Add properties for CCS and stdev CCS, propagate to geometry object as needed

Author: smcolby

isicle/geometry.py

@@ -24,7 +24,10 @@ class Geometry(GeometryInterface):
         "_frequency",
         "_molden",
         "_charge",
-        "_connectivity"
+        "_connectivity",
+        "_formal_charge",
+        "_ccs",
+        "_ccs_std"
         ]
     _default_value = None
 
@@ -154,6 +157,34 @@ def formal_charge(self):
 
         return Chem.rdmolops.GetFormalCharge(self.to_mol())
 
+    @property
+    def ccs(self):
+        """
+        Get CCS of the molecule.
+
+        Returns
+        -------
+        float
+            Collision cross section.
+
+        """
+
+        return self._ccs
+
+    @property
+    def ccs_std(self):
+        """
+        Get standard deviation of CCS prediction of the molecule.
+
+        Returns
+        -------
+        float
+            Standard deviation of collision cross section.
+
+        """
+
+        return self._ccs_std
+
     def view(self):
         """
         View internal rdkit mol object representation.

isicle/mobility.py

@@ -191,6 +191,9 @@ def finish(self):
             except UnicodeDecodeError:
                 result[ext] = contents
 
+        # Propagate geometry object
+        result["geometry"] = self.geom
+
         # Assign to attribute
         self.result = result
         return self.result

isicle/parse.py

@@ -835,7 +835,16 @@ def parse(self):
             elif "standard deviation (percent)" in line:
                 done = True
         if done is True:
-            self.result["ccs"] = {"mean": ccs_mn, "std": ccs_std}
+            self.result["ccs"] = ccs_mn
+            self.result["ccs_std"] = ccs_std
+        
+        self.result["geometry"] = self.data["geometry"]
+
+        # Update geometry attributes
+        self.result["geometry"].add___dict__(
+            {"_" + k: v for k, v in self.result.items() if k not in ["geometry"]},
+            override=True
+        )
 
         return self.result