Automorphisms, isomorphisms, symmetry classes and canonical labelling

I've just been spending some time ensuring that Tim's new symmetry and isomorphism code in Open Babel can be accessed from Python (you can already access it from C++). It didn't make it into the 2.3.0 official release but I'll push it out into the Windows Python in the next while.

First the symmetry classes and canonical labelling. These can be calculated and accessed as follows (the test molecule is shown in the image above):

import pybel
ob = pybel.ob

mol = pybel.readstring("smi", "c1c(O)cccc1(O)")

gs = ob.OBGraphSym(mol.OBMol)
symclasses = ob.vectorUnsignedInt()
gs.GetSymmetry(symclasses)

print symclasses
# <openbabel.vectorUnsignedInt; proxy of <Swig Object of type 'std::vector< unsigned int > *' at 0x004DFE90> >
print list(symclasses)

# [4, 5, 1, 3, 2, 3, 5, 1]

canonlabels = ob.vectorUnsignedInt()
ob.CanonicalLabels(mol.OBMol, symclasses, canonlabels)
print list(canonlabels)

# [4, 2, 1, 3, 5, 7, 6, 8]

Does the molecule have any automorphisms?

automorphs = ob.vvpairUIntUInt()
ob.FindAutomorphisms(mol.OBMol, automorphs, symclasses)
for x in automorphs:
    print x

# ((0, 0), (1, 6), (6, 1), (2, 7), (7, 2), (3, 5), (5, 3), (4, 4))
# ((0, 0), (1, 1), (2, 2), (3, 3), (4, 4), (5, 5), (6, 6), (7, 7))

Next we'll use the example molecule as a query to see how it matches another identical molecule which has the atoms in a different order:

query = ob.CompileMoleculeQuery(mol.OBMol)
mapper = ob.OBIsomorphismMapper.GetInstance(query)

mol_b = pybel.readstring("smi", "c1(O)cccc(O)c1")

isomorph = ob.vpairUIntUInt()
mapper.MapFirst(mol_b.OBMol, isomorph)
print list(isomorph)

# [(0, 7), (1, 5), (3, 4), (4, 3), (5, 2), (6, 0), (2, 6), (7, 1)]

isomorphs = ob.vvpairUIntUInt()
mapper.MapAll(mol_b.OBMol, isomorphs)
for x in isomorphs:
    print x

# ((0, 7), (1, 5), (3, 4), (4, 3), (5, 2), (6, 0), (2, 6), (7, 1))
# ((0, 7), (1, 0), (2, 1), (3, 2), (4, 3), (5, 4), (6, 5), (7, 6))