Which SMSD are you using? I don't have control over the downstream one. On Wed, 28 Aug 2019 at 10:16, Tim Dudgeon <[email protected]> wrote:
> Unfortunately other parts of my code are using new features such as > IAtomContainer.atoms() so whilst switching to the legacy IAtomContainer > avoids the alignment problem it looks to be a no go as a solution. > > Would switching to the legacy classes in the org.openscience.cdk.smsd > package be an option or do I just need to wait for the problem to be fixed? > > > On 28/08/2019 08:15, John Mayfield wrote: > > 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 >>> >>
_______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
