Rajarshi Guha wrote:
Ok, now hydrogen adder is working and atom count is correct, thank you.
Please can you solve another doubt?
Into the ethane molecule I have to search a substructure whose pattern
is specified by this SMARTS:
C(~C)(~H)
the code should be this:
IMolecularDescriptor descriptor = new AromaticBondsCountDescriptor();
Object[] params = {true};
descriptor.setParameters(params);
IAtomContainer ac = sp.parseSmiles("CC");
CDKHueckelAromaticityDetector.detectAromaticity(ac);
CDKHydrogenAdder hd =
CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
hd.addImplicitHydrogens(ac);
AtomContainerManipulator.convertImplicitToExplicitHydrogens(ac);
String pattern=?????? // What is the correct string to use here?
SMARTSQueryTool querytool = new SMARTSQueryTool(pattern);
boolean result = querytool.matches(ac);
System.out.println(result);
What is the correct string to use as pattern?
Best Regards, Thank you
GF
>
> It's a good idea to use the current code from SVN since hydrogen
> addition and aromaticity detection has been very much improved.
>
> The following code (based on the nightly build) works correctly:
>
> IMolecularDescriptor descriptor = new AromaticBondsCountDescriptor();
> Object[] params = {true};
> descriptor.setParameters(params);
>
> SmilesParser sp = new
> SmilesParser(DefaultChemObjectBuilder.getInstance());
> IAtomContainer mol = sp.parseSmiles("c1ccccc1"); // ethanol
>
> CDKHueckelAromaticityDetector.detectAromaticity(mol);
> CDKHydrogenAdder hd =
> CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
> hd.addImplicitHydrogens(mol);
> AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
>
> System.out.println(mol.getAtomCount());
>
> -------------------------------------------------------------------
> Rajarshi Guha <[EMAIL PROTECTED]>
> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
> -------------------------------------------------------------------
> All the passions make us commit faults; love makes us commit the most
> ridiculous ones.
> -- La Rochefoucauld
>
>
--
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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