Thanks for you reply.
I sooved my problem but I got another:
IMolecularDescriptor descriptor = new
AromaticBondsCountDescriptor();
Object[] params = {true};
descriptor.setParameters(params);
SmilesParser sp = new
SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol = sp.parseSmiles("c1ccccc1"); // ethanol
HydrogenAdder hd = new HydrogenAdder();
hd.addExplicitHydrogensToSatisfyValency(mol);
System.out.println(mol.getAtomCount());
assertEquals(6, ((IntegerResult)
descriptor.calculate(mol).getValue()).intValue());
it prints 18 total atoms instead of 12 (6C + 6H).
Why?
Cheers,
GF.
>
> On Dec 6, 2007, at 7:58 AM, Gianfranco wrote:
>
>> Dear all
>>
>> this SMARTS query
>>
>> this.xQuery_263 = SMARTSParser.parse("Li-H");
>
> Hmm, I would've thought that the atomic symbol would be accepted
> (since Daylight says that all SMILES atomic symbols are legal SMARTS
> symbols), but Daylights depictmatch page does not accept Li as a
> SMARTS either.
>
> In any case if you use [#3H] as the pattern it will parse correctly.
>
> BTW, I don't know anything about your application but it is preferred
> to use SMARTSQueryTool for SMARTS matching as it provides handy helper
> methods
>
> -------------------------------------------------------------------
> Rajarshi Guha <[EMAIL PROTECTED]>
> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
> -------------------------------------------------------------------
> Got Mole problems? Call Avogadro at 6.02 x 10^23.
>
>
--
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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