Added cjson.py which can be used to read cjson current method added i…

…s get_atoms_coords which will get the co-ordinates of all atoms

Signed-off-by: aditya <[email protected]>

.vscode/settings.json

@@ -0,0 +1,6 @@
+{
+    "cSpell.words": [
+        "avogadrolibs",
+        "Cjson"
+    ]
+}

python/avogadro/cjson.py

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+import json
+class Cjson:
+    def __init__(self):
+        print("cjson configured successfully start your operations")
+    def __open_file(self, filePath):
+        with open(filePath, 'r') as cjsonFile:
+            py_dict_data = json.load(cjsonFile)
+            return py_dict_data
+    def __to_cjson(self, element_coords):
+        dict = {"element-coordinates" :element_coords}
+        cjsonData = json.dumps(dict, indent=4)
+        print(cjsonData)
+    def get_atoms_coords(self,filePath):
+        data = self.__open_file(filePath)
+        coords = data["atoms"]["coords"]["3d"]
+        elements = data["atoms"]["elements"]["number"]
+        # element_coords = {}
+        element_coords = [(*coords[i*3:(i+1)*3], elements[i]) for i in range(0, int(len(coords) / 3))]
+        print(type(element_coords))
+        self.__to_cjson(element_coords)
+