minor cleaning

cosymlib/molecule/__init__.py

@@ -40,7 +40,6 @@ def __init__(self, geometry,
         self._electronic_structure = electronic_structure
         self._symmetry = geometry._symmetry
         self._shape = geometry._shape
-        self._symmetry.set_electronic_structure(electronic_structure)
 
     def molecule_copy(self):
         return deepcopy(self)
@@ -80,7 +79,6 @@ def electronic_structure(self):
                                                              multiplicity=eh.get_multiplicity(),
                                                              alpha_occupancy=[1]*eh.get_alpha_electrons(),
                                                              beta_occupancy=[1]*eh.get_beta_electrons())
-            self.symmetry.set_electronic_structure(self._electronic_structure)
 
         return self._electronic_structure
 
@@ -94,12 +92,6 @@ def symmetry(self):
     def shape(self):
         return self._shape
 
-    # TODO: Old method (to be deprecated)
-    @set_parameters
-    def OLD_get_mo_symmetry(self, group, axis=None, axis2=None, center=None):
-        warn('This method is deprecated', DeprecationWarning)
-        return self.symmetry._get_wfnsym_results(group)
-
     # New ones (to substitute get_mo_symmetry)
     @set_parameters
     def get_mo_irreducible_representations(self, group, axis=None, axis2=None, center=None):
@@ -171,6 +163,7 @@ def get_symbols(self):
     def get_pointgroup(self, tol=0.01):
         """
         Get the symmetry point group
+
         :param tol: The tolerance
         :type tol: float
         :return: The point group

cosymlib/symmetry/__init__.py

@@ -54,15 +54,22 @@ def __init__(self,
                  ):
 
         try:
+            # Interpret as Geometry or molecule
             self._coordinates = structure.get_positions()
             self._symbols = structure.get_symbols()
             self._connectivity = structure.get_connectivity()
         except AttributeError:
-            # Interpret as numpy array of coordinates
+            # Interpret as numpy array of coordinates or list of lists
             self._coordinates = structure
             self._symbols = None
             self._connectivity = None
 
+        # If molecule object add electronic structure
+        try:
+            self._electronic_structure = structure.electronic_structure
+        except AttributeError:
+            self._electronic_structure = None
+
         self._central_atom = central_atom
         self._center = center
         self._connect_thresh = connect_thresh
@@ -71,11 +78,6 @@ def __init__(self,
         self._axis2 = axis2
         self._results = {}
 
-        try:
-            self._electronic_structure = structure.electronic_structure
-        except AttributeError:
-            self._electronic_structure = None
-
     # Modifier methods
     def set_parameters(self, parameters_dict):
         """
@@ -118,6 +120,8 @@ def _get_symgroup_results(self, group):
         return self._results[key]
 
     def _get_wfnsym_results(self, group):
+        if self._electronic_structure is None:
+            raise Exception('Electronic structure not set')
 
         key = _get_key_wfnsym(group, self._axis, self._axis2, self._center, self._electronic_structure.alpha_occupancy,
                               self._electronic_structure.beta_occupancy)

cosymlib/utils.py

@@ -64,8 +64,8 @@ def plot_molecular_orbital_diagram(molecule, wfnsym, mo_range=None):
 
 
 def swap_vectors(v1, v2, position):
-    vector1 = v1.copy()
-    vector2 = v2.copy()
+    vector1 = v1.get_copy()
+    vector2 = v2.get_copy()
     for i in range(len(v1)):
         if i >= position:
             vector1[i] = v2[i]

scripts/shape_map

@@ -7,7 +7,7 @@ import argparse
 import sys
 import yaml
 
-parser = argparse.ArgumentParser(description='Shape_map ')
+parser = argparse.ArgumentParser(description='shape_map ')
 
 # positional arguments
 parser.add_argument(type=str,