Dear all,
I am working on task where I need to generate atom fingerprints based on
the occurence of a set of patterns in a molecule. Therefore, I am doing
some pattern matching and trying to get the atom indices.
I ran this ():
IAtomContainer molecule = sp.parseSmiles("CSCCSCO");
SMARTSQueryTool smarts_pattern = new SMARTSQueryTool("[#6]S[#6]");
boolean status = smarts_pattern.matches(molecule);
List<List<Integer>> indexes = smarts_pattern.getUniqueMatchingAtoms();
smarts_pattern.countMatches() returned 2. However, indexes = [[0, 1, 2]]
(Aren't I supposed to get 2 arrays here ?).
Trying smarts_pattern.getMatchingAtoms() did not change anything.
When I changed the structure to "CSCCSC(O)CCCSCC",
smarts_pattern.countMatches() returned 4, which is wrong too.
And indexes = [[0, 1, 2], [9, 10, 11]].
I am using CDK-1.4.11.
Please could you help me understand this and get the correct result?
Regards,
Yannick
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