Remove duplicated method getNumberOfRadicalElectrons

Was identical to getRadicalCount

rmgpy/constraints.py

@@ -90,7 +90,7 @@ def failsSpeciesConstraints(species):
 
     maxRadicals = speciesConstraints.get('maximumRadicalElectrons', -1)
     if maxRadicals != -1:
-        if (struct.getNumberOfRadicalElectrons() > maxRadicals):
+        if (struct.getRadicalCount() > maxRadicals):
             return True
 
     maxIsotopes = speciesConstraints.get('maximumIsotopicAtoms', -1)

rmgpy/molecule/molecule.pxd

@@ -152,8 +152,6 @@ cdef class Molecule(Graph):
 
     cpdef int getNumAtoms(self, str element=?)
 
-    cpdef int getNumberOfRadicalElectrons(self)
-
     cpdef Graph copy(self, bint deep=?)
 
     cpdef deleteHydrogens(self)

rmgpy/molecule/molecule.py

@@ -849,7 +849,9 @@ def getMolecularWeight(self):
 
     def getRadicalCount(self):
         """
-        Return the number of unpaired electrons.
+        Return the total number of radical electrons on all atoms in the
+        molecule. In this function, monoradical atoms count as one, biradicals
+        count as two, etc.
         """
         cython.declare(atom=Atom, radicals=cython.short)
         radicals = 0
@@ -872,18 +874,6 @@ def getNumAtoms(self, element = None):
                     numAtoms += 1
             return numAtoms
 
-    def getNumberOfRadicalElectrons(self):
-        """
-        Return the total number of radical electrons on all atoms in the
-        molecule. In this function, monoradical atoms count as one, biradicals
-        count as two, etc. 
-        """
-        cython.declare(numRadicals=cython.int, atom=Atom)
-        numRadicals = 0
-        for atom in self.vertices:
-            numRadicals += atom.radicalElectrons
-        return numRadicals
-
     def copy(self, deep=False):
         """
         Create a copy of the current graph. If `deep` is ``True``, a deep copy

rmgpy/molecule/parser.py

@@ -431,7 +431,7 @@ def fixCharge(mol, u_indices):
         return
 
     is_charged = sum([abs(at.charge) for at in mol.atoms]) != 0
-    is_correct = mol.getNumberOfRadicalElectrons() == (mol.multiplicity - 1)
+    is_correct = mol.getRadicalCount() == (mol.multiplicity - 1)
     if mol.multiplicity < 3 or is_correct or not is_charged:
         return
 
@@ -667,7 +667,7 @@ def fix_triplet_to_singlet(mol, p_indices):
 
     for at in mol.atoms:
         index = mol.atoms.index(at) + 1
-        if mol.getNumberOfRadicalElectrons() == 2 and index in p_indices:
+        if mol.getRadicalCount() == 2 and index in p_indices:
             at.lonePairs += 1
             at.radicalElectrons -= 2
             p_indices.remove(index)
@@ -846,7 +846,7 @@ def fix_unsaturated_bond(mol, indices, aug_inchi):
     of atoms that should be unpaired electrons left. 
     """
 
-    correct = mol.getNumberOfRadicalElectrons() == (mol.multiplicity - 1)
+    correct = mol.getRadicalCount() == (mol.multiplicity - 1)
 
     if not correct and not indices:
         raise Exception( 'Cannot correct {} based on {} by converting unsaturated bonds into unpaired electrons...'\
@@ -856,5 +856,5 @@ def fix_unsaturated_bond(mol, indices, aug_inchi):
 
     while not correct and unsaturated and len(indices) > 1:
         mol = fix_unsaturated_bond_to_biradical(mol, aug_inchi.inchi, indices)
-        correct = mol.getNumberOfRadicalElectrons() == (mol.multiplicity - 1)
+        correct = mol.getRadicalCount() == (mol.multiplicity - 1)
         unsaturated = isUnsaturated(mol)