From 4b634b2cbfb751c9847c328dda30a09ff04e8427 Mon Sep 17 00:00:00 2001 From: Manuel Nuno Melo Date: Thu, 28 Jan 2016 17:16:19 +0100 Subject: [PATCH] Added _bytes_seek and _bytes_tell XDR methods On error xtc_seek now returns the system errno value, which is printed as is. This is more informative and fixes an IndexError looking up the error message, that occurred when xtc_seek failed and returned exdrNR. Added testing for _bytes_seek and _bytes_tell, also beyond 4GB filesize limits. --- package/CHANGELOG | 1 + package/MDAnalysis/lib/formats/src/xdrfile.c | 11 +- package/MDAnalysis/lib/formats/xdrlib.c | 2269 ++++++++++------- package/MDAnalysis/lib/formats/xdrlib.pyx | 77 +- .../MDAnalysisTests/formats/test_xdrlib.py | 28 + 5 files changed, 1455 insertions(+), 931 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index c7ab67430ec..a1185a3f6bf 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -26,6 +26,7 @@ API Changes 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) diff --git a/package/MDAnalysis/lib/formats/src/xdrfile.c b/package/MDAnalysis/lib/formats/src/xdrfile.c index 78aaf2eeaef..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 @@ -2607,7 +2608,13 @@ xdrstdio_getpos (XDR *xdrs) static int 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 1af0c88a229..818006b8a16 100644 --- a/package/MDAnalysis/lib/formats/xdrlib.c +++ b/package/MDAnalysis/lib/formats/xdrlib.c @@ -894,7 +894,7 @@ 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":95 @@ -919,7 +919,7 @@ struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile { }; -/* "MDAnalysis/lib/formats/xdrlib.pyx":293 +/* "MDAnalysis/lib/formats/xdrlib.pyx":353 * * * cdef class TRRFile(_XDRFile): # <<<<<<<<<<<<<< @@ -931,7 +931,7 @@ struct __pyx_obj_10MDAnalysis_3lib_7formats_6xdrlib_TRRFile { }; -/* "MDAnalysis/lib/formats/xdrlib.pyx":506 +/* "MDAnalysis/lib/formats/xdrlib.pyx":567 * * * cdef class XTCFile(_XDRFile): # <<<<<<<<<<<<<< @@ -1430,6 +1430,8 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *); +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int64_t(int64_t value); + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); #if CYTHON_CCOMPLEX @@ -1770,9 +1772,11 @@ 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"; @@ -1782,6 +1786,9 @@ 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_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"; @@ -1817,7 +1824,7 @@ 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[] = ""; @@ -1837,9 +1844,9 @@ 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 'SEEK_SET', 'SEEK_CUR', or 'SEEK_END'."; 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"; @@ -1865,6 +1872,7 @@ 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 {}"; @@ -1881,7 +1889,7 @@ 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; @@ -1900,6 +1908,7 @@ 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; @@ -1909,6 +1918,9 @@ 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; @@ -1919,7 +1931,7 @@ 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; @@ -1989,6 +2001,7 @@ 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; @@ -2023,6 +2036,7 @@ 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_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; @@ -2036,9 +2050,11 @@ 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 */ @@ -2103,9 +2119,9 @@ static PyObject *__pyx_tuple__6; static PyObject *__pyx_tuple__7; static PyObject *__pyx_tuple__8; static PyObject *__pyx_tuple__9; -static PyObject *__pyx_slice__26; static PyObject *__pyx_slice__27; static PyObject *__pyx_slice__28; +static PyObject *__pyx_slice__29; static PyObject *__pyx_tuple__10; static PyObject *__pyx_tuple__11; static PyObject *__pyx_tuple__12; @@ -2122,7 +2138,7 @@ static PyObject *__pyx_tuple__22; static PyObject *__pyx_tuple__23; static PyObject *__pyx_tuple__24; static PyObject *__pyx_tuple__25; -static PyObject *__pyx_tuple__29; +static PyObject *__pyx_tuple__26; static PyObject *__pyx_tuple__30; static PyObject *__pyx_tuple__31; static PyObject *__pyx_tuple__32; @@ -2130,6 +2146,7 @@ static PyObject *__pyx_tuple__33; static PyObject *__pyx_tuple__34; static PyObject *__pyx_tuple__35; static PyObject *__pyx_tuple__36; +static PyObject *__pyx_tuple__37; /* "MDAnalysis/lib/formats/xdrlib.pyx":131 * cdef int _has_offsets @@ -2917,7 +2934,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str * * 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 = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_6 = (__pyx_t_1 != 0); @@ -2927,7 +2944,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str * * 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 = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -2965,11 +2982,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str /* "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)) # <<<<<<<<<<<<<< * * 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 = 195; __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 = 195; __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))) { @@ -3012,13 +3029,13 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str * * 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":197 - * 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); # <<<<<<<<<<<<<< * @@ -3282,7 +3299,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_6open(str * * 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)) */ } @@ -3965,7 +3982,7 @@ 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 than 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 RuntimeError\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 @@ -3995,21 +4012,21 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek(st int __pyx_clineno = 0; __Pyx_RefNannySetupContext("seek", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":254 - * """ + /* "MDAnalysis/lib/formats/xdrlib.pyx":256 * cdef int64_t offset + * cdef int ok * 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 = 254; __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 = 254; __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":255 - * cdef int64_t offset + /* "MDAnalysis/lib/formats/xdrlib.pyx":257 + * cdef int ok * if frame == 0: * offset = 0 # <<<<<<<<<<<<<< * else: @@ -4017,9 +4034,9 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek(st */ __pyx_v_offset = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":254 - * """ + /* "MDAnalysis/lib/formats/xdrlib.pyx":256 * cdef int64_t offset + * cdef int ok * if frame == 0: # <<<<<<<<<<<<<< * offset = 0 * else: @@ -4027,7 +4044,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek(st goto __pyx_L3; 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__pyx_t_1 = 0; if (__pyx_t_2) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":258 + /* "MDAnalysis/lib/formats/xdrlib.pyx":260 * else: * if frame >= self.offsets.size: * raise RuntimeError('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 = 258; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __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 = 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 = 258; __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":257 + /* "MDAnalysis/lib/formats/xdrlib.pyx":259 * offset = 0 * else: * if frame >= self.offsets.size: # <<<<<<<<<<<<<< @@ -4068,25 +4085,25 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek(st */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":259 + /* "MDAnalysis/lib/formats/xdrlib.pyx":261 * if frame >= self.offsets.size: * raise RuntimeError('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 = 259; __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__; 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if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 265; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __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":236 @@ -4226,7 +4224,327 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek(st return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":268 +/* "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. + * + */ + +/* Python wrapper */ +static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_21_bytes_seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); 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__pyx_lineno = 384; __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))) { @@ -4750,17 +5132,17 @@ 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 = 324; __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 = 384; __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 = 324; __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 = 384; __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 = 324; __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 = 384; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } @@ -4769,26 +5151,26 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs __pyx_t_2 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":323 + /* "MDAnalysis/lib/formats/xdrlib.pyx":383 * def calc_offsets(self): * """read byte offsets from TRR file directly""" * if not self.is_open: # <<<<<<<<<<<<<< * return np.array([]) - * cdef int n_frames = 0 + * cdef int ok */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":325 - * if not self.is_open: + /* "MDAnalysis/lib/formats/xdrlib.pyx":386 * return np.array([]) + * cdef int ok * cdef int n_frames = 0 # <<<<<<<<<<<<<< * cdef int est_nframes = 0 * cdef int64_t* offsets = NULL */ __pyx_v_n_frames = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":326 - * return np.array([]) + /* "MDAnalysis/lib/formats/xdrlib.pyx":387 + * cdef int ok * cdef int n_frames = 0 * cdef int est_nframes = 0 # <<<<<<<<<<<<<< * cdef int64_t* offsets = NULL @@ -4796,7 +5178,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs */ __pyx_v_est_nframes = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":327 + /* "MDAnalysis/lib/formats/xdrlib.pyx":388 * cdef int n_frames = 0 * cdef int est_nframes = 0 * cdef int64_t* offsets = NULL # <<<<<<<<<<<<<< @@ -4805,17 +5187,17 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_2calc_offs */ __pyx_v_offsets = NULL; - /* "MDAnalysis/lib/formats/xdrlib.pyx":328 + /* "MDAnalysis/lib/formats/xdrlib.pyx":389 * 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: * raise RuntimeError("TRR couldn't calculate offsets, error={}".format( */ - __pyx_t_7 = __Pyx_PyObject_AsString(__pyx_v_self->__pyx_base.fname); 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if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __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 = 391; __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 = 330; __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 = 391; __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 = 330; __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 = 391; __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":330 + /* "MDAnalysis/lib/formats/xdrlib.pyx":391 * ok = read_trr_n_frames(self.fname, &n_frames, &est_nframes, &offsets); * if ok != 0: * 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 = 330; __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 = 391; __pyx_clineno = __LINE__; 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if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":362 + /* "MDAnalysis/lib/formats/xdrlib.pyx":423 * 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: {}. 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__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":363 + /* "MDAnalysis/lib/formats/xdrlib.pyx":424 * if not self.is_open: * raise RuntimeError('No file opened') * if self.mode != 'r': # <<<<<<<<<<<<<< @@ -5167,7 +5549,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":367 + /* "MDAnalysis/lib/formats/xdrlib.pyx":428 * 'in mode "r"'.format('self.mode')) * * cdef int return_code = 1 # <<<<<<<<<<<<<< @@ -5176,7 +5558,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ __pyx_v_return_code = 1; - /* "MDAnalysis/lib/formats/xdrlib.pyx":368 + /* "MDAnalysis/lib/formats/xdrlib.pyx":429 * * cdef int return_code = 1 * cdef int step = 0 # <<<<<<<<<<<<<< @@ -5185,7 +5567,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ __pyx_v_step = 0; 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if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __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 = 378; __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 = 439; __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 = 378; __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 = 439; __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 = 378; __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 = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_box = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":380 + /* "MDAnalysis/lib/formats/xdrlib.pyx":441 * cdef np.ndarray box = np.empty((DIMS, DIMS), dtype=DTYPE) * * return_code = read_trr(self.xfp, self.n_atoms, &step, # <<<<<<<<<<<<<< @@ -5397,7 +5779,7 @@ 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":389 + /* "MDAnalysis/lib/formats/xdrlib.pyx":450 * # results in an integer error while reading. 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- /* "MDAnalysis/lib/formats/xdrlib.pyx":392 + /* "MDAnalysis/lib/formats/xdrlib.pyx":453 * 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 = 392; __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 = 453; __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 = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __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 = 453; __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; @@ -5465,42 +5847,42 @@ 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 = 391; __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 = 452; __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 = 391; __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 = 452; __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 = 391; __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 = 452; __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":391 + /* "MDAnalysis/lib/formats/xdrlib.pyx":452 * 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 = 391; __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 = 452; __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 = 391; __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 = 452; __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 = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":389 + /* "MDAnalysis/lib/formats/xdrlib.pyx":450 * # 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 \ # <<<<<<<<<<<<<< @@ -5509,9 +5891,9 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":397 + /* "MDAnalysis/lib/formats/xdrlib.pyx":458 * # 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 @@ -5520,8 +5902,8 @@ 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":398 - * # then we just can't read it and stop there which is not to bad. + /* "MDAnalysis/lib/formats/xdrlib.pyx":459 + * # 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 @@ -5529,7 +5911,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ __pyx_v_self->__pyx_base.reached_eof = 1; - /* "MDAnalysis/lib/formats/xdrlib.pyx":399 + /* "MDAnalysis/lib/formats/xdrlib.pyx":460 * if return_code == EENDOFFILE or return_code == EINTEGER: * self.reached_eof = True * raise StopIteration # <<<<<<<<<<<<<< @@ -5537,11 +5919,11 @@ 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 = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":397 + /* "MDAnalysis/lib/formats/xdrlib.pyx":458 * # 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 @@ -5550,7 +5932,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru default: break; } - /* "MDAnalysis/lib/formats/xdrlib.pyx":401 + /* "MDAnalysis/lib/formats/xdrlib.pyx":462 * raise StopIteration * * if return_code == EOK: # <<<<<<<<<<<<<< @@ -5560,7 +5942,7 @@ 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":402 + /* "MDAnalysis/lib/formats/xdrlib.pyx":463 * * if return_code == EOK: * self.current_frame += 1 # <<<<<<<<<<<<<< @@ -5569,7 +5951,7 @@ 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":401 + /* "MDAnalysis/lib/formats/xdrlib.pyx":462 * raise StopIteration * * if return_code == EOK: # <<<<<<<<<<<<<< @@ -5578,55 +5960,55 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":404 + /* "MDAnalysis/lib/formats/xdrlib.pyx":465 * 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 = 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_HASX)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __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 = 465; __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 = 465; __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":405 + /* "MDAnalysis/lib/formats/xdrlib.pyx":466 * * 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 = 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_HASV)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __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 = 466; __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 = 466; __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":406 + /* "MDAnalysis/lib/formats/xdrlib.pyx":467 * 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 = 406; __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 = 467; __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 = 406; __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 = 467; __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 = 406; __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 = 467; __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":407 + /* "MDAnalysis/lib/formats/xdrlib.pyx":468 * has_v = bool(has_prop & HASV) * has_f = bool(has_prop & HASF) * return TRRFrame(xyz, velocity, forces, box, step, time, lmbda, # <<<<<<<<<<<<<< @@ -5634,16 +6016,16 @@ 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 = 407; __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 = 468; __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 = 407; __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 = 468; __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 = 407; __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 = 468; __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 = 407; __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 = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "MDAnalysis/lib/formats/xdrlib.pyx":408 + /* "MDAnalysis/lib/formats/xdrlib.pyx":469 * has_f = bool(has_prop & HASF) * return TRRFrame(xyz, velocity, forces, box, step, time, lmbda, * has_x, has_v, has_f) # <<<<<<<<<<<<<< @@ -5662,7 +6044,7 @@ 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 = 407; __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 = 468; __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; @@ -5697,7 +6079,7 @@ 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 = 407; __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 = 468; __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; @@ -5705,7 +6087,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru __pyx_t_4 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":341 + /* "MDAnalysis/lib/formats/xdrlib.pyx":402 * return nd_offsets[:n_frames] * * def read(self): # <<<<<<<<<<<<<< @@ -5737,7 +6119,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":410 +/* "MDAnalysis/lib/formats/xdrlib.pyx":471 * has_x, has_v, has_f) * * def write(self, xyz, velocity, forces, box, int step, float time, # <<<<<<<<<<<<<< @@ -5789,41 +6171,41 @@ 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 = 410; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __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 = 410; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __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 = 410; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __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 = 410; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __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 = 410; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __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 = 410; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __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 = 410; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, 7); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __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 = 410; __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 = 471; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 8) { goto __pyx_L5_argtuple_error; @@ -5841,14 +6223,14 @@ 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]; 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__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 = 471; __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 = 472; __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 = 472; __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 = 410; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 1, 8, 8, PyTuple_GET_SIZE(__pyx_args)); 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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 486; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":485 + /* "MDAnalysis/lib/formats/xdrlib.pyx":546 * 'are trying to write {} atoms.'.format( * self.n_atoms, forces.shape[0])) * if not np.allclose(self.box, box, rtol=0, atol=1e-2): # <<<<<<<<<<<<<< @@ -6763,7 +7145,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str } __pyx_L7:; - /* "MDAnalysis/lib/formats/xdrlib.pyx":491 + /* "MDAnalysis/lib/formats/xdrlib.pyx":552 * * cdef int return_code * return_code = write_trr(self.xfp, self.n_atoms, step, time, # <<<<<<<<<<<<<< @@ -6772,7 +7154,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ __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":496 + /* "MDAnalysis/lib/formats/xdrlib.pyx":557 * velocity_ptr, * forces_ptr) * if return_code != EOK: # <<<<<<<<<<<<<< @@ -6782,26 +7164,26 @@ 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":497 + /* "MDAnalysis/lib/formats/xdrlib.pyx":558 * 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 = 497; __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 = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "MDAnalysis/lib/formats/xdrlib.pyx":498 + /* "MDAnalysis/lib/formats/xdrlib.pyx":559 * 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 = 498; __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 = 559; __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 = 498; __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); 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__pyx_lineno = 538; __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 = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } @@ -7087,7 +7469,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs __pyx_t_2 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":537 + /* "MDAnalysis/lib/formats/xdrlib.pyx":598 * def calc_offsets(self): * """Calculate offsets from XTC file directly""" * if not self.is_open: # <<<<<<<<<<<<<< @@ -7096,7 +7478,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":539 + /* "MDAnalysis/lib/formats/xdrlib.pyx":600 * if not self.is_open: * return np.array([]) * cdef int n_frames = 0 # <<<<<<<<<<<<<< @@ -7105,7 +7487,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs */ __pyx_v_n_frames = 0; 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if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 542; __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 = 603; __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":543 + /* "MDAnalysis/lib/formats/xdrlib.pyx":604 * cdef int64_t* offsets = NULL * ok = read_xtc_n_frames(self.fname, &n_frames, &est_nframes, &offsets); * if ok != 0: # <<<<<<<<<<<<<< @@ -7143,26 +7525,26 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_2calc_offs __pyx_t_1 = ((__pyx_v_ok != 0) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":544 + /* "MDAnalysis/lib/formats/xdrlib.pyx":605 * ok = read_xtc_n_frames(self.fname, &n_frames, &est_nframes, &offsets); 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__pyx_lineno = 544; __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 = 605; __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":544 + /* "MDAnalysis/lib/formats/xdrlib.pyx":605 * ok = read_xtc_n_frames(self.fname, &n_frames, &est_nframes, &offsets); * if ok != 0: * 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 = 544; __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 = 605; __pyx_clineno = __LINE__; 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__pyx_lineno = 550; __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 = 611; __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 = 550; __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 = 611; __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 = 550; __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 = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); 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__Pyx_RefNannySetupContext("read", 0); - /* "MDAnalysis/lib/formats/xdrlib.pyx":573 + /* "MDAnalysis/lib/formats/xdrlib.pyx":634 * Something must have happened reading the file * """ * if self.reached_eof: # <<<<<<<<<<<<<< @@ -7373,20 +7755,20 @@ 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":574 + /* "MDAnalysis/lib/formats/xdrlib.pyx":635 * """ * 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 = 574; __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 = 635; __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 = 574; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":573 + /* "MDAnalysis/lib/formats/xdrlib.pyx":634 * Something must have happened reading the file * """ * if self.reached_eof: # <<<<<<<<<<<<<< @@ -7395,7 +7777,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":575 + /* "MDAnalysis/lib/formats/xdrlib.pyx":636 * if self.reached_eof: * raise RuntimeError('Reached last frame in XTC, seek to 0') * if not self.is_open: # <<<<<<<<<<<<<< @@ -7405,20 +7787,20 @@ 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":576 + /* "MDAnalysis/lib/formats/xdrlib.pyx":637 * 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: {}. 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__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 = 586; __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 = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_box = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":588 + /* "MDAnalysis/lib/formats/xdrlib.pyx":649 * cdef np.ndarray box = np.empty((DIMS, DIMS), dtype=DTYPE) * * return_code = read_xtc(self.xfp, self.n_atoms, &step, # <<<<<<<<<<<<<< @@ -7585,7 +7967,7 @@ 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":591 + /* "MDAnalysis/lib/formats/xdrlib.pyx":652 * &time, box.data, * xyz.data, &prec) * if return_code != EOK and return_code != EENDOFFILE: # <<<<<<<<<<<<<< @@ -7603,26 +7985,26 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru } if (__pyx_t_3) { - /* "MDAnalysis/lib/formats/xdrlib.pyx":592 + /* "MDAnalysis/lib/formats/xdrlib.pyx":653 * 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 = 592; __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 = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - /* "MDAnalysis/lib/formats/xdrlib.pyx":593 + /* "MDAnalysis/lib/formats/xdrlib.pyx":654 * 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 = 593; __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 = 654; __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 = 593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __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 = 654; __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; @@ -7636,42 +8018,42 @@ 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 = 592; __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 = 653; __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 = 592; __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 = 653; __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 = 592; __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 = 653; __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":592 + /* "MDAnalysis/lib/formats/xdrlib.pyx":653 * 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 = 592; __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 = 653; __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 = 592; __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 = 653; __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 = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":591 + /* "MDAnalysis/lib/formats/xdrlib.pyx":652 * &time, box.data, * xyz.data, &prec) * if return_code != EOK and return_code != EENDOFFILE: # <<<<<<<<<<<<<< @@ -7680,7 +8062,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":595 + /* "MDAnalysis/lib/formats/xdrlib.pyx":656 * error_message[return_code])) * * if return_code == EENDOFFILE: # <<<<<<<<<<<<<< @@ -7690,7 +8072,7 @@ 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":596 + /* "MDAnalysis/lib/formats/xdrlib.pyx":657 * * if return_code == EENDOFFILE: * self.reached_eof = True # <<<<<<<<<<<<<< @@ -7699,7 +8081,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ __pyx_v_self->__pyx_base.reached_eof = 1; - /* "MDAnalysis/lib/formats/xdrlib.pyx":597 + /* "MDAnalysis/lib/formats/xdrlib.pyx":658 * if return_code == EENDOFFILE: * self.reached_eof = True * raise StopIteration # <<<<<<<<<<<<<< @@ -7707,9 +8089,9 @@ 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 = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":595 + /* "MDAnalysis/lib/formats/xdrlib.pyx":656 * error_message[return_code])) * * if return_code == EENDOFFILE: # <<<<<<<<<<<<<< @@ -7718,7 +8100,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":599 + /* "MDAnalysis/lib/formats/xdrlib.pyx":660 * raise StopIteration * * if return_code == EOK: # <<<<<<<<<<<<<< @@ -7728,7 +8110,7 @@ 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":600 + /* "MDAnalysis/lib/formats/xdrlib.pyx":661 * * if return_code == EOK: * self.current_frame += 1 # <<<<<<<<<<<<<< @@ -7737,7 +8119,7 @@ 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":599 + /* "MDAnalysis/lib/formats/xdrlib.pyx":660 * raise StopIteration * * if return_code == EOK: # <<<<<<<<<<<<<< @@ -7746,7 +8128,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":601 + /* "MDAnalysis/lib/formats/xdrlib.pyx":662 * if return_code == EOK: * self.current_frame += 1 * return XTCFrame(xyz, box, step, time, prec) # <<<<<<<<<<<<<< @@ -7754,13 +8136,13 @@ 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 = 601; __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 = 662; __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 = 601; __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 = 662; __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 = 601; __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 = 662; __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 = 601; __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 = 662; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_8 = NULL; __pyx_t_9 = 0; @@ -7774,7 +8156,7 @@ 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 = 601; __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 = 662; __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; @@ -7794,7 +8176,7 @@ 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 = 601; __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 = 662; __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; @@ -7802,7 +8184,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru __pyx_t_4 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":555 + /* "MDAnalysis/lib/formats/xdrlib.pyx":616 * return nd_offsets[:n_frames] * * def read(self): # <<<<<<<<<<<<<< @@ -7829,7 +8211,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru return __pyx_r; } -/* "MDAnalysis/lib/formats/xdrlib.pyx":603 +/* "MDAnalysis/lib/formats/xdrlib.pyx":664 * return XTCFrame(xyz, box, step, time, prec) * * def write(self, xyz, box, int step, float time, float precision=1000): # <<<<<<<<<<<<<< @@ -7875,17 +8257,17 @@ 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 = 603; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __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 = 603; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("write", 0, 4, 5, 2); 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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 = 656; __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 = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_11); - /* "MDAnalysis/lib/formats/xdrlib.pyx":657 + /* "MDAnalysis/lib/formats/xdrlib.pyx":718 * raise ValueError('Previous frames used precision of {}. You ' * 'are trying to use {}'.format( * self.precision, precision)) # <<<<<<<<<<<<<< * * cdef int return_code */ - __pyx_t_6 = PyFloat_FromDouble(__pyx_v_self->precision); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __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 = 718; __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 = 657; __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 = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = NULL; __pyx_t_10 = 0; @@ -8393,7 +8775,7 @@ 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 = 656; __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 = 717; __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; @@ -8404,31 +8786,31 @@ 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 = 656; __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 = 717; __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":655 + /* "MDAnalysis/lib/formats/xdrlib.pyx":716 * 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 = 655; __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 = 716; __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 = 655; __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 = 716; __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 = 655; __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":654 + /* "MDAnalysis/lib/formats/xdrlib.pyx":715 * 'are trying to write {} box.'.format( * self.box, box)) * if self.precision != precision: # <<<<<<<<<<<<<< @@ -8439,7 +8821,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str } __pyx_L4:; - /* "MDAnalysis/lib/formats/xdrlib.pyx":661 + /* "MDAnalysis/lib/formats/xdrlib.pyx":722 * cdef int return_code * return_code = write_xtc(self.xfp, self.n_atoms, step, time, * &box_view[0, 0], # <<<<<<<<<<<<<< @@ -8459,10 +8841,10 @@ 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 = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "MDAnalysis/lib/formats/xdrlib.pyx":662 + /* "MDAnalysis/lib/formats/xdrlib.pyx":723 * return_code = write_xtc(self.xfp, self.n_atoms, step, time, * &box_view[0, 0], * &xyz_view[0, 0], precision) # <<<<<<<<<<<<<< @@ -8482,10 +8864,10 @@ 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 = 662; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "MDAnalysis/lib/formats/xdrlib.pyx":660 + /* "MDAnalysis/lib/formats/xdrlib.pyx":721 * * cdef int return_code * return_code = write_xtc(self.xfp, self.n_atoms, step, time, # <<<<<<<<<<<<<< @@ -8494,7 +8876,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str */ __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":663 + /* "MDAnalysis/lib/formats/xdrlib.pyx":724 * &box_view[0, 0], * &xyz_view[0, 0], precision) * if return_code != EOK: # <<<<<<<<<<<<<< @@ -8504,26 +8886,26 @@ 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":664 + /* "MDAnalysis/lib/formats/xdrlib.pyx":725 * &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 = 664; __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 = 725; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_11); - /* "MDAnalysis/lib/formats/xdrlib.pyx":665 + /* "MDAnalysis/lib/formats/xdrlib.pyx":726 * 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 = 665; __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 = 726; __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 = 665; __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 = 726; __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; @@ -8537,42 +8919,42 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str } } if (!__pyx_t_5) { - 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 725; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "MDAnalysis/lib/formats/xdrlib.pyx":663 + /* "MDAnalysis/lib/formats/xdrlib.pyx":724 * &box_view[0, 0], * &xyz_view[0, 0], precision) * if return_code != EOK: # <<<<<<<<<<<<<< @@ -8581,14 +8963,14 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str */ } - /* "MDAnalysis/lib/formats/xdrlib.pyx":667 + /* "MDAnalysis/lib/formats/xdrlib.pyx":728 * 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":603 + /* "MDAnalysis/lib/formats/xdrlib.pyx":664 * return XTCFrame(xyz, box, step, time, prec) * * def write(self, xyz, box, int step, float time, float precision=1000): # <<<<<<<<<<<<<< @@ -8789,7 +9171,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) */ - 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__pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__19, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__20, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF_SET(__pyx_v_format, __pyx_t_5); @@ -11094,7 +11476,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ * * */ - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_MemoryError, __pyx_tuple__20, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_MemoryError, __pyx_tuple__21, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_Raise(__pyx_t_5, 0, 0, 0); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; @@ -11378,7 +11760,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ * * if self.dtype_is_object: */ - 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__pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__23, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__24, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_Raise(__pyx_t_6, 0, 0, 0); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; @@ -15235,7 +15617,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_7strides___get__(st * * return tuple([stride for stride in self.view.strides[:self.view.ndim]]) */ - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__24, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__25, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 523; __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; @@ -15352,7 +15734,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_10suboffsets___get_ __Pyx_XDECREF(__pyx_r); __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_self->view.ndim); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyNumber_Multiply(__pyx_tuple__25, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyNumber_Multiply(__pyx_tuple__26, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_r = __pyx_t_3; @@ -16692,9 +17074,9 @@ static PyObject *_unellipsify(PyObject *__pyx_v_index, int __pyx_v_ndim) { __Pyx_GOTREF(__pyx_t_7); { Py_ssize_t __pyx_temp; for (__pyx_temp=0; __pyx_temp < ((__pyx_v_ndim - __pyx_t_8) + 1); __pyx_temp++) { - __Pyx_INCREF(__pyx_slice__26); - __Pyx_GIVEREF(__pyx_slice__26); - PyList_SET_ITEM(__pyx_t_7, __pyx_temp, __pyx_slice__26); + __Pyx_INCREF(__pyx_slice__27); + __Pyx_GIVEREF(__pyx_slice__27); + PyList_SET_ITEM(__pyx_t_7, __pyx_temp, __pyx_slice__27); } } __pyx_t_9 = __Pyx_PyList_Extend(__pyx_v_result, __pyx_t_7); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -16727,7 +17109,7 @@ static PyObject *_unellipsify(PyObject *__pyx_v_index, int __pyx_v_ndim) { * else: */ /*else*/ { - __pyx_t_9 = __Pyx_PyList_Append(__pyx_v_result, __pyx_slice__27); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyList_Append(__pyx_v_result, __pyx_slice__28); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_L7:; @@ -16872,9 +17254,9 @@ static PyObject *_unellipsify(PyObject *__pyx_v_index, int __pyx_v_ndim) { __Pyx_GOTREF(__pyx_t_3); { Py_ssize_t __pyx_temp; for (__pyx_temp=0; __pyx_temp < __pyx_v_nslices; __pyx_temp++) { - __Pyx_INCREF(__pyx_slice__28); - __Pyx_GIVEREF(__pyx_slice__28); - PyList_SET_ITEM(__pyx_t_3, __pyx_temp, __pyx_slice__28); + __Pyx_INCREF(__pyx_slice__29); + __Pyx_GIVEREF(__pyx_slice__29); + PyList_SET_ITEM(__pyx_t_3, __pyx_temp, __pyx_slice__29); } } __pyx_t_9 = __Pyx_PyList_Extend(__pyx_v_result, __pyx_t_3); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -17001,7 +17383,7 @@ static PyObject *assert_direct_dimensions(Py_ssize_t *__pyx_v_suboffsets, int __ * * */ - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__29, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__30, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_Raise(__pyx_t_5, 0, 0, 0); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; @@ -22369,9 +22751,11 @@ 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} }; @@ -23309,7 +23693,7 @@ 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}, @@ -23328,6 +23712,7 @@ 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}, @@ -23337,6 +23722,9 @@ 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}, @@ -23347,7 +23735,7 @@ 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}, @@ -23417,6 +23805,7 @@ 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}, @@ -23451,13 +23840,14 @@ 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_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 = 267; __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 = 323; __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 = 152; __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 = 189; __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 = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -23489,104 +23879,115 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple_); __Pyx_GIVEREF(__pyx_tuple_); - /* "MDAnalysis/lib/formats/xdrlib.pyx":258 + /* "MDAnalysis/lib/formats/xdrlib.pyx":260 * else: * if frame >= self.offsets.size: * raise RuntimeError('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 = 258; __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":360 + /* "MDAnalysis/lib/formats/xdrlib.pyx":313 + * whn = SEEK_END + * elif whence != "SEEK_SET": + * raise ValueError("Parameter 'whence' must be one of 'SEEK_SET', " # <<<<<<<<<<<<<< + * "'SEEK_CUR', or 'SEEK_END'.") + * offst = offset + */ + __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_s_Parameter_whence_must_be_one_of); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 313; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__3); + __Pyx_GIVEREF(__pyx_tuple__3); + + /* "MDAnalysis/lib/formats/xdrlib.pyx":421 * """ * 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 = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__3); - __Pyx_GIVEREF(__pyx_tuple__3); + __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_s_Reached_last_frame_in_TRR_seek_t); if (unlikely(!__pyx_tuple__4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__4); + __Pyx_GIVEREF(__pyx_tuple__4); - /* "MDAnalysis/lib/formats/xdrlib.pyx":362 + /* "MDAnalysis/lib/formats/xdrlib.pyx":423 * 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 = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__4); - __Pyx_GIVEREF(__pyx_tuple__4); + __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_s_No_file_opened); if (unlikely(!__pyx_tuple__5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__5); + __Pyx_GIVEREF(__pyx_tuple__5); - /* "MDAnalysis/lib/formats/xdrlib.pyx":365 + /* "MDAnalysis/lib/formats/xdrlib.pyx":426 * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. Reading only allow ' * 'in mode "r"'.format('self.mode')) # <<<<<<<<<<<<<< * * cdef int 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 = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__5); - __Pyx_GIVEREF(__pyx_tuple__5); + __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 426; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__6); + __Pyx_GIVEREF(__pyx_tuple__6); - /* "MDAnalysis/lib/formats/xdrlib.pyx":438 + /* "MDAnalysis/lib/formats/xdrlib.pyx":499 * if self.mode != 'w' : * raise RuntimeError('File opened in mode: {}. 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Reading only allow ' * 'in mode "r"'.format('self.mode')) # <<<<<<<<<<<<<< * * cdef int 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 = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__9); - __Pyx_GIVEREF(__pyx_tuple__9); + __pyx_tuple__10 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__10); + __Pyx_GIVEREF(__pyx_tuple__10); - /* "MDAnalysis/lib/formats/xdrlib.pyx":636 + /* "MDAnalysis/lib/formats/xdrlib.pyx":697 * 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 = 636; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__10); - __Pyx_GIVEREF(__pyx_tuple__10); + __pyx_tuple__11 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__11); + __Pyx_GIVEREF(__pyx_tuple__11); /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":218 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) @@ -23595,9 +23996,9 @@ static int __Pyx_InitCachedConstants(void) { * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) */ - __pyx_tuple__11 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple__11)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__11); - __Pyx_GIVEREF(__pyx_tuple__11); + __pyx_tuple__12 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple__12)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__12); + __Pyx_GIVEREF(__pyx_tuple__12); /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":222 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) @@ -23606,9 +24007,9 @@ static int __Pyx_InitCachedConstants(void) { * * info.buf = PyArray_DATA(self) */ - __pyx_tuple__12 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__12)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__12); - __Pyx_GIVEREF(__pyx_tuple__12); + __pyx_tuple__13 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__13)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__13); + __Pyx_GIVEREF(__pyx_tuple__13); /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":259 * if ((descr.byteorder == c'>' and little_endian) or @@ -23617,9 +24018,9 @@ static int __Pyx_InitCachedConstants(void) { * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ - __pyx_tuple__13 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__13)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__13); - __Pyx_GIVEREF(__pyx_tuple__13); + __pyx_tuple__14 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__14)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__14); + __Pyx_GIVEREF(__pyx_tuple__14); /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":799 * @@ -23628,9 +24029,9 @@ static int __Pyx_InitCachedConstants(void) { * * if ((child.byteorder == c'>' and little_endian) or */ - __pyx_tuple__14 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__14)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__14); - __Pyx_GIVEREF(__pyx_tuple__14); + __pyx_tuple__15 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__15)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__15); + __Pyx_GIVEREF(__pyx_tuple__15); /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":803 * if ((child.byteorder == c'>' and little_endian) or @@ -23639,9 +24040,9 @@ static int __Pyx_InitCachedConstants(void) { * # One could encode it in the format string and have Cython * # complain instead, BUT: < and > in format strings also imply */ - __pyx_tuple__15 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__15)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__15); - __Pyx_GIVEREF(__pyx_tuple__15); + __pyx_tuple__16 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__16)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__16); + __Pyx_GIVEREF(__pyx_tuple__16); /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":823 * t = child.type_num @@ -23650,9 +24051,9 @@ static int __Pyx_InitCachedConstants(void) { * * # Until ticket #99 is fixed, use integers to avoid warnings */ - __pyx_tuple__16 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__16)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__16); - __Pyx_GIVEREF(__pyx_tuple__16); + __pyx_tuple__17 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__17)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__17); + __Pyx_GIVEREF(__pyx_tuple__17); /* "View.MemoryView":129 * @@ -23661,9 +24062,9 @@ static int __Pyx_InitCachedConstants(void) { * * if itemsize <= 0: */ - __pyx_tuple__17 = PyTuple_Pack(1, __pyx_kp_s_Empty_shape_tuple_for_cython_arr); if (unlikely(!__pyx_tuple__17)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__17); - __Pyx_GIVEREF(__pyx_tuple__17); + __pyx_tuple__18 = PyTuple_Pack(1, __pyx_kp_s_Empty_shape_tuple_for_cython_arr); if (unlikely(!__pyx_tuple__18)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__18); + __Pyx_GIVEREF(__pyx_tuple__18); /* "View.MemoryView":132 * @@ -23672,9 +24073,9 @@ static int __Pyx_InitCachedConstants(void) { * * if not isinstance(format, bytes): */ - __pyx_tuple__18 = PyTuple_Pack(1, __pyx_kp_s_itemsize_0_for_cython_array); if (unlikely(!__pyx_tuple__18)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__18); - __Pyx_GIVEREF(__pyx_tuple__18); + __pyx_tuple__19 = PyTuple_Pack(1, __pyx_kp_s_itemsize_0_for_cython_array); if (unlikely(!__pyx_tuple__19)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__19); + __Pyx_GIVEREF(__pyx_tuple__19); /* "View.MemoryView":135 * @@ -23683,9 +24084,9 @@ static int __Pyx_InitCachedConstants(void) { * self._format = format # keep a reference to the byte string * self.format = self._format */ - __pyx_tuple__19 = PyTuple_Pack(1, __pyx_n_s_ASCII); if (unlikely(!__pyx_tuple__19)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__19); - __Pyx_GIVEREF(__pyx_tuple__19); + __pyx_tuple__20 = PyTuple_Pack(1, __pyx_n_s_ASCII); if (unlikely(!__pyx_tuple__20)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__20); + __Pyx_GIVEREF(__pyx_tuple__20); /* "View.MemoryView":144 * @@ -23694,9 +24095,9 @@ static int __Pyx_InitCachedConstants(void) { * * */ - __pyx_tuple__20 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_shape_and_str); if (unlikely(!__pyx_tuple__20)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__20); - __Pyx_GIVEREF(__pyx_tuple__20); + __pyx_tuple__21 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_shape_and_str); if (unlikely(!__pyx_tuple__21)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__21); + __Pyx_GIVEREF(__pyx_tuple__21); /* "View.MemoryView":172 * self.data = malloc(self.len) @@ -23705,9 +24106,9 @@ static int __Pyx_InitCachedConstants(void) { * * if self.dtype_is_object: */ - __pyx_tuple__21 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_array_data); if (unlikely(!__pyx_tuple__21)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__21); - __Pyx_GIVEREF(__pyx_tuple__21); + __pyx_tuple__22 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_array_data); if (unlikely(!__pyx_tuple__22)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__22); + __Pyx_GIVEREF(__pyx_tuple__22); /* "View.MemoryView":188 * bufmode = PyBUF_F_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS @@ -23716,9 +24117,9 @@ static int __Pyx_InitCachedConstants(void) { * info.buf = self.data * info.len = self.len */ - __pyx_tuple__22 = PyTuple_Pack(1, __pyx_kp_s_Can_only_create_a_buffer_that_is); if (unlikely(!__pyx_tuple__22)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__22); - __Pyx_GIVEREF(__pyx_tuple__22); + __pyx_tuple__23 = PyTuple_Pack(1, __pyx_kp_s_Can_only_create_a_buffer_that_is); 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goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__26); __Pyx_INCREF(__pyx_int_neg_1); __Pyx_GIVEREF(__pyx_int_neg_1); - PyTuple_SET_ITEM(__pyx_tuple__25, 0, __pyx_int_neg_1); - __Pyx_GIVEREF(__pyx_tuple__25); + PyTuple_SET_ITEM(__pyx_tuple__26, 0, __pyx_int_neg_1); + __Pyx_GIVEREF(__pyx_tuple__26); /* "View.MemoryView":640 * if item is Ellipsis: @@ -23763,9 +24164,9 @@ static int __Pyx_InitCachedConstants(void) { * seen_ellipsis = True * else: */ - __pyx_slice__26 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__26)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_slice__26); - __Pyx_GIVEREF(__pyx_slice__26); + __pyx_slice__27 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__27)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__27); + __Pyx_GIVEREF(__pyx_slice__27); /* "View.MemoryView":643 * seen_ellipsis = True @@ -23774,9 +24175,9 @@ static int __Pyx_InitCachedConstants(void) { * have_slices = True * else: */ - __pyx_slice__27 = PySlice_New(Py_None, Py_None, Py_None); 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__pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__29); + __Pyx_GIVEREF(__pyx_slice__29); /* "View.MemoryView":661 * for suboffset in suboffsets[:ndim]: @@ -23796,31 +24197,31 @@ static int __Pyx_InitCachedConstants(void) { * * */ - __pyx_tuple__29 = PyTuple_Pack(1, __pyx_kp_s_Indirect_dimensions_not_supporte); if (unlikely(!__pyx_tuple__29)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__29); - __Pyx_GIVEREF(__pyx_tuple__29); + __pyx_tuple__30 = PyTuple_Pack(1, __pyx_kp_s_Indirect_dimensions_not_supporte); if (unlikely(!__pyx_tuple__30)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__30); + __Pyx_GIVEREF(__pyx_tuple__30); - /* "MDAnalysis/lib/formats/xdrlib.pyx":290 + /* "MDAnalysis/lib/formats/xdrlib.pyx":350 * * * 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); 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if (unlikely(!__pyx_tuple__32)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__32); + __Pyx_GIVEREF(__pyx_tuple__32); /* "View.MemoryView":278 * return self.name @@ -23829,9 +24230,9 @@ static int __Pyx_InitCachedConstants(void) { * cdef strided = Enum("") # default * cdef indirect = Enum("") */ - __pyx_tuple__32 = PyTuple_Pack(1, __pyx_kp_s_strided_and_direct_or_indirect); if (unlikely(!__pyx_tuple__32)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__32); - __Pyx_GIVEREF(__pyx_tuple__32); + __pyx_tuple__33 = PyTuple_Pack(1, __pyx_kp_s_strided_and_direct_or_indirect); if (unlikely(!__pyx_tuple__33)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__33); + __Pyx_GIVEREF(__pyx_tuple__33); /* "View.MemoryView":279 * @@ -23840,9 +24241,9 @@ static int __Pyx_InitCachedConstants(void) { * cdef indirect = Enum("") * */ - __pyx_tuple__33 = PyTuple_Pack(1, __pyx_kp_s_strided_and_direct); 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__35); + __Pyx_GIVEREF(__pyx_tuple__35); /* "View.MemoryView":283 * @@ -23862,9 +24263,9 @@ static int __Pyx_InitCachedConstants(void) { * cdef indirect_contiguous = Enum("") * */ - __pyx_tuple__35 = PyTuple_Pack(1, __pyx_kp_s_contiguous_and_direct); if (unlikely(!__pyx_tuple__35)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__35); - __Pyx_GIVEREF(__pyx_tuple__35); + __pyx_tuple__36 = PyTuple_Pack(1, __pyx_kp_s_contiguous_and_direct); if (unlikely(!__pyx_tuple__36)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__36); + __Pyx_GIVEREF(__pyx_tuple__36); /* "View.MemoryView":284 * @@ -23873,9 +24274,9 @@ static int __Pyx_InitCachedConstants(void) { * * */ - __pyx_tuple__36 = PyTuple_Pack(1, __pyx_kp_s_contiguous_and_indirect); if (unlikely(!__pyx_tuple__36)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__36); - __Pyx_GIVEREF(__pyx_tuple__36); + __pyx_tuple__37 = PyTuple_Pack(1, __pyx_kp_s_contiguous_and_indirect); if (unlikely(!__pyx_tuple__37)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__37); + __Pyx_GIVEREF(__pyx_tuple__37); __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -23992,14 +24393,14 @@ PyMODINIT_FUNC PyInit_xdrlib(void) if (PyObject_SetAttrString(__pyx_m, "_XDRFile", (PyObject *)&__pyx_type_10MDAnalysis_3lib_7formats_6xdrlib__XDRFile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __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 = 293; __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 = 353; __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 = 293; __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 = 353; __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 = 506; __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 = 567; __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 = 506; __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 = 567; __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; 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if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __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 = 268; __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 = 324; __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":290 + /* "MDAnalysis/lib/formats/xdrlib.pyx":350 * * * 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 = 290; __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 = 350; __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 = 290; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__31, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __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 = 290; __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 = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/formats/xdrlib.pyx":503 + /* "MDAnalysis/lib/formats/xdrlib.pyx":564 * * * 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 = 503; __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 = 564; __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 = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__32, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __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 = 503; __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 = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; /* "MDAnalysis/lib/formats/xdrlib.pyx":1 @@ -24305,7 +24706,7 @@ PyMODINIT_FUNC PyInit_xdrlib(void) * cdef strided = Enum("") # default * cdef indirect = Enum("") */ - __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__32, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__33, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__35, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_XGOTREF(indirect); __Pyx_DECREF_SET(indirect, __pyx_t_3); @@ -24347,7 +24748,7 @@ PyMODINIT_FUNC PyInit_xdrlib(void) * cdef indirect_contiguous = Enum("") * */ - __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__35, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__36, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_XGOTREF(contiguous); __Pyx_DECREF_SET(contiguous, __pyx_t_3); @@ -24361,7 +24762,7 @@ PyMODINIT_FUNC PyInit_xdrlib(void) * * */ - __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__36, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__37, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_XGOTREF(indirect_contiguous); __Pyx_DECREF_SET(indirect_contiguous, __pyx_t_3); @@ -27062,6 +27463,32 @@ static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) { 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(int64_t) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int64_t) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(int64_t) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(int64_t) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } 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(int64_t), + little, !is_unsigned); + } +} + 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; diff --git a/package/MDAnalysis/lib/formats/xdrlib.pyx b/package/MDAnalysis/lib/formats/xdrlib.pyx index d6e4218e813..e3a96be2e19 100644 --- a/package/MDAnalysis/lib/formats/xdrlib.pyx +++ b/package/MDAnalysis/lib/formats/xdrlib.pyx @@ -18,7 +18,7 @@ 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 cdef extern from 'include/xdrfile.h': ctypedef struct XDRFILE: @@ -70,7 +70,7 @@ cdef enum: EMAGIC = 9 EMEMORY = 10 EENDOFFILE = 11 - ENOTFOUND = 11 + ENOTFOUND = 12 error_message = ['OK', 'header', 'string', 'double', 'integer', 'float', 'unsigned integer', 'compression', @@ -192,7 +192,7 @@ 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); @@ -236,7 +236,7 @@ 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. @@ -248,9 +248,11 @@ cdef class _XDRFile: Raises ------ RuntimeError - If you seek for more frames than are available + If you seek for more frames than are available or if the + seek fails (the low-level system error is reported). """ cdef int64_t offset + cdef int ok if frame == 0: offset = 0 else: @@ -260,10 +262,64 @@ cdef class _XDRFile: 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])) + # 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 RuntimeError("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. + + RuntimeError + If the seek fails (the low-level system error is reported). + """ + cdef int whn = SEEK_SET + cdef int ok + cdef int64_t offst + + if whence == "SEEK_CUR": + whn = SEEK_CUR + elif whence == "SEEK_END": + whn = SEEK_END + elif whence != "SEEK_SET": + raise ValueError("Parameter 'whence' must be one of 'SEEK_SET', " + "'SEEK_CUR', or 'SEEK_END'.") + offst = offset + self.reached_eof = False + ok = xdr_seek(self.xfp, offst, whn) + if ok != 0: + # See the comments to seek() for hints on errno meaning. + raise RuntimeError("XDR seek failed with " + "system errno={}".format(ok)) + @property def offsets(self): """get byte offsets from current xdr file @@ -286,6 +342,10 @@ 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') @@ -322,6 +382,7 @@ cdef class TRRFile(_XDRFile): """read byte offsets from TRR file directly""" if not self.is_open: return np.array([]) + cdef int ok cdef int n_frames = 0 cdef int est_nframes = 0 cdef int64_t* offsets = NULL @@ -393,7 +454,7 @@ 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 diff --git a/testsuite/MDAnalysisTests/formats/test_xdrlib.py b/testsuite/MDAnalysisTests/formats/test_xdrlib.py index 291f9de2354..fe0b19c2629 100644 --- a/testsuite/MDAnalysisTests/formats/test_xdrlib.py +++ b/testsuite/MDAnalysisTests/formats/test_xdrlib.py @@ -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