[Joelib-help] addHydrogens, modification counter, joelib conversion to joelib2

[Stephanie C. <SC...@sc...>]

Hi,

I have some JoeLib code I am trying to convert to JoeLib2.

When I run the JoeLib2 code, I get this error for some smiles string inputs (example below). But it runs just fine in the JoeLib code. Did I miss something in the conversion?

Exception in thread "main" java.lang.RuntimeException: : Molecule modification counter must be zero.
       at joelib2.molecule.types.AtomPropertyHelper.accessAtomProperty(Unknown Source)
       at joelib2.molecule.types.AtomPropertyHelper.getLabelCache(Unknown Source)
       at joelib2.molecule.types.AtomPropertyHelper.getBooleanAtomProperty(Unknown Source)
       at joelib2.molecule.types.AtomPropertyHelper.getBooleanAtomProperty(Unknown Source)
       at joelib2.feature.types.atomlabel.AtomIsAlphaBetaUnsaturated.isValue(Unknown Source)
       at joelib2.molecule.AtomHelper.getNBV3Dvalence1(Unknown Source)
       at joelib2.molecule.AtomHelper.getNewBondVector3D(Unknown Source)
       at joelib2.molecule.ProtonationHelper.addHydrogens(Unknown Source)
       at joelib2.molecule.BasicConformerMolecule.addHydrogens(Unknown Source)
       at edu.scripps.fl.match.test.CleanMoleculeJoeLib2Test.main(CleanMoleculeJoeLib2Test.java:20)


What I really don't understand is that just before I run the function mol.addHydrogens() the modificationCounter is 0.

JoeLib:

JOESmilesParser parser = new JOESmilesParser();
              JOEAromaticTyper typer = JOEAromaticTyper.instance();
              JOEMol mol = new JOEMol();
              parser.smiToMol(mol, "c1(N2CCC(O)CC2)c3c(nc(cc(c4cccc(OC)c4)n5)n15)CCCC3");
              typer.assignAromaticFlags(mol);
              mol.addHydrogens();
              for(AtomIterator ait = mol.atomIterator(); ait.hasNext(); ) {
                     JOEAtom atom = ait.nextAtom();
                     if (atom.isCarbon() && atom.getFormalCharge() > 0)
                           atom.setFormalCharge(0);
              }


JoeLib2:

SMILESParser parser = new SMILESParser();
              AromaticityTyper typer = BasicAromaticityTyper.instance();
              Molecule mol = new BasicConformerMolecule();
              parser.smiles2molecule(mol, "c1(N2CCC(O)CC2)c3c(nc(cc(c4cccc(OC)c4)n5)n15)CCCC3");
              typer.assignAromaticFlags(mol, null, null);
              mol.addHydrogens();
              for(AtomIterator ait = mol.atomIterator(); ait.hasNext(); ) {
                     Atom atom = ait.nextAtom();
                     if (atom.getAtomicNumber() == 6 && atom.getFormalCharge() > 0)
                           atom.setFormalCharge(0);
              }


Thank you for your help,

Stephanie