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 this
ability).
Pattern ptrn = Pattern.findIdentical(mdlQuery); // of
Pattern.findSubstructure(mdlQuery).
for (Mol m : mols)
ptrn.matches(m);
Unfortunately it doesn't look like either V2000/V3000 load this information
and is only available via SMARTS. It should be too hard to add basic
support (atom lists etc) but I know V3000 gets crazy with sphere/distance
exclusions etc.
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