Merge pull request #1604 from ReactionMechanismGenerator/group_is

Added GroupAtom isNitrogen() and isCarbon() methods

rmgpy/molecule/group.pxd

@@ -73,6 +73,10 @@ cdef class GroupAtom(Vertex):
 
     cpdef bint isSulfur(self)
 
+    cpdef bint isNitrogen(self)
+
+    cpdef bint isCarbon(self)
+
     cpdef list countBonds(self, wildcards = ?)
 
     cpdef bint hasWildcards(self)

rmgpy/molecule/group.py

@@ -442,7 +442,7 @@ def isSpecificCaseOf(self, other):
                         return False
         else:
             if group.lonePairs: return False
-        #Each charge in self must have an equivalent in other
+        # Each charge in self must have an equivalent in other
         if self.charge:
             for charge1 in self.charge:
                 if group.charge:
@@ -462,7 +462,6 @@ def isSpecificCaseOf(self, other):
         # Otherwise self is in fact a specific case of other
         return True
 
-
     def isSurfaceSite(self):
         """
         Return ``True`` if the atom represents a surface site or ``False`` if not.
@@ -472,31 +471,42 @@ def isSurfaceSite(self):
 
     def isOxygen(self):
         """
-        Return ``True`` if the atom represents an oxygen atom or ``False`` if
-        not.
+        Return ``True`` if the atom represents an oxygen atom or ``False`` if not.
         """
         allOxygens = [atomTypes['O']] + atomTypes['O'].specific
-        checkList=[x in allOxygens for x in self.atomType]
-
+        checkList = [x in allOxygens for x in self.atomType]
         return all(checkList)
 
     def isSulfur(self):
         """
-        Return ``True`` if the atom represents an sulfur atom or ``False`` if
-        not.
+        Return ``True`` if the atom represents an sulfur atom or ``False`` if not.
         """
         allSulfur = [atomTypes['S']] + atomTypes['S'].specific
-        checkList=[x in allSulfur for x in self.atomType]
+        checkList = [x in allSulfur for x in self.atomType]
+        return all(checkList)
 
+    def isNitrogen(self):
+        """
+        Return ``True`` if the atom represents an sulfur atom or ``False`` if not.
+        """
+        allNitrogen = [atomTypes['N']] + atomTypes['N'].specific
+        checkList = [x in allNitrogen for x in self.atomType]
+        return all(checkList)
+
+    def isCarbon(self):
+        """
+        Return ``True`` if the atom represents an sulfur atom or ``False`` if not.
+        """
+        allCarbon = [atomTypes['C']] + atomTypes['C'].specific
+        checkList = [x in allCarbon for x in self.atomType]
         return all(checkList)
 
     def hasWildcards(self):
         """
         Return ``True`` if the atom has wildcards in any of the attributes:
-        atomtype, electronpairs, lone pairs, charge, and bond order. Returns
+        atomtype, radical electrons, lone pairs, charge, and bond order. Returns
         ''False'' if no attribute has wildcards.
         """
-
         if len(self.atomType) > 1:
             return True
         elif len(self.radicalElectrons) > 1 or len(self.radicalElectrons) == 0:
@@ -506,7 +516,6 @@ def hasWildcards(self):
         for bond in self.bonds.values():
             if len(bond.order) > 1:
                 return True
-
         return False
 
     def countBonds(self, wildcards = False):
@@ -516,7 +525,7 @@ def countBonds(self, wildcards = False):
         If the argument wildcards is turned off then any bonds with multiple
         options for bond orders will not be counted
         """
-        #count up number of bonds
+        # count up number of bonds
         single = 0; rDouble = 0; oDouble = 0; sDouble = 0; triple = 0; quadruple = 0; benzene = 0
         for atom2, bond12 in self.bonds.iteritems():
             if not wildcards and len(bond12.order) > 1:

rmgpy/statmech/conformer.pyx

@@ -338,13 +338,13 @@ cdef class Conformer(RMGObject):
         Finally, the reduced moment of inertia is evaluated from the moment of inertia 
         of each top via the formula (I1*I2)/(I1+I2).  
         
-        Option corresponds to 3 possible ways of calculating the internal reduced moment of inertia
-        as discussed in East and Radom [2]
+        ``option`` is an integer corresponding to one of three possible ways of calculating the internal reduced moment
+        of inertia, as discussed in East and Radom [2]
         
         +----------+---------------------------------------------------------------------------------------------------+
         |option = 1|moments of inertia of each rotating group calculated about the axis containing the twisting bond   |
         +----------+---------------------------------------------------------------------------------------------------+
-        |option = 2|(unimplemented) each moment of inertia of each rotating group is calculated about an axis parallel |
+        |option = 2|each moment of inertia of each rotating group is calculated about an axis parallel                 |
         |          |to the twisting bond and passing through its center of mass                                        |
         +----------+---------------------------------------------------------------------------------------------------+
         |option = 3|moments of inertia of each rotating group calculated about the axis passing through the            |
@@ -371,9 +371,11 @@ cdef class Conformer(RMGObject):
 
         # Check that exactly one pivot atom is in the specified top
         if pivots[0] not in top1 and pivots[1] not in top1:
-            raise ValueError('No pivot atom included in top; you must specify which pivot atom belongs with the specified top.')
+            raise ValueError('No pivot atom included in top; you must specify which pivot atom belongs with the'
+                             ' specified top.')
         elif pivots[0] in top1 and pivots[1] in top1:
-            raise ValueError('Both pivot atoms included in top; you must specify only one pivot atom that belongs with the specified top.')
+            raise ValueError('Both pivot atoms included in top; you must specify only one pivot atom that belongs'
+                             ' with the specified top.')
 
         # Enumerate atoms in other top
         top2 = [i+1 for i in range(Natoms) if i+1 not in top1]
@@ -412,8 +414,9 @@ cdef class Conformer(RMGObject):
             # Determine moments of inertia of each top
             I1 = 0.0
             for atom in top1:
-                r1 = coordinates[atom-1,:] - top1CenterOfMass #shift to the center of mass (goes through center of mass)
-                r1 -= numpy.dot(r1, axis) * axis #remove components parallel to the bond axis
+                # shift to the center of mass (goes through center of mass)
+                r1 = coordinates[atom-1,:] - top1CenterOfMass
+                r1 -= numpy.dot(r1, axis) * axis  # remove components parallel to the bond axis
                 I1 += mass[atom-1] * numpy.linalg.norm(r1)**2
             I2 = 0.0
             for atom in top2:
@@ -442,9 +445,9 @@ cdef class Conformer(RMGObject):
 
         else:
 
-            raise ValueError("option {0} unimplemented or non-existant".format(option))
+            raise ValueError('Option {0} is invalid. Should be either 1, 2, or 3.'.format(option))
 
-        return I1*I2/(I1+I2)
+        return I1 * I2 / (I1 + I2)
 
     @cython.boundscheck(False)
     @cython.wraparound(False)