Re: [Cdk-devel] basic molecule handling

[Ola S. <Ola...@fa...>]

John,

With some legacy code for reading molecules I run into:

java.lang.NullPointerException: Aromaticity model requires implicit hydrogen count is set.

when trying your suggested:

Aromaticity arom = new Aromaticity(ElectronDonation.daylight(),
                Cycles.or(Cycles.all(), Cycles.all(6)));
         arom.apply(atomcontainer);

Could you help me out how to set implicit hydrogen count? I really have no interest in a major rewrite of my legacy code for the moment...

Thanks,

Ola

On 9 jun 2015, at 14:08, Ola Spjuth <Ola...@fa...<mailto:Ola...@fa...>> wrote:

Thanks, John!

Ola

On 8 jun 2015, at 23:08, John M <joh...@gm...<mailto:joh...@gm...>> wrote:

https://gist.github.com/johnmay/711a42227f86fb339e9f
​


BufferedReader     brdr   = ...;



// create once and reuse

IChemObjectBuilder bldr   = SilentChemObjectBuilder.getInstance();

Aromaticity        arom   = new Aromaticity(ElectronDonation.daylight(),

                                            Cycles.or(Cycles.all(), Cycles.all(6)));



// SMILES, implicit h already present

SmilesParser smipar = new SmilesParser(bldr);

String line;

while ((line = brdr.readLine()) != null) {

    try {

        IAtomContainer mol = smipar.parseSmiles(line);

        arom.apply(mol);

        AtomContainerManipulator.suppressHydrogens(mol);

    } catch (InvalidSmilesException ex) {

        // log.. normally bad Kekulé input

    } catch (CDKException e) {

        // log.. complex ring system couldn't calc arom - avoid SSSR

    }

}



// SDfile V2000, implicit h already present

MDLV2000Reader mdlr = new MDLV2000Reader(brdr);

IAtomContainer mol;

while ((mol = mdlr.read(bldr.newInstance(IAtomContainer.class, 0,0,0,0))) != null) {

    try {

        arom.apply(mol);

        AtomContainerManipulator.suppressHydrogens(mol);

    } catch (CDKException e) {

        // log.. complex ring system couldn't calc arom - avoid SSSR

    }

}



// InChI, implicit h already present

// CML, implicit h maybe present -> atom type + guess hydrogen counts

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