fixed get_connectivity function. Now returns None if no connectivity …

…is found

added geometric symmetry measure n (=multi) values tot the print function in Cosymlib class
adapted the symgroup properties names to the new names of symgroupy version 0.5.7

cosymlib/__init__.py

@@ -295,6 +295,8 @@ def print_geometric_measure_info(self, label, multi=1, central_atom=0, center=No
                 txt += '{:12.8f} {:12.8f} {:12.8f}\n'.format(array[0], array[1], array[2])
             txt += '\n'
             txt += 'Symmetry measure {:.5f}\n'.format(molecule.geometry.get_symmetry_measure(**kwargs))
+            txt += 'Symmetry {} lower values:  '.format(multi)
+            txt += ' '.join(format(csm, '.5f') for csm in molecule.geometry._symmetry.csm_multi(label, multi)) + '\n'
             txt += sep_line
 
         output.write(txt)

cosymlib/symmetry/__init__.py

@@ -105,7 +105,8 @@ def _get_symgroup_results(self, group):
         """
 
         # Crude calculation call methods
-        key = _get_key_symgroup(group, self._center, self._central_atom, self._connectivity, self._multi, self._connect_thresh)
+        key = _get_key_symgroup(group, self._center, self._central_atom, self._connectivity, self._multi,
+                                self._connect_thresh)
         if key not in self._results:
             self._results[key] = Symgroupy(self._coordinates,
                                            group=group,
@@ -200,7 +201,7 @@ def reference_axis(self, label):
         """
         return self._get_symgroup_results(label).reference_axis
 
-    def cms_multi(self, label, multi=1):
+    def csm_multi(self, label, multi=1):
         """
         Get symmetry measure of the optimum N axis
 
@@ -212,7 +213,7 @@ def cms_multi(self, label, multi=1):
         :rtype: list
         """
         self._multi = multi
-        return self._get_symgroup_results(label).cms_multi
+        return self._get_symgroup_results(label).csm_multi
 
     def axis_multi(self, label, multi=1):
         """

cosymlib/tools/__init__.py

@@ -74,7 +74,10 @@ def generate_connectivity_from_geometry(geometry, thresh=1.2):
         warn('failed to generate connectivity')
         return None
 
-    return (np.array(np.where(relative_differences < thresh - 1)).T + 1).tolist()
+    if not (np.array(np.where(relative_differences < thresh - 1)).T + 1).tolist():
+        return None
+    else:
+        return (np.array(np.where(relative_differences < thresh - 1)).T + 1).tolist()
 
 
 def get_connectivity_matrix(connectivity, ndim):