On Tuesday 26 June 2007 22:54, Rajarshi Guha wrote: > I'm looking at one of the SmilesParserTest cases, specifically > testSFBug956921(). > > The function looks like: > > String smiles = "[cH-]1cccc1"; > IMolecule mol = sp.parseSmiles(smiles); > Assert.assertEquals(5, mol.getAtomCount()); > // each atom should have 1 implicit hydrogen, and two neighbors > > However when I look at the result of the SMILES parsing I see that > the first carbon has 1 implicit hydrogen (as returned by > atom.getHydrogenCount()) but all others are null - indicating that > they have not been set. I guess this is related to the new attributes being objects - so by default the implicit H count is null, the first atom gets 1. Question is: Shall the smiles parser set them all to 0? Always? Or only if at least one H is in the smiles? > But, if in the above code I change the SMILES to c1ccccc1 and then > rerun, all the atoms are reported to have 0 implicit hydrogens, 0? or null? > whereas this should be for each atom. Don't understand this. Sorry. -- Stefan Kuhn BSc MA IPB Halle AG Bioinformatik & Massenspektrometrie Weinberg 3 06120 Halle http://www.ipb-halle.de http://msbi.bic-gh.de [EMAIL PROTECTED] +49 (0) 345 5582 1474 Fax.+49 (0) 345 5582 1409
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