Merge pull request #468 from ReactionMechanismGenerator/fixGroupsAlgo…

…rithm

Fix group algorithm that was breaking database tests.  
When matching a structure against a functional group, labeled atoms in the structure but not the group are to be ignored. Previously we temporarily removed the atoms before doing the graph isomorphism. This now causes problems with the sort method which is used at the start of the isomorphism check. So now we just mark the atoms that should be ignored, and ignore them in the VF2 subgraph algorithm.  Seems to work (or at least passes the unit tests).

.travis.yml

@@ -32,6 +32,7 @@ install:
 
 script: 
   - make test
+  - make test-database
   - make eg1
   - make eg4
   - make eg5

rmgpy/data/base.py

@@ -948,18 +948,17 @@ def matchNodeToStructure(self, node, structure, atoms, strict=False):
                 # Passed semantic checks, so add to maps of already-matched atoms
                 initialMap[atom] = center
             # Labeled atoms in the structure that are not in the group should
-            # not be considered in the isomorphism check, so remove them temporarily
+            # not be considered in the isomorphism check, so flag them temporarily
             # Without this we would hit a lot of nodes that are ambiguous
-            removedAtoms = []
-            for label, atom in structure.getLabeledAtoms().iteritems():
-                if label not in centers:
-                    removedAtoms.append(atom)
-                    structure.atoms.remove(atom)
+            flaggedAtoms = [atom for label, atom in structure.getLabeledAtoms().iteritems() if label not in centers]
+            for atom in flaggedAtoms: atom.ignore = True
+
             # use mapped (labeled) atoms to try to match subgraph
             result = structure.isSubgraphIsomorphic(group, initialMap)
-            # Restore atoms removed in previous step
-            for atom in removedAtoms:
-                structure.atoms.append(atom)
+
+            # Restore atoms flagged in previous step
+            for atom in flaggedAtoms: atom.ignore = False
+
             return result
 
     def descendTree(self, structure, atoms, root=None, strict=False):

rmgpy/molecule/graph.pxd

@@ -33,6 +33,7 @@ cdef class Vertex(object):
     cdef public short sortingLabel
     cdef public bint terminal
     cdef public Vertex mapping
+    cdef public bint ignore
 
     cpdef Vertex copy(self)
 

rmgpy/molecule/graph.pyx

@@ -57,6 +57,7 @@ cdef class Vertex(object):
     def __init__(self):
         self.edges = {}
         self.resetConnectivityValues()
+        self.ignore = False
 
     def __reduce__(self):
         """

rmgpy/molecule/vf2.pyx

@@ -168,6 +168,8 @@ cdef class VF2:
             if self.findAll:
                 mapping = {}
                 for vertex2 in self.graph2.vertices:
+                    if vertex2.ignore:
+                        continue
                     assert vertex2.mapping is not None
                     assert vertex2.mapping.mapping is vertex2
                     mapping[vertex2.mapping] = vertex2
@@ -178,6 +180,8 @@ cdef class VF2:
         # Create list of pairs of candidates for inclusion in mapping
         hasTerminals = False
         for vertex2 in self.graph2.vertices:
+            if vertex2.ignore:
+                continue
             if vertex2.terminal:
                 # graph2 has terminals, so graph1 also must have terminals
                 hasTerminals = True
@@ -186,6 +190,8 @@ cdef class VF2:
             vertex2 = self.graph2.vertices[0]
 
         for vertex1 in self.graph1.vertices:
+            if vertex1.ignore:
+                continue
             # If terminals are available, then skip vertices in the first
             # graph that are not terminals
             if hasTerminals and not vertex1.terminal: continue