Okay code is likely adding atoms/bonds in the wrong order, will fix it. On Tue, 27 Aug 2019 at 18:18, Tim Dudgeon <[email protected]> wrote:
> Hi John, > > Yes, turning off AtomContainer2 avoids the error. > > > On 27/08/2019 16:31, John Mayfield wrote: > > Hmm odd, in legacy so expected but tests seem okay. Can you try turning > off AtomContainer2, https://github.com/cdk/cdk/wiki/AtomContainer2 > > On Tue, 27 Aug 2019 at 14:19, Tim Dudgeon <[email protected]> wrote: > >> Hi folks, >> >> I'm getting a NPE from AtomAtomMapping.getCommonFragmentAsSMILES() in >> certain cases. >> An example is below - the two structures differ only for a Cl <-> Br >> change. >> >> This is using the org.openscience.smsd.AtomAtomMapping, >> org.openscience.smsd.Isomorphism and >> org.openscience.smsd.tools.ExtAtomContainerManipulator classes. >> Not sure if those guys are active on this list? >> >> >> IAtomContainer query = smilesParser.parseSmiles('BrC1CCC(Cc2ccccc2)C1') >> IAtomContainer target = smilesParser.parseSmiles('ClC1CCC(Cc2ccccc2)C1') >> >> StructureDiagramGenerator sdg = new StructureDiagramGenerator() >> sdg.generateCoordinates(query) >> >> ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(query) >> ExtAtomContainerManipulator.aromatizeMolecule(query) >> >> ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(target) >> ExtAtomContainerManipulator.aromatizeMolecule(target) >> >> Isomorphism comparison = new Isomorphism(query, target, Algorithm.DEFAULT, >> true, false, false) >> AtomAtomMapping mapping = comparison.getFirstAtomMapping() >> String mcsSmiles = mapping.getCommonFragmentAsSMILES() >> >> The error I get is: >> >> java.lang.NullPointerException >> at >> org.openscience.cdk.silent.AtomContainer2.getAtomRefUnsafe(AtomContainer2.java:172) >> at >> org.openscience.cdk.silent.AtomContainer2.getBond(AtomContainer2.java:612) >> at >> org.openscience.smsd.AtomAtomMapping.getCommonFragment(AtomAtomMapping.java:332) >> at >> org.openscience.smsd.AtomAtomMapping.getCommonFragmentAsSMILES(AtomAtomMapping.java:371) >> at >> org.squonk.fragnet.depict.ChemUtilsSpec.alignMolecule2(ChemUtilsSpec.groovy:81) >> >> >> >> >> _______________________________________________ >> Cdk-user mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> >
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