Just a note on this - in CDK 1.5 the Pattern class is preferred as the
universal isomorphism tester is actually doing MCS (much harder).
Pattern ptrn = Pattern.findIdentical(butane);
for (Mol m : mols)
ptrn.matches(m);
In general though this is the slowest way to do it (n^2) vs (n log n) with
Hi John,
If the reader produces and IQueryAtomContainer IQueryAtoms/IQueryBonds then
it's simply a matter of passing it into the Pattern class (of UIT). This
will do a test of the query against real molecules - if you want to check
if one query equals another that's more tricky (I think RDKit has
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