The tests used by PerlMol are available at http://cpansearch.perl.org/src/ITUB/Chemistry-File-SMARTS-0.22/t/pats/ .
Each test looks like this: -------- Pattern: [R2] Options: permute 0 overlap 1 Mol: CCC12CC1CC2 Matched: (a4) Matched: (a6) Matched: () --------- The only trick is to know that the matched atom numbers are "global" atom numbers counting both the pattern and the molecule. In the example above, a1 is the pattern atom and a2..a8 are the atoms in the molecule. As for the options line, those are options affecting the substructure search in PerlMol. These are explained in http://search.cpan.org/~itub/Chemistry-Pattern-0.27/Pattern.pm . Cheers, Ivan
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