On Jul 2, 2007, at 3:57 PM, Stefan Kuhn wrote:
> 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?
The change I made in SmilesParser.java is around line 680 and looks
like:
Integer hcount = atom.getHydrogenCount() == CDKConstants.UNSET ?
0 : atom.getHydrogenCount()
if (hcount > 0)
{
atom.setHydrogenCount(hcount - 1);
}
This is only qualitatively different from the original which had
assumed the implicit H count was 0, so I'm not sure what happened
>> 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?
0
>> whereas this should be for each atom.
> Don't understand this. Sorry.
Sorry, that have been '2 for each atom'
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