v_self->precision = __pyx_v_precision; - /* "MDAnalysis/lib/formats/xdrlib.pyx":640 + /* "MDAnalysis/lib/formats/xdrlib.pyx":696 * cdef DTYPE_T[:, ::1] box_view = np.ascontiguousarray(box, dtype=DTYPE) * * if self.current_frame == 0: # <<<<<<<<<<<<<< @@ -8138,7 +8594,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str goto __pyx_L4; } - /* "MDAnalysis/lib/formats/xdrlib.pyx":645 + /* "MDAnalysis/lib/formats/xdrlib.pyx":701 * self.precision = precision * else: * if self.n_atoms != xyz.shape[0]: # <<<<<<<<<<<<<< @@ -8146,42 +8602,42 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str * 'are trying to write {} atoms.'.format( */ /*else*/ { - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_xyz, __pyx_n_s_shape); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_xyz, __pyx_n_s_shape); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyObject_RichCompare(__pyx_t_4, __pyx_t_6, Py_NE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_RichCompare(__pyx_t_4, __pyx_t_6, Py_NE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_2) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":647 + /* "MDAnalysis/lib/formats/xdrlib.pyx":703 * if self.n_atoms != xyz.shape[0]: * raise ValueError('Previous frames contained {} atoms. You ' * 'are trying to write {} atoms.'.format( # <<<<<<<<<<<<<< * self.n_atoms, xyz.shape[1])) * if not np.allclose(self.box, box, rtol=0, atol=1e-2): */ - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_contained_atoms, __pyx_n_s_format); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_contained_atoms, __pyx_n_s_format); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - /* "MDAnalysis/lib/formats/xdrlib.pyx":648 + /* "MDAnalysis/lib/formats/xdrlib.pyx":704 * raise ValueError('Previous frames contained {} atoms. You ' * 'are trying to write {} atoms.'.format( * self.n_atoms, xyz.shape[1])) # <<<<<<<<<<<<<< * if not np.allclose(self.box, box, rtol=0, atol=1e-2): * raise ValueError('Previous frames contained {} box. You ' */ - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 648; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_self->__pyx_base.n_atoms); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_xyz, __pyx_n_s_shape); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 648; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_xyz, __pyx_n_s_shape); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_9 = __Pyx_GetItemInt(__pyx_t_5, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_9 = __Pyx_GetItemInt(__pyx_t_5, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_5 = NULL; @@ -8196,7 +8652,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str __pyx_t_10 = 1; } } - __pyx_t_11 = PyTuple_New(2+__pyx_t_10); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = PyTuple_New(2+__pyx_t_10); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_11); if (__pyx_t_5) { __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_5); __pyx_t_5 = NULL; @@ -8207,31 +8663,31 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str PyTuple_SET_ITEM(__pyx_t_11, 1+__pyx_t_10, __pyx_t_9); __pyx_t_4 = 0; __pyx_t_9 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_11, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_11, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":646 + /* "MDAnalysis/lib/formats/xdrlib.pyx":702 * else: * if self.n_atoms != xyz.shape[0]: * raise ValueError('Previous frames contained {} atoms. You ' # <<<<<<<<<<<<<< * 'are trying to write {} atoms.'.format( * self.n_atoms, xyz.shape[1])) */ - __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":645 + /* "MDAnalysis/lib/formats/xdrlib.pyx":701 * self.precision = precision * else: * if self.n_atoms != xyz.shape[0]: # <<<<<<<<<<<<<< @@ -8240,19 +8696,19 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":649 + /* "MDAnalysis/lib/formats/xdrlib.pyx":705 * 'are trying to write {} atoms.'.format( * self.n_atoms, xyz.shape[1])) * if not np.allclose(self.box, box, rtol=0, atol=1e-2): # <<<<<<<<<<<<<< * raise ValueError('Previous frames contained {} box. You ' * 'are trying to write {} box.'.format( */ - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_allclose); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_allclose); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(((PyObject *)__pyx_v_self->__pyx_base.box)); __Pyx_GIVEREF(((PyObject *)__pyx_v_self->__pyx_base.box)); @@ -8260,31 +8716,31 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str __Pyx_INCREF(__pyx_v_box); __Pyx_GIVEREF(__pyx_v_box); PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_box); - __pyx_t_11 = PyDict_New(); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = PyDict_New(); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_11); - if (PyDict_SetItem(__pyx_t_11, __pyx_n_s_rtol, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_11, __pyx_n_s_atol, __pyx_float_1eneg_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_3, __pyx_t_11); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_11, __pyx_n_s_rtol, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_11, __pyx_n_s_atol, __pyx_float_1eneg_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_3, __pyx_t_11); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; - __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_t_1 = ((!__pyx_t_2) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":651 + /* "MDAnalysis/lib/formats/xdrlib.pyx":707 * if not np.allclose(self.box, box, rtol=0, atol=1e-2): * raise ValueError('Previous frames contained {} box. You ' * 'are trying to write {} box.'.format( # <<<<<<<<<<<<<< * self.box, box)) * if self.precision != precision: */ - __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_contained_box_Yo, __pyx_n_s_format); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 651; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_contained_box_Yo, __pyx_n_s_format); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_11); - /* "MDAnalysis/lib/formats/xdrlib.pyx":652 + /* "MDAnalysis/lib/formats/xdrlib.pyx":708 * raise ValueError('Previous frames contained {} box. You ' * 'are trying to write {} box.'.format( * self.box, box)) # <<<<<<<<<<<<<< @@ -8303,7 +8759,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str __pyx_t_10 = 1; } } - __pyx_t_6 = PyTuple_New(2+__pyx_t_10); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 651; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(2+__pyx_t_10); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); if (__pyx_t_3) { __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3); __pyx_t_3 = NULL; @@ -8314,31 +8770,31 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str __Pyx_INCREF(__pyx_v_box); __Pyx_GIVEREF(__pyx_v_box); PyTuple_SET_ITEM(__pyx_t_6, 1+__pyx_t_10, __pyx_v_box); - __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_6, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 651; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_6, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":650 + /* "MDAnalysis/lib/formats/xdrlib.pyx":706 * self.n_atoms, xyz.shape[1])) * if not np.allclose(self.box, box, rtol=0, atol=1e-2): * raise ValueError('Previous frames contained {} box. You ' # <<<<<<<<<<<<<< * 'are trying to write {} box.'.format( * self.box, box)) */ - __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_11); __Pyx_GIVEREF(__pyx_t_9); PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_9); __pyx_t_9 = 0; - __pyx_t_9 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_11, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_11, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; __Pyx_Raise(__pyx_t_9, 0, 0, 0); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":649 + /* "MDAnalysis/lib/formats/xdrlib.pyx":705 * 'are trying to write {} atoms.'.format( * self.n_atoms, xyz.shape[1])) * if not np.allclose(self.box, box, rtol=0, atol=1e-2): # <<<<<<<<<<<<<< @@ -8347,7 +8803,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":653 + /* "MDAnalysis/lib/formats/xdrlib.pyx":709 * 'are trying to write {} box.'.format( * self.box, box)) * if self.precision != precision: # <<<<<<<<<<<<<< @@ -8357,26 +8813,26 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str __pyx_t_1 = ((__pyx_v_self->precision != __pyx_v_precision) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":655 + /* "MDAnalysis/lib/formats/xdrlib.pyx":711 * if self.precision != precision: * raise ValueError('Previous frames used precision of {}. You ' * 'are trying to use {}'.format( # <<<<<<<<<<<<<< * self.precision, precision)) * */ - __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_used_precision_o, __pyx_n_s_format); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_used_precision_o, __pyx_n_s_format); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_11); - /* "MDAnalysis/lib/formats/xdrlib.pyx":656 + /* "MDAnalysis/lib/formats/xdrlib.pyx":712 * raise ValueError('Previous frames used precision of {}. You ' * 'are trying to use {}'.format( * self.precision, precision)) # <<<<<<<<<<<<<< * - * cdef int return_code + * return_code = write_xtc(self.xfp, self.n_atoms, step, time, */ - __pyx_t_6 = PyFloat_FromDouble(__pyx_v_self->precision); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_v_self->precision); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_3 = PyFloat_FromDouble(__pyx_v_precision); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble(__pyx_v_precision); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = NULL; __pyx_t_10 = 0; @@ -8390,7 +8846,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str __pyx_t_10 = 1; } } - __pyx_t_5 = PyTuple_New(2+__pyx_t_10); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(2+__pyx_t_10); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); if (__pyx_t_4) { __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4); __pyx_t_4 = NULL; @@ -8401,31 +8857,31 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str PyTuple_SET_ITEM(__pyx_t_5, 1+__pyx_t_10, __pyx_t_3); __pyx_t_6 = 0; __pyx_t_3 = 0; - __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_5, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_5, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":654 + /* "MDAnalysis/lib/formats/xdrlib.pyx":710 * self.box, box)) * if self.precision != precision: * raise ValueError('Previous frames used precision of {}. You ' # <<<<<<<<<<<<<< * 'are trying to use {}'.format( * self.precision, precision)) */ - __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_11); __Pyx_GIVEREF(__pyx_t_9); PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_9); __pyx_t_9 = 0; - __pyx_t_9 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_11, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_11, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; __Pyx_Raise(__pyx_t_9, 0, 0, 0); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":653 + /* "MDAnalysis/lib/formats/xdrlib.pyx":709 * 'are trying to write {} box.'.format( * self.box, box)) * if self.precision != precision: # <<<<<<<<<<<<<< @@ -8436,8 +8892,8 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str } __pyx_L4:; - /* "MDAnalysis/lib/formats/xdrlib.pyx":660 - * cdef int return_code + /* "MDAnalysis/lib/formats/xdrlib.pyx":715 + * * return_code = write_xtc(self.xfp, self.n_atoms, step, time, * &box_view[0, 0], # <<<<<<<<<<<<<< * &xyz_view[0, 0], precision) @@ -8456,10 +8912,10 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str } else if (unlikely(__pyx_t_13 >= __pyx_v_box_view.shape[1])) __pyx_t_8 = 1; if (unlikely(__pyx_t_8 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_8); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "MDAnalysis/lib/formats/xdrlib.pyx":661 + /* "MDAnalysis/lib/formats/xdrlib.pyx":716 * return_code = write_xtc(self.xfp, self.n_atoms, step, time, * &box_view[0, 0], * &xyz_view[0, 0], precision) # <<<<<<<<<<<<<< @@ -8479,19 +8935,19 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str } else if (unlikely(__pyx_t_15 >= __pyx_v_xyz_view.shape[1])) __pyx_t_8 = 1; if (unlikely(__pyx_t_8 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_8); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "MDAnalysis/lib/formats/xdrlib.pyx":659 + /* "MDAnalysis/lib/formats/xdrlib.pyx":714 + * self.precision, precision)) * - * cdef int return_code * return_code = write_xtc(self.xfp, self.n_atoms, step, time, # <<<<<<<<<<<<<< * &box_view[0, 0], * &xyz_view[0, 0], precision) */ __pyx_v_return_code = write_xtc(__pyx_v_self->__pyx_base.xfp, __pyx_v_self->__pyx_base.n_atoms, __pyx_v_step, __pyx_v_time, ((float (*)[3])(&(*((__pyx_t_10MDAnalysis_3lib_7formats_6xdrlib_DTYPE_T *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_7formats_6xdrlib_DTYPE_T *) ( /* dim=0 */ (__pyx_v_box_view.data + __pyx_t_12 * __pyx_v_box_view.strides[0]) )) + __pyx_t_13)) ))))), ((rvec *)(&(*((__pyx_t_10MDAnalysis_3lib_7formats_6xdrlib_DTYPE_T *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_7formats_6xdrlib_DTYPE_T *) ( /* dim=0 */ (__pyx_v_xyz_view.data + __pyx_t_14 * __pyx_v_xyz_view.strides[0]) )) + __pyx_t_15)) ))))), __pyx_v_precision); - /* "MDAnalysis/lib/formats/xdrlib.pyx":662 + /* "MDAnalysis/lib/formats/xdrlib.pyx":717 * &box_view[0, 0], * &xyz_view[0, 0], precision) * if return_code != EOK: # <<<<<<<<<<<<<< @@ -8501,26 +8957,26 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str __pyx_t_1 = ((__pyx_v_return_code != __pyx_e_10MDAnalysis_3lib_7formats_6xdrlib_EOK) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":663 + /* "MDAnalysis/lib/formats/xdrlib.pyx":718 * &xyz_view[0, 0], precision) * if return_code != EOK: * raise RuntimeError('XTC write error: {}'.format( # <<<<<<<<<<<<<< * error_message[return_code])) * */ - __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_XTC_write_error, __pyx_n_s_format); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_XTC_write_error, __pyx_n_s_format); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_11); - /* "MDAnalysis/lib/formats/xdrlib.pyx":664 + /* "MDAnalysis/lib/formats/xdrlib.pyx":719 * if return_code != EOK: * raise RuntimeError('XTC write error: {}'.format( * error_message[return_code])) # <<<<<<<<<<<<<< * * self.current_frame += 1 */ - __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_error_message); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_5, __pyx_v_return_code, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_5, __pyx_v_return_code, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_5 = NULL; @@ -8534,42 +8990,42 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str } } if (!__pyx_t_5) { - __pyx_t_9 = __Pyx_PyObject_CallOneArg(__pyx_t_11, __pyx_t_3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_CallOneArg(__pyx_t_11, __pyx_t_3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_GOTREF(__pyx_t_9); } else { - __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5); __pyx_t_5 = NULL; __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_6, 0+1, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_6, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_6, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":663 + /* "MDAnalysis/lib/formats/xdrlib.pyx":718 * &xyz_view[0, 0], precision) * if return_code != EOK: * raise RuntimeError('XTC write error: {}'.format( # <<<<<<<<<<<<<< * error_message[return_code])) * */ - __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_11); __Pyx_GIVEREF(__pyx_t_9); PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_9); __pyx_t_9 = 0; - __pyx_t_9 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_11, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_t_11, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; __Pyx_Raise(__pyx_t_9, 0, 0, 0); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":662 + /* "MDAnalysis/lib/formats/xdrlib.pyx":717 * &box_view[0, 0], * &xyz_view[0, 0], precision) * if return_code != EOK: # <<<<<<<<<<<<<< @@ -8578,14 +9034,14 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":666 + /* "MDAnalysis/lib/formats/xdrlib.pyx":721 * error_message[return_code])) * * self.current_frame += 1 # <<<<<<<<<<<<<< */ __pyx_v_self->__pyx_base.current_frame = (__pyx_v_self->__pyx_base.current_frame + 1); - /* "MDAnalysis/lib/formats/xdrlib.pyx":602 + /* "MDAnalysis/lib/formats/xdrlib.pyx":658 * return XTCFrame(xyz, box, step, time, prec) * * def write(self, xyz, box, int step, float time, float precision=1000): # <<<<<<<<<<<<<< @@ -8614,7 +9070,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str return __pyx_r; } -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":197 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -8664,7 +9120,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_GIVEREF(__pyx_v_info->obj); } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":203 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":203 * # of flags * * if info == NULL: return # <<<<<<<<<<<<<< @@ -8677,7 +9133,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L0; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":206 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":206 * * cdef int copy_shape, i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -8686,7 +9142,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":207 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":207 * cdef int copy_shape, i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -8695,7 +9151,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":209 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":209 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -8704,7 +9160,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":211 * ndim = PyArray_NDIM(self) * * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -8714,7 +9170,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":212 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":212 * * if sizeof(npy_intp) != sizeof(Py_ssize_t): * copy_shape = 1 # <<<<<<<<<<<<<< @@ -8723,7 +9179,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_copy_shape = 1; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":211 * ndim = PyArray_NDIM(self) * * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -8733,7 +9189,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":214 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":214 * copy_shape = 1 * else: * copy_shape = 0 # <<<<<<<<<<<<<< @@ -8745,7 +9201,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L4:; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":216 * copy_shape = 0 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -8759,7 +9215,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L6_bool_binop_done; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":217 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":217 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -8770,7 +9226,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L6_bool_binop_done:; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":216 * copy_shape = 0 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -8779,7 +9235,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (__pyx_t_1) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":218 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -8792,7 +9248,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":216 * copy_shape = 0 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -8801,7 +9257,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":220 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -8815,7 +9271,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9_bool_binop_done; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":221 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":221 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -8826,7 +9282,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L9_bool_binop_done:; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":220 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -8835,7 +9291,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (__pyx_t_1) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":222 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -8848,7 +9304,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":220 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -8857,7 +9313,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":224 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":224 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -8866,7 +9322,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":225 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":225 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -8875,7 +9331,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":226 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if copy_shape: # <<<<<<<<<<<<<< @@ -8885,7 +9341,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (__pyx_v_copy_shape != 0); if (__pyx_t_1) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":229 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) # <<<<<<<<<<<<<< @@ -8894,7 +9350,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2))); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":230 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":230 * # This is allocated as one block, strides first. * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -8903,7 +9359,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":231 * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -8914,7 +9370,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":232 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -8923,7 +9379,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":233 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -8933,7 +9389,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":226 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if copy_shape: # <<<<<<<<<<<<<< @@ -8943,7 +9399,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L11; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":235 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -8953,7 +9409,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":236 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -8964,7 +9420,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L11:; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":237 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -8973,7 +9429,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":238 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":238 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -8982,7 +9438,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":239 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":239 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -8991,7 +9447,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":242 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -9000,7 +9456,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":243 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -9012,7 +9468,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":246 * cdef int offset * * cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<< @@ -9021,7 +9477,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":248 * cdef bint hasfields = PyDataType_HASFIELDS(descr) * * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< @@ -9039,7 +9495,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_L15_bool_binop_done:; if (__pyx_t_1) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":250 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":250 * if not hasfields and not copy_shape: * # do not call releasebuffer * info.obj = None # <<<<<<<<<<<<<< @@ -9052,7 +9508,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = Py_None; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":248 * cdef bint hasfields = PyDataType_HASFIELDS(descr) * * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< @@ -9062,7 +9518,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L14; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":253 * else: * # need to call releasebuffer * info.obj = self # <<<<<<<<<<<<<< @@ -9078,7 +9534,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L14:; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":255 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":255 * info.obj = self * * if not hasfields: # <<<<<<<<<<<<<< @@ -9088,7 +9544,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0); if (__pyx_t_1) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":256 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":256 * * if not hasfields: * t = descr.type_num # <<<<<<<<<<<<<< @@ -9098,7 +9554,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":257 * if not hasfields: * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -9118,7 +9574,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L20_next_or:; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":258 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -9135,7 +9591,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L19_bool_binop_done:; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":257 * if not hasfields: * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -9144,7 +9600,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (__pyx_t_1) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":259 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -9157,7 +9613,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":257 * if not hasfields: * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -9166,7 +9622,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":260 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -9178,7 +9634,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_b; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":261 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -9189,7 +9645,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_B; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":262 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -9200,7 +9656,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_h; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":263 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -9211,7 +9667,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_H; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":264 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -9222,7 +9678,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_i; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":265 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -9233,7 +9689,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_I; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":266 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -9244,7 +9700,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_l; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -9255,7 +9711,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_L; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -9266,7 +9722,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_q; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -9277,7 +9733,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Q; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -9288,7 +9744,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_f; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -9299,7 +9755,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_d; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -9310,7 +9766,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_g; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -9321,7 +9777,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zf; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -9332,7 +9788,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zd; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -9343,7 +9799,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zg; break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -9355,7 +9811,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":278 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -9381,7 +9837,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":279 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -9390,7 +9846,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":280 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -9400,7 +9856,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":255 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":255 * info.obj = self * * if not hasfields: # <<<<<<<<<<<<<< @@ -9409,7 +9865,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":282 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":282 * return * else: * info.format = stdlib.malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -9419,7 +9875,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)malloc(0xFF)); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":283 * else: * info.format = stdlib.malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -9428,7 +9884,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":284 * info.format = stdlib.malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -9437,7 +9893,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":285 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":285 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -9447,7 +9903,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_f = __pyx_t_7; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":288 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":288 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -9457,7 +9913,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":197 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -9489,7 +9945,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P return __pyx_r; } -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":290 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":290 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -9513,7 +9969,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":291 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -9523,7 +9979,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":292 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * stdlib.free(info.format) # <<<<<<<<<<<<<< @@ -9532,7 +9988,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ free(__pyx_v_info->format); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":291 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -9541,7 +9997,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":293 * if PyArray_HASFIELDS(self): * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -9551,7 +10007,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":294 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":294 * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * stdlib.free(info.strides) # <<<<<<<<<<<<<< @@ -9560,7 +10016,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ free(__pyx_v_info->strides); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":293 * if PyArray_HASFIELDS(self): * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -9569,7 +10025,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":290 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":290 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -9581,7 +10037,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __Pyx_RefNannyFinishContext(); } -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":770 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":770 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -9598,7 +10054,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":771 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":771 * * cdef inline object PyArray_MultiIterNew1(a): * return PyArray_MultiIterNew(1, a) # <<<<<<<<<<<<<< @@ -9612,7 +10068,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":770 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":770 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -9631,7 +10087,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ return __pyx_r; } -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":773 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":773 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -9648,7 +10104,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 0); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":774 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":774 * * cdef inline object PyArray_MultiIterNew2(a, b): * return PyArray_MultiIterNew(2, a, b) # <<<<<<<<<<<<<< @@ -9662,7 +10118,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":773 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":773 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -9681,7 +10137,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ return __pyx_r; } -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":776 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":776 * return PyArray_MultiIterNew(2, a, b) * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< @@ -9698,7 +10154,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 0); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":777 * * cdef inline object PyArray_MultiIterNew3(a, b, c): * return PyArray_MultiIterNew(3, a, b, c) # <<<<<<<<<<<<<< @@ -9712,7 +10168,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":776 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":776 * return PyArray_MultiIterNew(2, a, b) * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< @@ -9731,7 +10187,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ return __pyx_r; } -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":779 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":779 * return PyArray_MultiIterNew(3, a, b, c) * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< @@ -9748,7 +10204,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew4", 0); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":780 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":780 * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): * return PyArray_MultiIterNew(4, a, b, c, d) # <<<<<<<<<<<<<< @@ -9762,7 +10218,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":779 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":779 * return PyArray_MultiIterNew(3, a, b, c) * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< @@ -9781,7 +10237,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ return __pyx_r; } -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":782 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":782 * return PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< @@ -9798,7 +10254,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew5", 0); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":783 * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): * return PyArray_MultiIterNew(5, a, b, c, d, e) # <<<<<<<<<<<<<< @@ -9812,7 +10268,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":782 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":782 * return PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< @@ -9831,7 +10287,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ return __pyx_r; } -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":785 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":785 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -9863,7 +10319,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_util_dtypestring", 0); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":790 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":790 * * cdef dtype child * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -9872,7 +10328,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_endian_detector = 1; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":791 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":791 * cdef dtype child * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -9881,7 +10337,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":794 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":794 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -9904,7 +10360,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_childname, __pyx_t_3); __pyx_t_3 = 0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":795 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":795 * * for childname in descr.names: * fields = descr.fields[childname] # <<<<<<<<<<<<<< @@ -9921,7 +10377,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_fields, ((PyObject*)__pyx_t_3)); __pyx_t_3 = 0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":796 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":796 * for childname in descr.names: * fields = descr.fields[childname] * child, new_offset = fields # <<<<<<<<<<<<<< @@ -9960,7 +10416,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_new_offset, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":798 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":798 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -9977,7 +10433,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0); if (__pyx_t_6) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":799 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":799 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -9990,7 +10446,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":798 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":798 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -9999,7 +10455,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":801 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -10019,7 +10475,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L8_next_or:; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":802 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -10036,7 +10492,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = __pyx_t_7; __pyx_L7_bool_binop_done:; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":801 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -10045,7 +10501,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (__pyx_t_6) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":803 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":803 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -10058,7 +10514,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":801 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -10067,7 +10523,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":813 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -10083,7 +10539,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":814 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -10092,7 +10548,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":815 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":815 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -10101,7 +10557,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":816 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -10112,7 +10568,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":818 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":818 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -10122,7 +10578,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":820 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":820 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -10132,7 +10588,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":821 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":821 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -10144,7 +10600,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":822 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":822 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -10154,7 +10610,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (__pyx_t_6) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":823 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -10167,7 +10623,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":822 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":822 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -10176,7 +10632,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":826 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -10194,7 +10650,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":827 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -10212,7 +10668,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":828 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":828 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -10230,7 +10686,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":829 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -10248,7 +10704,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":830 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":830 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -10266,7 +10722,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":831 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -10284,7 +10740,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":832 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -10302,7 +10758,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":833 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -10320,7 +10776,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":834 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -10338,7 +10794,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":835 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":835 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -10356,7 +10812,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":836 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -10374,7 +10830,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":837 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -10392,7 +10848,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":838 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -10410,7 +10866,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":839 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -10430,7 +10886,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":840 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -10450,7 +10906,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":841 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -10470,7 +10926,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":842 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -10488,7 +10944,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":844 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -10512,7 +10968,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":845 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":845 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -10521,7 +10977,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":820 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":820 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -10531,7 +10987,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":849 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":849 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -10544,7 +11000,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":794 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":794 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -10554,7 +11010,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":850 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -10564,7 +11020,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":785 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":785 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -10589,7 +11045,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":966 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":966 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -10604,7 +11060,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":968 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":968 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -10615,7 +11071,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":969 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":969 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -10624,7 +11080,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_baseptr = NULL; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":968 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":968 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -10634,7 +11090,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a goto __pyx_L3; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":971 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":971 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< @@ -10644,7 +11100,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a /*else*/ { Py_INCREF(__pyx_v_base); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":972 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":972 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< @@ -10655,7 +11111,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":973 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":973 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< @@ -10664,7 +11120,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":974 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":974 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -10673,7 +11129,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":966 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":966 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -10685,7 +11141,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976 +/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":976 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -10699,7 +11155,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":977 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -10709,7 +11165,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); if (__pyx_t_1) { - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":978 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":978 * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: * return None # <<<<<<<<<<<<<< @@ -10721,7 +11177,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; goto __pyx_L0; - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":977 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -10730,7 +11186,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":980 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":980 * return None * else: * return arr.base # <<<<<<<<<<<<<< @@ -10742,7 +11198,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py goto __pyx_L0; } - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":976 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -17342,7 +17798,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ * new_ndim += 1 * else: */ - (__pyx_v_p_dst->suboffsets[__pyx_v_new_ndim]) = -1L; + (__pyx_v_p_dst->suboffsets[__pyx_v_new_ndim]) = -1; /* "View.MemoryView":716 * p_dst.strides[new_ndim] = 0 @@ -18075,7 +18531,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * else: * stop = shape */ - __pyx_v_stop = -1L; + __pyx_v_stop = -1; /* "View.MemoryView":823 * stop = shape @@ -18431,7 +18887,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P * cdef Py_ssize_t itemsize = view.itemsize * cdef char *resultp */ - __pyx_v_suboffset = -1L; + __pyx_v_suboffset = -1; /* "View.MemoryView":871 * Py_ssize_t dim) except NULL: @@ -19721,7 +20177,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem if ((__pyx_v_suboffsets != 0)) { __pyx_t_4 = (__pyx_v_suboffsets[__pyx_v_dim]); } else { - __pyx_t_4 = -1L; + __pyx_t_4 = -1; } (__pyx_v_dst->suboffsets[__pyx_v_dim]) = __pyx_t_4; } @@ -20032,7 +20488,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ * if mslice.shape[i] > 1: * c_stride = mslice.strides[i] */ - for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1L; __pyx_t_1-=1) { + for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { __pyx_v_i = __pyx_t_1; /* "View.MemoryView":1081 @@ -20585,7 +21041,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ * stride = stride * shape[idx] */ /*else*/ { - for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1L; __pyx_t_2-=1) { + for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) { __pyx_v_idx = __pyx_t_2; /* "View.MemoryView":1159 @@ -20757,7 +21213,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, * * fill_contig_strides_array(&tmpslice.shape[0], &tmpslice.strides[0], itemsize, */ - (__pyx_v_tmpslice->suboffsets[__pyx_v_i]) = -1L; + (__pyx_v_tmpslice->suboffsets[__pyx_v_i]) = -1; } /* "View.MemoryView":1190 @@ -21802,7 +22258,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic * mslice.shape[i + offset] = mslice.shape[i] * mslice.strides[i + offset] = mslice.strides[i] */ - for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1L; __pyx_t_1-=1) { + for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { __pyx_v_i = __pyx_t_1; /* "View.MemoryView":1304 @@ -21869,7 +22325,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslic * * */ - (__pyx_v_mslice->suboffsets[__pyx_v_i]) = -1L; + (__pyx_v_mslice->suboffsets[__pyx_v_i]) = -1; } /* "View.MemoryView":1297 @@ -22366,9 +22822,11 @@ static PyMethodDef __pyx_methods_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile[] = {"__exit__", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_11__exit__, METH_VARARGS|METH_KEYWORDS, __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_10__exit__}, {"__next__", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_15__next__, METH_NOARGS|METH_COEXIST, 0}, {"seek", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_19seek, METH_O, __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek}, - {"offsets", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_21offsets, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20offsets}, - {"set_offsets", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_23set_offsets, METH_O, __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22set_offsets}, - {"tell", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_25tell, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_24tell}, + {"_bytes_seek", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_21_bytes_seek, METH_VARARGS|METH_KEYWORDS, __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_20_bytes_seek}, + {"offsets", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_23offsets, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_22offsets}, + {"set_offsets", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_25set_offsets, METH_O, __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_24set_offsets}, + {"tell", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_27tell, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_26tell}, + {"_bytes_tell", (PyCFunction)__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_29_bytes_tell, METH_NOARGS, __pyx_doc_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_28_bytes_tell}, {0, 0, 0, 0} }; @@ -23306,7 +23764,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_DTYPE, __pyx_k_DTYPE, sizeof(__pyx_k_DTYPE), 0, 0, 1, 1}, {&__pyx_n_s_Ellipsis, __pyx_k_Ellipsis, sizeof(__pyx_k_Ellipsis), 0, 0, 1, 1}, {&__pyx_kp_s_Empty_shape_tuple_for_cython_arr, __pyx_k_Empty_shape_tuple_for_cython_arr, sizeof(__pyx_k_Empty_shape_tuple_for_cython_arr), 0, 0, 1, 0}, - {&__pyx_kp_s_File_does_not_exists, __pyx_k_File_does_not_exists, sizeof(__pyx_k_File_does_not_exists), 0, 0, 1, 0}, + {&__pyx_kp_s_File_does_not_exist, __pyx_k_File_does_not_exist, sizeof(__pyx_k_File_does_not_exist), 0, 0, 1, 0}, {&__pyx_kp_s_File_opened_in_mode_Reading_only, __pyx_k_File_opened_in_mode_Reading_only, sizeof(__pyx_k_File_opened_in_mode_Reading_only), 0, 0, 1, 0}, {&__pyx_kp_s_File_opened_in_mode_Writing_only, __pyx_k_File_opened_in_mode_Writing_only, sizeof(__pyx_k_File_opened_in_mode_Writing_only), 0, 0, 1, 0}, {&__pyx_kp_u_Format_string_allocated_too_shor, __pyx_k_Format_string_allocated_too_shor, sizeof(__pyx_k_Format_string_allocated_too_shor), 0, 1, 0, 0}, @@ -23316,6 +23774,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_Indirect_dimensions_not_supporte, __pyx_k_Indirect_dimensions_not_supporte, sizeof(__pyx_k_Indirect_dimensions_not_supporte), 0, 0, 1, 0}, {&__pyx_kp_s_Invalid_mode_expected_c_or_fortr, __pyx_k_Invalid_mode_expected_c_or_fortr, sizeof(__pyx_k_Invalid_mode_expected_c_or_fortr), 0, 0, 1, 0}, {&__pyx_kp_s_Invalid_shape_in_axis_d_d, __pyx_k_Invalid_shape_in_axis_d_d, sizeof(__pyx_k_Invalid_shape_in_axis_d_d), 0, 0, 1, 0}, + {&__pyx_n_s_KeyError, __pyx_k_KeyError, sizeof(__pyx_k_KeyError), 0, 0, 1, 1}, {&__pyx_n_s_MemoryError, __pyx_k_MemoryError, sizeof(__pyx_k_MemoryError), 0, 0, 1, 1}, {&__pyx_kp_s_MemoryView_of_r_at_0x_x, __pyx_k_MemoryView_of_r_at_0x_x, sizeof(__pyx_k_MemoryView_of_r_at_0x_x), 0, 0, 1, 0}, {&__pyx_kp_s_MemoryView_of_r_object, __pyx_k_MemoryView_of_r_object, sizeof(__pyx_k_MemoryView_of_r_object), 0, 0, 1, 0}, @@ -23325,6 +23784,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_b_O, __pyx_k_O, sizeof(__pyx_k_O), 0, 0, 0, 1}, {&__pyx_n_s_OK, __pyx_k_OK, sizeof(__pyx_k_OK), 0, 0, 1, 1}, {&__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_k_Out_of_bounds_on_buffer_access_a, sizeof(__pyx_k_Out_of_bounds_on_buffer_access_a), 0, 0, 1, 0}, + {&__pyx_kp_s_Parameter_whence_must_be_one_of, __pyx_k_Parameter_whence_must_be_one_of, sizeof(__pyx_k_Parameter_whence_must_be_one_of), 0, 0, 1, 0}, {&__pyx_kp_s_Previous_frames_contained_atoms, __pyx_k_Previous_frames_contained_atoms, sizeof(__pyx_k_Previous_frames_contained_atoms), 0, 0, 1, 0}, {&__pyx_kp_s_Previous_frames_contained_box_Yo, __pyx_k_Previous_frames_contained_box_Yo, sizeof(__pyx_k_Previous_frames_contained_box_Yo), 0, 0, 1, 0}, {&__pyx_kp_s_Previous_frames_forces_contained, __pyx_k_Previous_frames_forces_contained, sizeof(__pyx_k_Previous_frames_forces_contained), 0, 0, 1, 0}, @@ -23334,6 +23794,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_Reached_last_frame_in_TRR_seek_t, __pyx_k_Reached_last_frame_in_TRR_seek_t, sizeof(__pyx_k_Reached_last_frame_in_TRR_seek_t), 0, 0, 1, 0}, {&__pyx_kp_s_Reached_last_frame_in_XTC_seek_t, __pyx_k_Reached_last_frame_in_XTC_seek_t, sizeof(__pyx_k_Reached_last_frame_in_XTC_seek_t), 0, 0, 1, 0}, {&__pyx_n_s_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 0, 0, 1, 1}, + {&__pyx_n_s_SEEK_CUR, __pyx_k_SEEK_CUR, sizeof(__pyx_k_SEEK_CUR), 0, 0, 1, 1}, + {&__pyx_n_s_SEEK_END, __pyx_k_SEEK_END, sizeof(__pyx_k_SEEK_END), 0, 0, 1, 1}, + {&__pyx_n_s_SEEK_SET, __pyx_k_SEEK_SET, sizeof(__pyx_k_SEEK_SET), 0, 0, 1, 1}, {&__pyx_n_s_StopIteration, __pyx_k_StopIteration, sizeof(__pyx_k_StopIteration), 0, 0, 1, 1}, {&__pyx_n_s_TRRFrame, __pyx_k_TRRFrame, sizeof(__pyx_k_TRRFrame), 0, 0, 1, 1}, {&__pyx_kp_s_TRR_Read_Error_occured, __pyx_k_TRR_Read_Error_occured, sizeof(__pyx_k_TRR_Read_Error_occured), 0, 0, 1, 0}, @@ -23344,7 +23807,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_Unable_to_convert_item_to_object, __pyx_k_Unable_to_convert_item_to_object, sizeof(__pyx_k_Unable_to_convert_item_to_object), 0, 0, 1, 0}, {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1}, {&__pyx_kp_s_XDRLIB_read_error, __pyx_k_XDRLIB_read_error, sizeof(__pyx_k_XDRLIB_read_error), 0, 0, 1, 0}, - {&__pyx_kp_s_XDR_seek_failed_error_message, __pyx_k_XDR_seek_failed_error_message, sizeof(__pyx_k_XDR_seek_failed_error_message), 0, 0, 1, 0}, + {&__pyx_kp_s_XDR_seek_failed_with_system_errn, __pyx_k_XDR_seek_failed_with_system_errn, sizeof(__pyx_k_XDR_seek_failed_with_system_errn), 0, 0, 1, 0}, {&__pyx_n_s_XTCFrame, __pyx_k_XTCFrame, sizeof(__pyx_k_XTCFrame), 0, 0, 1, 1}, {&__pyx_kp_s_XTC_Read_Error_occured, __pyx_k_XTC_Read_Error_occured, sizeof(__pyx_k_XTC_Read_Error_occured), 0, 0, 1, 0}, {&__pyx_kp_s_XTC_couldn_t_calculate_offsets_e, __pyx_k_XTC_couldn_t_calculate_offsets_e, sizeof(__pyx_k_XTC_couldn_t_calculate_offsets_e), 0, 0, 1, 0}, @@ -23396,6 +23859,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_integer, __pyx_k_integer, sizeof(__pyx_k_integer), 0, 0, 1, 1}, {&__pyx_n_s_itemsize, __pyx_k_itemsize, sizeof(__pyx_k_itemsize), 0, 0, 1, 1}, {&__pyx_kp_s_itemsize_0_for_cython_array, __pyx_k_itemsize_0_for_cython_array, sizeof(__pyx_k_itemsize_0_for_cython_array), 0, 0, 1, 0}, + {&__pyx_n_s_keys, __pyx_k_keys, sizeof(__pyx_k_keys), 0, 0, 1, 1}, {&__pyx_n_s_lambda, __pyx_k_lambda, sizeof(__pyx_k_lambda), 0, 0, 1, 1}, {&__pyx_n_s_magic, __pyx_k_magic, sizeof(__pyx_k_magic), 0, 0, 1, 1}, {&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1}, @@ -23414,6 +23878,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 0, 1, 1}, {&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1}, {&__pyx_n_s_obj, __pyx_k_obj, sizeof(__pyx_k_obj), 0, 0, 1, 1}, + {&__pyx_n_s_offset, __pyx_k_offset, sizeof(__pyx_k_offset), 0, 0, 1, 1}, {&__pyx_n_s_offsets, __pyx_k_offsets, sizeof(__pyx_k_offsets), 0, 0, 1, 1}, {&__pyx_n_s_open, __pyx_k_open, sizeof(__pyx_k_open), 0, 0, 1, 1}, {&__pyx_n_s_os_path, __pyx_k_os_path, sizeof(__pyx_k_os_path), 0, 0, 1, 1}, @@ -23448,17 +23913,20 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_velocity, __pyx_k_velocity, sizeof(__pyx_k_velocity), 0, 0, 1, 1}, {&__pyx_n_b_w, __pyx_k_w, sizeof(__pyx_k_w), 0, 0, 0, 1}, {&__pyx_n_s_w, __pyx_k_w, sizeof(__pyx_k_w), 0, 0, 1, 1}, + {&__pyx_n_s_whence, __pyx_k_whence, sizeof(__pyx_k_whence), 0, 0, 1, 1}, + {&__pyx_n_s_whence_vals, __pyx_k_whence_vals, sizeof(__pyx_k_whence_vals), 0, 0, 1, 1}, {&__pyx_kp_s_x_box_step_time_prec, __pyx_k_x_box_step_time_prec, sizeof(__pyx_k_x_box_step_time_prec), 0, 0, 1, 0}, {&__pyx_kp_s_x_v_f_box_step_time_lmbda_hasx_h, __pyx_k_x_v_f_box_step_time_lmbda_hasx_h, sizeof(__pyx_k_x_v_f_box_step_time_lmbda_hasx_h), 0, 0, 1, 0}, {&__pyx_n_s_xyz, __pyx_k_xyz, sizeof(__pyx_k_xyz), 0, 0, 1, 1}, {0, 0, 0, 0, 0, 0, 0} }; static int __Pyx_InitCachedBuiltins(void) { - __pyx_builtin_property = __Pyx_GetBuiltinName(__pyx_n_s_property); if (!__pyx_builtin_property) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 266; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_IOError = __Pyx_GetBuiltinName(__pyx_n_s_IOError); if (!__pyx_builtin_IOError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_StopIteration = __Pyx_GetBuiltinName(__pyx_n_s_StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 227; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_property = __Pyx_GetBuiltinName(__pyx_n_s_property); if (!__pyx_builtin_property) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_IOError = __Pyx_GetBuiltinName(__pyx_n_s_IOError); if (!__pyx_builtin_IOError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_StopIteration = __Pyx_GetBuiltinName(__pyx_n_s_StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_KeyError = __Pyx_GetBuiltinName(__pyx_n_s_KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_MemoryError = __Pyx_GetBuiltinName(__pyx_n_s_MemoryError); if (!__pyx_builtin_MemoryError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -23475,117 +23943,117 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":232 + /* "MDAnalysis/lib/formats/xdrlib.pyx":234 * def __len__(self): * if not self.is_open: * raise RuntimeError('No file currently opened') # <<<<<<<<<<<<<< * return self.offsets.size * */ - __pyx_tuple_ = PyTuple_Pack(1, __pyx_kp_s_No_file_currently_opened); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple_ = PyTuple_Pack(1, __pyx_kp_s_No_file_currently_opened); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple_); __Pyx_GIVEREF(__pyx_tuple_); - /* "MDAnalysis/lib/formats/xdrlib.pyx":257 + /* "MDAnalysis/lib/formats/xdrlib.pyx":260 * else: * if frame >= self.offsets.size: - * raise RuntimeError('Trying to seek over max number of frames') # <<<<<<<<<<<<<< + * raise IOError('Trying to seek over max number of frames') # <<<<<<<<<<<<<< * offset = self.offsets[frame] * self.reached_eof = False */ - __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_s_Trying_to_seek_over_max_number_o); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_s_Trying_to_seek_over_max_number_o); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__2); __Pyx_GIVEREF(__pyx_tuple__2); - /* "MDAnalysis/lib/formats/xdrlib.pyx":359 + /* "MDAnalysis/lib/formats/xdrlib.pyx":416 * """ * if self.reached_eof: * raise RuntimeError('Reached last frame in TRR, seek to 0') # <<<<<<<<<<<<<< * if not self.is_open: * raise RuntimeError('No file opened') */ - __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_s_Reached_last_frame_in_TRR_seek_t); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_s_Reached_last_frame_in_TRR_seek_t); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__3); __Pyx_GIVEREF(__pyx_tuple__3); - /* "MDAnalysis/lib/formats/xdrlib.pyx":361 + /* "MDAnalysis/lib/formats/xdrlib.pyx":418 * raise RuntimeError('Reached last frame in TRR, seek to 0') * if not self.is_open: * raise RuntimeError('No file opened') # <<<<<<<<<<<<<< * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. Reading only allow ' */ - __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_s_No_file_opened); if (unlikely(!__pyx_tuple__4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_s_No_file_opened); if (unlikely(!__pyx_tuple__4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__4); __Pyx_GIVEREF(__pyx_tuple__4); - /* "MDAnalysis/lib/formats/xdrlib.pyx":364 + /* "MDAnalysis/lib/formats/xdrlib.pyx":421 * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. Reading only allow ' * 'in mode "r"'.format('self.mode')) # <<<<<<<<<<<<<< * - * cdef int return_code = 1 + * return_code = 1 */ - __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__5); __Pyx_GIVEREF(__pyx_tuple__5); - /* "MDAnalysis/lib/formats/xdrlib.pyx":437 + /* "MDAnalysis/lib/formats/xdrlib.pyx":494 * if self.mode != 'w' : * raise RuntimeError('File opened in mode: {}. Writing only allow ' * 'in mode "w"'.format('self.mode')) # <<<<<<<<<<<<<< * * cdef float* xyz_ptr = NULL */ - __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__6); __Pyx_GIVEREF(__pyx_tuple__6); - /* "MDAnalysis/lib/formats/xdrlib.pyx":573 + /* "MDAnalysis/lib/formats/xdrlib.pyx":629 * """ * if self.reached_eof: * raise RuntimeError('Reached last frame in XTC, seek to 0') # <<<<<<<<<<<<<< * if not self.is_open: * raise RuntimeError('No file opened') */ - __pyx_tuple__7 = PyTuple_Pack(1, __pyx_kp_s_Reached_last_frame_in_XTC_seek_t); if (unlikely(!__pyx_tuple__7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__7 = PyTuple_Pack(1, __pyx_kp_s_Reached_last_frame_in_XTC_seek_t); if (unlikely(!__pyx_tuple__7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 629; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__7); __Pyx_GIVEREF(__pyx_tuple__7); - /* "MDAnalysis/lib/formats/xdrlib.pyx":575 + /* "MDAnalysis/lib/formats/xdrlib.pyx":631 * raise RuntimeError('Reached last frame in XTC, seek to 0') * if not self.is_open: * raise RuntimeError('No file opened') # <<<<<<<<<<<<<< * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. Reading only allow ' */ - __pyx_tuple__8 = PyTuple_Pack(1, __pyx_kp_s_No_file_opened); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 575; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__8 = PyTuple_Pack(1, __pyx_kp_s_No_file_opened); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__8); __Pyx_GIVEREF(__pyx_tuple__8); - /* "MDAnalysis/lib/formats/xdrlib.pyx":578 + /* "MDAnalysis/lib/formats/xdrlib.pyx":634 * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. Reading only allow ' * 'in mode "r"'.format('self.mode')) # <<<<<<<<<<<<<< * - * cdef int return_code = 1 + * return_code = 1 */ - __pyx_tuple__9 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__9 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__9); __Pyx_GIVEREF(__pyx_tuple__9); - /* "MDAnalysis/lib/formats/xdrlib.pyx":635 + /* "MDAnalysis/lib/formats/xdrlib.pyx":691 * if self.mode != 'w': * raise RuntimeError('File opened in mode: {}. Writing only allow ' * 'in mode "w"'.format('self.mode')) # <<<<<<<<<<<<<< * * cdef DTYPE_T[:, ::1] xyz_view = np.ascontiguousarray(xyz, dtype=DTYPE) */ - __pyx_tuple__10 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__10 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__10); __Pyx_GIVEREF(__pyx_tuple__10); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":218 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -23596,7 +24064,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__11); __Pyx_GIVEREF(__pyx_tuple__11); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":222 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -23607,7 +24075,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__12); __Pyx_GIVEREF(__pyx_tuple__12); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":259 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -23618,7 +24086,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__13); __Pyx_GIVEREF(__pyx_tuple__13); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":799 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":799 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -23629,7 +24097,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__14); __Pyx_GIVEREF(__pyx_tuple__14); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":803 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":803 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -23640,7 +24108,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__15); __Pyx_GIVEREF(__pyx_tuple__15); - /* "../../../../.virtualenvs/mda-p2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 + /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":823 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -23797,25 +24265,25 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__29); __Pyx_GIVEREF(__pyx_tuple__29); - /* "MDAnalysis/lib/formats/xdrlib.pyx":289 + /* "MDAnalysis/lib/formats/xdrlib.pyx":346 * * * TRRFrame = namedtuple('TRRFrame', 'x v f box step time lmbda hasx hasv hasf') # <<<<<<<<<<<<<< * * */ - __pyx_tuple__30 = PyTuple_Pack(2, __pyx_n_s_TRRFrame, __pyx_kp_s_x_v_f_box_step_time_lmbda_hasx_h); if (unlikely(!__pyx_tuple__30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__30 = PyTuple_Pack(2, __pyx_n_s_TRRFrame, __pyx_kp_s_x_v_f_box_step_time_lmbda_hasx_h); if (unlikely(!__pyx_tuple__30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__30); __Pyx_GIVEREF(__pyx_tuple__30); - /* "MDAnalysis/lib/formats/xdrlib.pyx":502 + /* "MDAnalysis/lib/formats/xdrlib.pyx":558 * * * XTCFrame = namedtuple('XTCFrame', 'x box step time prec') # <<<<<<<<<<<<<< * * */ - __pyx_tuple__31 = PyTuple_Pack(2, __pyx_n_s_XTCFrame, __pyx_kp_s_x_box_step_time_prec); if (unlikely(!__pyx_tuple__31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__31 = PyTuple_Pack(2, __pyx_n_s_XTCFrame, __pyx_kp_s_x_box_step_time_prec); if (unlikely(!__pyx_tuple__31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__31); __Pyx_GIVEREF(__pyx_tuple__31); @@ -23984,19 +24452,19 @@ PyMODINIT_FUNC PyInit_xdrlib(void) /*--- Variable export code ---*/ /*--- Function export code ---*/ /*--- Type init code ---*/ - if (PyType_Ready(&__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 96; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile.tp_print = 0; - if (PyObject_SetAttrString(__pyx_m, "_XDRFile", (PyObject *)&__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "_XDRFile", (PyObject *)&__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 96; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile = &__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile; __pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_TRRFile.tp_base = __pyx_ptype_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile; - if (PyType_Ready(&__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_TRRFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_TRRFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_TRRFile.tp_print = 0; - if (PyObject_SetAttrString(__pyx_m, "TRRFile", (PyObject *)&__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_TRRFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "TRRFile", (PyObject *)&__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_TRRFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_10MDAnalysis_3lib_7formats_6xdrlib_TRRFile = &__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_TRRFile; __pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_XTCFile.tp_base = __pyx_ptype_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile; - if (PyType_Ready(&__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_XTCFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 505; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_XTCFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 561; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_XTCFile.tp_print = 0; - if (PyObject_SetAttrString(__pyx_m, "XTCFile", (PyObject *)&__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_XTCFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 505; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "XTCFile", (PyObject *)&__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_XTCFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 561; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_10MDAnalysis_3lib_7formats_6xdrlib_XTCFile = &__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib_XTCFile; if (PyType_Ready(&__pyx_type___pyx_array) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 101; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type___pyx_array.tp_print = 0; @@ -24048,14 +24516,38 @@ PyMODINIT_FUNC PyInit_xdrlib(void) if (__Pyx_patch_abc() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif - /* "MDAnalysis/lib/formats/xdrlib.pyx":74 - * ENOTFOUND = 11 + /* "MDAnalysis/lib/formats/xdrlib.pyx":22 + * + * from libc.stdio cimport SEEK_SET, SEEK_CUR, SEEK_END + * _whence_vals = {"SEEK_SET": SEEK_SET, "SEEK_CUR": SEEK_CUR, "SEEK_END": SEEK_END} # <<<<<<<<<<<<<< + * + * cdef extern from 'include/xdrfile.h': + */ + __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = __Pyx_PyInt_From_int(SEEK_SET); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_SEEK_SET, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_PyInt_From_int(SEEK_CUR); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_SEEK_CUR, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = __Pyx_PyInt_From_int(SEEK_END); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_SEEK_END, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (PyDict_SetItem(__pyx_d, __pyx_n_s_whence_vals, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + + /* "MDAnalysis/lib/formats/xdrlib.pyx":76 + * ENOTFOUND = 12 * * error_message = ['OK', 'header', 'string', 'double', 'integer', # <<<<<<<<<<<<<< * 'float', 'unsigned integer', 'compression', * 'close', 'magic', 'memory', 'endoffile', */ - __pyx_t_2 = PyList_New(13); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyList_New(13); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_n_s_OK); __Pyx_GIVEREF(__pyx_n_s_OK); @@ -24096,64 +24588,64 @@ PyMODINIT_FUNC PyInit_xdrlib(void) __Pyx_INCREF(__pyx_n_s_notfound); __Pyx_GIVEREF(__pyx_n_s_notfound); PyList_SET_ITEM(__pyx_t_2, 12, __pyx_n_s_notfound); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_error_message, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_error_message, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":80 + /* "MDAnalysis/lib/formats/xdrlib.pyx":82 * * import cython * import numpy as np # <<<<<<<<<<<<<< * from os.path import exists * from collections import namedtuple */ - __pyx_t_2 = __Pyx_Import(__pyx_n_s_numpy, 0, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_Import(__pyx_n_s_numpy, 0, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":81 + /* "MDAnalysis/lib/formats/xdrlib.pyx":83 * import cython * import numpy as np * from os.path import exists # <<<<<<<<<<<<<< * from collections import namedtuple * */ - __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_n_s_exists); __Pyx_GIVEREF(__pyx_n_s_exists); PyList_SET_ITEM(__pyx_t_2, 0, __pyx_n_s_exists); - __pyx_t_3 = __Pyx_Import(__pyx_n_s_os_path, __pyx_t_2, -1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_Import(__pyx_n_s_os_path, __pyx_t_2, -1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_exists); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_ImportFrom(__pyx_t_3, __pyx_n_s_exists); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_exists, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_exists, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":82 + /* "MDAnalysis/lib/formats/xdrlib.pyx":84 * import numpy as np * from os.path import exists * from collections import namedtuple # <<<<<<<<<<<<<< * * np.import_array() */ - __pyx_t_3 = PyList_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyList_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_n_s_namedtuple); __Pyx_GIVEREF(__pyx_n_s_namedtuple); PyList_SET_ITEM(__pyx_t_3, 0, __pyx_n_s_namedtuple); - __pyx_t_2 = __Pyx_Import(__pyx_n_s_collections, __pyx_t_3, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_Import(__pyx_n_s_collections, __pyx_t_3, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_ImportFrom(__pyx_t_2, __pyx_n_s_namedtuple); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_ImportFrom(__pyx_t_2, __pyx_n_s_namedtuple); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_namedtuple, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_namedtuple, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":84 + /* "MDAnalysis/lib/formats/xdrlib.pyx":86 * from collections import namedtuple * * np.import_array() # <<<<<<<<<<<<<< @@ -24162,22 +24654,22 @@ PyMODINIT_FUNC PyInit_xdrlib(void) */ import_array(); - /* "MDAnalysis/lib/formats/xdrlib.pyx":87 + /* "MDAnalysis/lib/formats/xdrlib.pyx":89 * * ctypedef np.float32_t DTYPE_T * DTYPE = np.float32 # <<<<<<<<<<<<<< * cdef int DIMS = 3 * cdef int HASX = 1 */ - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_float32); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_float32); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - if (PyDict_SetItem(__pyx_d, __pyx_n_s_DTYPE, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_DTYPE, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":88 + /* "MDAnalysis/lib/formats/xdrlib.pyx":90 * ctypedef np.float32_t DTYPE_T * DTYPE = np.float32 * cdef int DIMS = 3 # <<<<<<<<<<<<<< @@ -24186,7 +24678,7 @@ PyMODINIT_FUNC PyInit_xdrlib(void) */ __pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_DIMS = 3; - /* "MDAnalysis/lib/formats/xdrlib.pyx":89 + /* "MDAnalysis/lib/formats/xdrlib.pyx":91 * DTYPE = np.float32 * cdef int DIMS = 3 * cdef int HASX = 1 # <<<<<<<<<<<<<< @@ -24195,7 +24687,7 @@ PyMODINIT_FUNC PyInit_xdrlib(void) */ __pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_HASX = 1; - /* "MDAnalysis/lib/formats/xdrlib.pyx":90 + /* "MDAnalysis/lib/formats/xdrlib.pyx":92 * cdef int DIMS = 3 * cdef int HASX = 1 * cdef int HASV = 2 # <<<<<<<<<<<<<< @@ -24204,7 +24696,7 @@ PyMODINIT_FUNC PyInit_xdrlib(void) */ __pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_HASV = 2; - /* "MDAnalysis/lib/formats/xdrlib.pyx":91 + /* "MDAnalysis/lib/formats/xdrlib.pyx":93 * cdef int HASX = 1 * cdef int HASV = 2 * cdef int HASF = 4 # <<<<<<<<<<<<<< @@ -24213,63 +24705,63 @@ PyMODINIT_FUNC PyInit_xdrlib(void) */ __pyx_v_10MDAnalysis_3lib_7formats_6xdrlib_HASF = 4; - /* "MDAnalysis/lib/formats/xdrlib.pyx":267 + /* "MDAnalysis/lib/formats/xdrlib.pyx":320 * * @property * def offsets(self): # <<<<<<<<<<<<<< * """get byte offsets from current xdr file * */ - __pyx_t_3 = __Pyx_GetNameInClass((PyObject *)__pyx_ptype_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile, __pyx_n_s_offsets); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 267; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetNameInClass((PyObject *)__pyx_ptype_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile, __pyx_n_s_offsets); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 320; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - /* "MDAnalysis/lib/formats/xdrlib.pyx":266 - * self.current_frame = frame + /* "MDAnalysis/lib/formats/xdrlib.pyx":319 + * raise IOError("XDR seek failed with system errno={}".format(ok)) * * @property # <<<<<<<<<<<<<< * def offsets(self): * """get byte offsets from current xdr file */ - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 266; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_property, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 266; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_property, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - if (PyDict_SetItem((PyObject *)__pyx_ptype_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile->tp_dict, __pyx_n_s_offsets, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 267; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem((PyObject *)__pyx_ptype_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile->tp_dict, __pyx_n_s_offsets, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 320; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; PyType_Modified(__pyx_ptype_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile); - /* "MDAnalysis/lib/formats/xdrlib.pyx":289 + /* "MDAnalysis/lib/formats/xdrlib.pyx":346 * * * TRRFrame = namedtuple('TRRFrame', 'x v f box step time lmbda hasx hasv hasf') # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_namedtuple); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_namedtuple); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__30, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__30, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - if (PyDict_SetItem(__pyx_d, __pyx_n_s_TRRFrame, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_TRRFrame, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":502 + /* "MDAnalysis/lib/formats/xdrlib.pyx":558 * * * XTCFrame = namedtuple('XTCFrame', 'x box step time prec') # <<<<<<<<<<<<<< * * */ - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_namedtuple); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_namedtuple); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__31, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__31, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - if (PyDict_SetItem(__pyx_d, __pyx_n_s_XTCFrame, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_XTCFrame, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; /* "MDAnalysis/lib/formats/xdrlib.pyx":1 @@ -24655,12 +25147,8 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec } #else static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; + PyObject* args = PyTuple_Pack(1, arg); + return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL; } #endif @@ -25213,32 +25701,32 @@ static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED switch (size) { case -2: if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); break; } case 2: if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); break; } case -3: if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); break; } case 3: if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); break; } case -4: if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); break; } case 4: if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); break; } #if PyLong_SHIFT < 30 && PyLong_SHIFT != 15 @@ -25268,6 +25756,94 @@ static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED } #endif +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->exc_type; + *value = tstate->exc_value; + *tb = tstate->exc_traceback; + Py_XINCREF(*type); + Py_XINCREF(*value); + Py_XINCREF(*tb); +#else + PyErr_GetExcInfo(type, value, tb); +#endif +} +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = type; + tstate->exc_value = value; + tstate->exc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(type, value, tb); +#endif +} + +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *local_type, *local_value, *local_tb; +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + local_type = tstate->curexc_type; + local_value = tstate->curexc_value; + local_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif + PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(tstate->curexc_type)) +#else + if (unlikely(PyErr_Occurred())) +#endif + goto bad; + #if PY_MAJOR_VERSION >= 3 + if (local_tb) { + if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) + goto bad; + } + #endif + Py_XINCREF(local_tb); + Py_XINCREF(local_type); + Py_XINCREF(local_value); + *type = local_type; + *value = local_value; + *tb = local_tb; +#if CYTHON_COMPILING_IN_CPYTHON + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = local_type; + tstate->exc_value = local_value; + tstate->exc_traceback = local_tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(local_type, local_value, local_tb); +#endif + return 0; +bad: + *type = 0; + *value = 0; + *tb = 0; + Py_XDECREF(local_type); + Py_XDECREF(local_value); + Py_XDECREF(local_tb); + return -1; +} + static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_SetString(PyExc_SystemError, "Missing type object"); @@ -26120,13 +26696,7 @@ static CYTHON_INLINE PyObject* __Pyx_decode_c_string( PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { Py_ssize_t length; if (unlikely((start < 0) | (stop < 0))) { - size_t slen = strlen(cstring); - if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { - PyErr_SetString(PyExc_OverflowError, - "c-string too long to convert to Python"); - return NULL; - } - length = (Py_ssize_t) slen; + length = strlen(cstring); if (start < 0) { start += length; if (start < 0) @@ -26146,94 +26716,6 @@ static CYTHON_INLINE PyObject* __Pyx_decode_c_string( } } -static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { -#if CYTHON_COMPILING_IN_CPYTHON - PyThreadState *tstate = PyThreadState_GET(); - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -#else - PyErr_GetExcInfo(type, value, tb); -#endif -} -static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { -#if CYTHON_COMPILING_IN_CPYTHON - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyThreadState *tstate = PyThreadState_GET(); - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(type, value, tb); -#endif -} - -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_COMPILING_IN_CPYTHON - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyThreadState *tstate = PyThreadState_GET(); - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_COMPILING_IN_CPYTHON - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; #if CYTHON_COMPILING_IN_CPYTHON @@ -26354,50 +26836,50 @@ static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED switch (size) { case -2: if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); break; } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | digits[0])); goto long_long; } case 2: if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); break; } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | digits[0])); goto long_long; } case -3: if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); break; } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); goto long_long; } case 3: if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); break; } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); goto long_long; } case -4: if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); break; } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); goto long_long; } case 4: if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); + a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); break; } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); + lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); goto long_long; } default: return PyLong_Type.tp_as_number->nb_add(op1, op2); @@ -26654,7 +27136,33 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #endif - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = (int) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } +} + +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) #define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) @@ -26701,27 +27209,27 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { case 2: if (8 * sizeof(int) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + return (int) (((((int)digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 3: if (8 * sizeof(int) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 4: if (8 * sizeof(int) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; @@ -26755,54 +27263,54 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { case -2: if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + return (int) -(((((int)digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 2: if (8 * sizeof(int) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + return (int) (((((int)digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case -3: if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + return (int) -(((((((int)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 3: if (8 * sizeof(int) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case -4: if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + return (int) -(((((((((int)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 4: if (8 * sizeof(int) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; @@ -26859,54 +27367,238 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { return (int) -1; } -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { - const int neg_one = (int) -1, const_zero = (int) 0; +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = (long) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { + if (sizeof(long) < sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { + } else if (sizeof(long) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); } } else { - if (sizeof(int) <= sizeof(long)) { + if (sizeof(long) <= sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { return PyLong_FromLongLong((PY_LONG_LONG) value); } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), + return _PyLong_FromByteArray(bytes, sizeof(long), little, !is_unsigned); } } -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { - const long neg_one = (long) -1, const_zero = (long) 0; +static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) { + const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int64_t) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int64_t, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int64_t) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int64_t) 0; + case 1: __PYX_VERIFY_RETURN_INT(int64_t, digit, digits[0]) + case 2: + if (8 * sizeof(int64_t) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int64_t) >= 2 * PyLong_SHIFT) { + return (int64_t) (((((int64_t)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int64_t) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int64_t) >= 3 * PyLong_SHIFT) { + return (int64_t) (((((((int64_t)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int64_t) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int64_t) >= 4 * PyLong_SHIFT) { + return (int64_t) (((((((((int64_t)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int64_t) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(int64_t) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int64_t, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (int64_t) 0; + case -1: __PYX_VERIFY_RETURN_INT(int64_t, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(int64_t, digit, +digits[0]) + case -2: + if (8 * sizeof(int64_t) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { + return (int64_t) -(((((int64_t)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 2: + if (8 * sizeof(int64_t) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { + return (int64_t) (((((int64_t)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case -3: + if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { + return (int64_t) -(((((((int64_t)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int64_t) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { + return (int64_t) (((((((int64_t)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case -4: + if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT) { + return (int64_t) -(((((((((int64_t)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int64_t) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT) { + return (int64_t) (((((((((int64_t)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + } +#endif + if (sizeof(int64_t) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(int64_t, long, PyLong_AsLong(x)) + } else if (sizeof(int64_t) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int64_t, PY_LONG_LONG, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int64_t val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int64_t) -1; + } + } else { + int64_t val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (int64_t) -1; + val = __Pyx_PyInt_As_int64_t(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int64_t"); + return (int64_t) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int64_t"); + return (int64_t) -1; +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int64_t(int64_t value) { + const int64_t neg_one = (int64_t) -1, const_zero = (int64_t) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { - if (sizeof(long) < sizeof(long)) { + if (sizeof(int64_t) < sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { + } else if (sizeof(int64_t) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + } else if (sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG)) { return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); } } else { - if (sizeof(long) <= sizeof(long)) { + if (sizeof(int64_t) <= sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + } else if (sizeof(int64_t) <= sizeof(PY_LONG_LONG)) { return PyLong_FromLongLong((PY_LONG_LONG) value); } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), + return _PyLong_FromByteArray(bytes, sizeof(int64_t), little, !is_unsigned); } } @@ -27338,27 +28030,27 @@ static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { case 2: if (8 * sizeof(char) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { - return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + return (char) (((((char)digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 3: if (8 * sizeof(char) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { - return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + return (char) (((((((char)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 4: if (8 * sizeof(char) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { - return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); + return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; @@ -27392,54 +28084,54 @@ static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { case -2: if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + return (char) -(((((char)digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 2: if (8 * sizeof(char) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + return (char) (((((char)digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case -3: if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + return (char) -(((((((char)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 3: if (8 * sizeof(char) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + return (char) (((((((char)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case -4: if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + return (char) -(((((((((char)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 4: if (8 * sizeof(char) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); + return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; @@ -27522,27 +28214,27 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { case 2: if (8 * sizeof(long) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + return (long) (((((long)digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 3: if (8 * sizeof(long) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 4: if (8 * sizeof(long) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; @@ -27576,54 +28268,54 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { case -2: if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + return (long) -(((((long)digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 2: if (8 * sizeof(long) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + return (long) (((((long)digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case -3: if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + return (long) -(((((((long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 3: if (8 * sizeof(long) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case -4: if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + return (long) -(((((((((long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; case 4: if (8 * sizeof(long) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } } break; @@ -28262,32 +28954,32 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { switch (size) { case 2: if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | digits[0])); } break; case -2: if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | digits[0])); } break; case 3: if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } break; case -3: if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } break; case 4: if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } break; case -4: if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); + return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); } break; } diff --git a/package/MDAnalysis/lib/formats/xdrlib.pyx b/package/MDAnalysis/lib/formats/xdrlib.pyx index df3d7e38c32..f7dd7e6ab59 100644 --- a/package/MDAnalysis/lib/formats/xdrlib.pyx +++ b/package/MDAnalysis/lib/formats/xdrlib.pyx @@ -18,7 +18,8 @@ cimport cython from cython_util cimport ptr_to_ndarray from libc.stdint cimport int64_t -from libc.stdio cimport SEEK_SET +from libc.stdio cimport SEEK_SET, SEEK_CUR, SEEK_END +_whence_vals = {"SEEK_SET": SEEK_SET, "SEEK_CUR": SEEK_CUR, "SEEK_END": SEEK_END} cdef extern from 'include/xdrfile.h': ctypedef struct XDRFILE: @@ -27,6 +28,7 @@ cdef extern from 'include/xdrfile.h': XDRFILE* xdrfile_open (char * path, char * mode) int xdrfile_close (XDRFILE * xfp) int xdr_seek(XDRFILE *xfp, int64_t pos, int whence) + int64_t xdr_tell(XDRFILE *xfp) ctypedef float matrix[3][3] ctypedef float rvec[3] @@ -69,7 +71,7 @@ cdef enum: EMAGIC = 9 EMEMORY = 10 EENDOFFILE = 11 - ENOTFOUND = 11 + ENOTFOUND = 12 error_message = ['OK', 'header', 'string', 'double', 'integer', 'float', 'unsigned integer', 'compression', @@ -143,11 +145,11 @@ cdef class _XDRFile: IOError If the TRR file can't be closed for some reason """ - cdef int res = 1 + res = 1 if self.is_open: res = xdrfile_close(self.xfp) self.is_open = False - if res != 0: + if res != EOK: raise IOError('Couldn\'t close file: {}, Error = XDRLIB-{}'.format( self.fname, error_message[res])) # forget old offsets in case we open a different file with the same instance. @@ -191,11 +193,11 @@ cdef class _XDRFile: if self.mode == 'r': if not exists(self.fname): - raise IOError('File does not exists: {}'.format(self.fname)) + raise IOError('File does not exist: {}'.format(self.fname)) return_code, self.n_atoms = self._calc_natoms(fname); - if return_code != 0: + if return_code != EOK: raise IOError('XDRLIB read error: {}'.format( error_message[return_code])) if self.n_atoms <= 0: @@ -235,9 +237,9 @@ cdef class _XDRFile: def seek(self, frame): """Seek to Frame. - Please note if that this function will generate internal file offsets if + Please note that this function will generate internal file offsets if they haven't been set before. For large file this means the first seek - can be very slow. Later seeks will be very fast + can be very slow. Later seeks will be very fast. Parameters ---------- @@ -246,23 +248,74 @@ cdef class _XDRFile: Raises ------ - RuntimeError - If you seek for more frames then are available + IOError + If you seek for more frames than are available or if the + seek fails (the low-level system error is reported). """ - cdef int offset + cdef int64_t offset if frame == 0: offset = 0 else: if frame >= self.offsets.size: - raise RuntimeError('Trying to seek over max number of frames') + raise IOError('Trying to seek over max number of frames') offset = self.offsets[frame] self.reached_eof = False ok = xdr_seek(self.xfp, offset, SEEK_SET) - if ok != 0: - raise RuntimeError("XDR seek failed, error-message={}".format( - error_message[ok])) + if ok != EOK: + # errno is the direct system error, not from the XDR library. + # errno=22 can be cryptic, since it means a wrong 'whence' + # parameter but it will also be issued when the resulting file + # offset is negative, or if the offset overflows the filesystem + # limit (ext3 is 16TB, for instance). + raise IOError("XDR seek failed with system errno={}".format(ok)) self.current_frame = frame + def _bytes_seek(self, offset, whence="SEEK_SET"): + """Low-level access to the stream repositioning xdr_seek call. + + Beware that this function will not update :attr:`current_frame`, + even on a successful seek, and might render the :class:`Reader` + unstable. + + Parameters + ---------- + offset : int + move the stream *offset* bytes relative to *whence* + (can be negative). + + whence : str, optional + must be one of: + "SEEK_SET": *offset* is applied relative to the beginning + of the file. + "SEEK_CUR": *offset* is applied relative to the current + position in the stream. + "SEEK_END": *offset* is applied relative to the end of + the file (a positive *offset* will seek beyond the + end of the file, without an error) + + Raises + ------ + ValueError + If *whence* is not one of the expected strings. + + IOError + If the seek fails (the low-level system error is reported). + """ + cdef int whn + cdef int64_t offst + + try: + whn = _whence_vals[whence] + except KeyError: + raise ValueError("Parameter 'whence' must be " + "one of {}".format(tuple(_whence_vals.keys()))) + offst = offset + self.reached_eof = False + ok = xdr_seek(self.xfp, offst, whn) + if ok != EOK: + # See the comments to seek() for hints on errno meaning. + raise IOError("XDR seek failed with system errno={}".format(ok)) + @property def offsets(self): """get byte offsets from current xdr file @@ -285,6 +338,10 @@ cdef class _XDRFile: """Get current frame""" return self.current_frame + def _bytes_tell(self): + """Low-level call to xdr_tell to get current byte offset.""" + return xdr_tell(self.xfp) + TRRFrame = namedtuple('TRRFrame', 'x v f box step time lmbda hasx hasv hasf') @@ -325,7 +382,7 @@ cdef class TRRFile(_XDRFile): cdef int est_nframes = 0 cdef int64_t* offsets = NULL ok = read_trr_n_frames(self.fname, &n_frames, &est_nframes, &offsets); - if ok != 0: + if ok != EOK: raise RuntimeError("TRR couldn't calculate offsets, error={}".format( error_message[ok])) # the read_xtc_n_frames allocates memory for the offsets with an @@ -363,7 +420,7 @@ cdef class TRRFile(_XDRFile): raise RuntimeError('File opened in mode: {}. Reading only allow ' 'in mode "r"'.format('self.mode')) - cdef int return_code = 1 + return_code = 1 cdef int step = 0 cdef int has_prop = 0 cdef float time = 0 @@ -392,7 +449,7 @@ cdef class TRRFile(_XDRFile): # In a trr the integer error seems to indicate that the file is ending. # There might be corrupted files where this is a legitimate error. But - # then we just can't read it and stop there which is not to bad. + # then we just can't read it and stop there which is not too bad. if return_code == EENDOFFILE or return_code == EINTEGER: self.reached_eof = True raise StopIteration @@ -486,7 +543,6 @@ cdef class TRRFile(_XDRFile): 'are trying to write {} box.'.format( self.box, box)) - cdef int return_code return_code = write_trr(self.xfp, self.n_atoms, step, time, _lambda, box_ptr, xyz_ptr, @@ -539,7 +595,7 @@ cdef class XTCFile(_XDRFile): cdef int est_nframes = 0 cdef int64_t* offsets = NULL ok = read_xtc_n_frames(self.fname, &n_frames, &est_nframes, &offsets); - if ok != 0: + if ok != EOK: raise RuntimeError("XTC couldn't calculate offsets, error={}".format( error_message[ok])) # the read_xtc_n_frames allocates memory for the offsets with an @@ -577,7 +633,7 @@ cdef class XTCFile(_XDRFile): raise RuntimeError('File opened in mode: {}. Reading only allow ' 'in mode "r"'.format('self.mode')) - cdef int return_code = 1 + return_code = 1 cdef int step cdef float time, prec @@ -655,7 +711,6 @@ cdef class XTCFile(_XDRFile): 'are trying to use {}'.format( self.precision, precision)) - cdef int return_code return_code = write_xtc(self.xfp, self.n_atoms, step, time, &box_view[0, 0], &xyz_view[0, 0], precision) diff --git a/testsuite/MDAnalysisTests/formats/test_xdrlib.py b/testsuite/MDAnalysisTests/formats/test_xdrlib.py index 291f9de2354..0bba21ca48b 100644 --- a/testsuite/MDAnalysisTests/formats/test_xdrlib.py +++ b/testsuite/MDAnalysisTests/formats/test_xdrlib.py @@ -46,7 +46,7 @@ def test_raise_not_existing(self): def test_open_wrong_mode(self): self.xdrfile('foo', 'e') - @raises(RuntimeError) + @raises(IOError) def test_over_seek(self): with self.xdrfile(self.multi_frame) as f: f.seek(100) @@ -91,6 +91,34 @@ def test_set_offsets(self): f.seek(6) f.read() + @raises(OverflowError) + def test_seek_overflow(self): + f = self.xdrfile(self.multi_frame) + f._bytes_seek(2**65) + + def test_seek_tell_all(self): + f = self.xdrfile(self.multi_frame) + for frame, offset in enumerate(self.offsets): + f.seek(frame) + assert f._bytes_tell() == offset + + def test_seek_tell_all_bytes(self): + f = self.xdrfile(self.multi_frame) + for offset in self.offsets: + f._bytes_seek(offset) + assert f._bytes_tell() == offset + + def test_seek_tell_largefile(self): + # Seeking/telling can be done on offsets larger than the file. + # Filesize won't change unless a write is done at the offset. + # We attempt to go just beyond a 4GB limit. + big_offset = 2**32+1000 + f = self.xdrfile(self.multi_frame) + f._bytes_seek(big_offset) + assert f._bytes_tell() == big_offset + # It should be safe to leave the read head so far away + # because the file is open read-only. + class Test_XTCFile(XDRFormatBaseTest): xdrfile = XTCFile