Merge pull request #37 from pnnl/md-refactor

Overhaul MD code to support decoupling of separate run/parsing functionality

isicle/geometry.py

@@ -24,8 +24,8 @@ def __init__(self, **kwargs):
         self.__dict__.update(dict.fromkeys(self._defaults, self._default_value))
         self.__dict__.update(kwargs)
 
-        if self.charge is None:
-            self.charge = self.get_charge()
+        # if self.charge is None:
+        #     self.charge = self.get_charge()
 
     def get_basename(self):
         """
@@ -395,9 +395,7 @@ def get_natoms(self):
 
         """
 
-        natoms = Chem.Mol.GetNumAtoms(self.to_mol())
-        self.__dict__["natoms"] = natoms
-        return self.__dict__["natoms"]
+        return Chem.Mol.GetNumAtoms(self.to_mol())
 
     def get_atom_indices(
         self, atoms=["C", "H"], lookup={"C": 6, "H": 1, "N": 7, "O": 8, "F": 9, "P": 15}

isicle/io.py

@@ -61,7 +61,7 @@ def load_xyz(path, charge=None):
     basename = os.path.splitext(os.path.basename(path))[0]
 
     # Initialize Geometry instance
-    geom = isicle.geometry.Geometry(mol=mol, charge=charge, basename=basename)
+    geom = isicle.geometry.Geometry(mol=mol, basename=basename)
 
     return geom