Dear all,
I find that if I use these SMILES as input
O=c2c(O)c(c1ccc(O)c(O)c1)sc3cccc(O)c23
O=c2c(O)c(c1ccc(O)c(O)c1)[nH]c3cccc(O)c23
O=c2c(O)c(c1ccc(O)c(O)c1)c(=O)c3cccc(O)c23
of this function
String smiles="O=c2c(O)c(c1ccc(O)c(O)c1)sc3cccc(O)c23";
SmilesParser sp = new
SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule m=sp.parseSmiles(smiles);
SSSRFinder sssrFinder = new SSSRFinder(m);
IRingSet rs = sssrFinder.findSSSR();
List list = RingPartitioner.partitionRings(rs);
RingSet tmp = null;
IAtomContainer test = null;
for (int z = 0; z < list.size(); z++){
tmp = (RingSet)list.get(z);
test = RingPartitioner.convertToAtomContainer(tmp);
mo = builder.newMolecule( test );
System.out.println( name + "\t" + sg.createSMILES( mo ) );
I observe that I loose the doublebond of the not-aromatic ring of the
bicyclic system (positions 2-3).
Is this a bug?
Thanks!
Gianfranco
--
Gianfranco Frau
CRS4 - Bioinformatics
Phone +39 070 9250 438
Loc. Pixina Manna Edificio 1 Pula 09010 (CA), Italy
http://www.bioinformatica.crs4.org
msn contact: [EMAIL PROTECTED]
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