Merge pull request #1427 from ghutchis/add-cjson-connect-python

Add some additional Python classes including cjson and connect

python/CMakeLists.txt

@@ -59,7 +59,9 @@ if (NOT WIN32)
                         INSTALL_RPATH ${_rpath_value})
 endif()
 
-install(FILES avogadro/__init__.py  COMPONENT python DESTINATION "${_python_module_install_dir}")
+# Install the python files.
+FILE(GLOB PY_SRCS "avogadro/*.py")
+install(FILES ${PY_SRCS} COMPONENT python DESTINATION "${_python_module_install_dir}")
 
 # Set the output directory so the python modules can be used from the build
 # tree.

python/avogadro/__init__.py

@@ -1,2 +1,4 @@
+from . import cjson
+from . import connect
 from . import core
 from . import io

python/avogadro/cjson.py

@@ -1,29 +1,41 @@
 """
 /******************************************************************************
   This source file is part of the Avogadro project.
-  This source code is released under the New BSD License, (the "License").
+  This source code is released under the 3-clause BSD License, (the "License").
 ******************************************************************************/
 """
 import json
-class Cjson:
+
+
+class cjson:
     """
-    This Class is intended to read Cjson files
-    with python libraries and perform certain
-    methods on files and convert them back to Cjson
-    files as required
+    This class is intended to read and write cjson (chemical json) files
+    and help manipulate them (e.g., change coordinates, elements, etc.)
+
+    The cjson format is a JSON format for chemical information. It is
+    intended to be a common exchange and storage format for chemical
+    information that is both human and machine readable. It is intended
+    to be easily extended to support new features and data types.
+
+    More information and the schema can be found at:
+    https://github.com/OpenChemistry/chemicaljson
     """
+
     def __init__(self):
         pass
+
     def __from_cjson(self, filePath):
-        '''Use to read CJson formats by converting them to python dictionaries'''
-        with open(filePath, 'r') as cjsonFile:
+        """Use to read cjson formats by converting them to python dictionaries"""
+        with open(filePath, "r") as cjsonFile:
             py_dict_data = json.load(cjsonFile)
             return py_dict_data
+
     def __to_cjson(self, cjson_dict_file):
-        '''It converts python dictionaries to CJson format'''
+        """It converts python dictionaries to cjson format"""
         cjsonData = json.dumps(cjson_dict_file, indent=4)
-        return (cjsonData)
-    def get_atoms_coords(self,filePath):
+        return cjsonData
+
+    def get_atoms_coords(self, filePath):
         """
         It helps to get the co-ordinates of individual elements/atoms in the format
         [
@@ -36,44 +48,52 @@ def get_atoms_coords(self,filePath):
         data = self.__from_cjson(filePath)
         coords = data["atoms"]["coords"]["3d"]
         elements = data["atoms"]["elements"]["number"]
-        element_coords = [(*coords[i*3:(i+1)*3], elements[i]) for i in range(0, int(len(coords) / 3))]
-        cjson_dict = {"element-coordinates" :element_coords}
+        element_coords = [
+            (*coords[i * 3 : (i + 1) * 3], elements[i])
+            for i in range(0, int(len(coords) / 3))
+        ]
+        cjson_dict = {"element-coordinates": element_coords}
         return self.__to_cjson(cjson_dict)
+
     def get_elements(self, filePath):
-        '''
+        """
         returns all the elements present in cjson file
-        '''
+        """
         data = self.__from_cjson(filePath)
         elements = data["atoms"]["elements"]["number"]
         return elements
-    def get_coordinates(self,filePath):
-        '''
+
+    def get_coordinates(self, filePath):
+        """
         returns the coordinate array
-        '''
+        """
         data = self.__from_cjson(filePath)
         coords = data["atoms"]["coords"]["3d"]
         return coords
+
     def set_atoms_coordinates(self, filePath, coords_array):
-        '''
+        """
         it updates the coordinates array in cjson file
-        '''
+        """
         data = self.__from_cjson(filePath)
         data["atoms"]["coords"]["3d"] = coords_array
         return self.__to_cjson(data)
+
     def set_elements(self, filePath, elements_array):
-        '''
+        """
         It sets all the elements present in the cjson file
         where elements are set/recognized by their atomic numbers
-        '''
+        """
         data = self.__from_cjson(filePath)
         data["atoms"]["elements"]["number"] = elements_array
         return self.__to_cjson(data)
+
     def set_coordinates(self, filePath, coords_array):
-        '''
+        """
         It helps to set all coordinates of the
         cjson file where coordinates of all elements
         can be changed by an input array of coords_array
-        '''
+        """
         data = self.__from_cjson(filePath)
         data["atoms"]["coords"]["3d"] = coords_array
-        return self.__to_cjson(data)
+        return self.__to_cjson(data)

python/avogadro/connect.py

@@ -0,0 +1,99 @@
+"""
+/******************************************************************************
+  This source file is part of the Avogadro project.
+  This source code is released under the 3-clause BSD License, (the "License").
+******************************************************************************/
+"""
+
+import json
+import os
+import socket
+import struct
+import sys
+import tempfile
+
+
+class connect:
+    """
+    Send JSON-RPC requests to Avogadro through a named pipe.
+
+    This class is intended to be used by external scripts that are
+    run on the same machine as Avogadro.
+
+    The named pipe is created by Avogadro and is named "avogadro".
+    If it does not exist, Avogadro is not running.
+    """
+
+    def __init__(self, name="avogadro"):
+        """
+        Connect to the local named pipe
+
+        :param name: The name of the named pipe.
+        """
+        # create socket and connect
+        try:
+            if os.name == "nt":
+                self.sock = open("//./pipe/" + name, "w+b", 0)
+            else:
+                self.sock.connect(tempfile.gettempdir() + "/" + name)
+                self.sock = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)
+
+        except Exception as exception:
+            print("error while connecting: " + str(exception))
+            print("Is Avogadro running?")
+
+    def __json(self, method, params={}):
+        """
+        Send a JSON-RPC request to the named pipe.
+        :param method: The JSON-RPC request method.
+        Send a message to the named pipe
+        :param file: file corresponding to method.
+
+        """
+        if method == "receive_message":
+            size = 1024
+            if os.name == "nt":
+                packet = self.sock.read(size)
+            else:
+                packet = self.sock.recv(size)
+
+            try:
+                return json.loads(str(packet[4:]))
+            except Exception as exception:
+                print("error: " + str(exception))
+                return {}
+        else:
+            msg = {
+                "jsonrpc": "2.0",
+                "id": 0,
+                "method": method,
+                "params": params,
+            }
+            json_msg = json.dumps(msg)
+            size = len(json_msg)
+            header = struct.pack(">I", size)
+            packet = header + json_msg.encode("ascii")
+            if os.name == "nt":
+                self.sock.write(packet)
+                self.sock.seek(0)
+            else:
+                self.sock.send(packet)
+
+    def open_file(self, file):
+        """Opens file"""
+        # param: file is filename input by the user in string
+        method = "openFile"
+        params = {"filename": file}
+        self.__json(method, params)
+        self.__json("receive_message")
+
+    def save_graphic(self, file):
+        """Save Graphic"""
+        method = "saveGraphic"
+        params = {"filename": file}
+        self.__json(method, params)
+        self.__json("receive_message")
+
+    def close(self):
+        """Close the socket to the named pipe"""
+        self.sock.close()

python/io.cpp

@@ -11,6 +11,7 @@
 #include <avogadro/quantumio/mopacaux.h>
 #include <avogadro/quantumio/nwchemjson.h>
 #include <avogadro/quantumio/nwchemlog.h>
+#include <avogadro/quantumio/orca.h>
 
 namespace py = pybind11;
 
@@ -68,12 +69,14 @@ PYBIND11_MODULE(io, m)
 
   /// Add the quantum IO formats, we should probably move them over soon, but
   /// get things working for now...
+  Io::FileFormatManager::registerFormat(new GAMESSUSOutput);
   Io::FileFormatManager::registerFormat(new GaussianFchk);
   Io::FileFormatManager::registerFormat(new GaussianCube);
   Io::FileFormatManager::registerFormat(new MoldenFile);
   Io::FileFormatManager::registerFormat(new MopacAux);
   Io::FileFormatManager::registerFormat(new NWChemJson);
   Io::FileFormatManager::registerFormat(new NWChemLog);
+  Io::FileFormatManager::registerFormat(new ORCAOutput);
 
   /// This class uses a singleton pattern, make it accessible through Python.
   py::class_<ffm>(m, "FileFormatManager")