Merge pull request #1360 from adityaomar3/manipulating-cjson

Added cjson.py which can be used to read cjson

.gitignore

@@ -1,2 +1,156 @@
 docs/build
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python/avogadro/cjson.py

@@ -0,0 +1,79 @@
+"""
+/******************************************************************************
+  This source file is part of the Avogadro project.
+  This source code is released under the New BSD License, (the "License").
+******************************************************************************/
+"""
+import json
+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
+    """
+    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:
+            py_dict_data = json.load(cjsonFile)
+            return py_dict_data
+    def __to_cjson(self, cjson_dict_file):
+        '''It converts python dictionaries to CJson format'''
+        cjsonData = json.dumps(cjson_dict_file, indent=4)
+        return (cjsonData)
+    def get_atoms_coords(self,filePath):
+        """
+        It helps to get the co-ordinates of individual elements/atoms in the format
+        [
+            x co-ordinate
+            y co-ordinate
+            z co-ordinate
+            Atomic Number of Element
+        ]
+        """
+        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}
+        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):
+        '''
+        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)