SMILES, InChI, Molfile have explicit valence models and thus their
hydrogens are set automatically on read. For other formats you need to add
them. The CDK doesn't do this by valence counting but rather through more
expensive atom typing. Very clunky:
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHydrogenAdder.getInstance(mol.getBuilder()).addImplicitHydrogens(mol);
If someone can point at the Tripos Mol2 valence model, am happy to add it.
Should be easy right as they encode the atom types in the format?
John
Regards,
John W May
john.wilkinson...@gmail.com
On 21 June 2016 at 17:22, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> I'm having difficulty reading Mol2 format files. Code is:
>
> def is = new FileInputStream("../../data/testfiles/ligand.mol2")
> def reader = new Mol2Reader(is)
> def file = reader.read(new ChemFile())
> def mol = ChemFileManipulator.getAllAtomContainers(file).get(0)
> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol)
> def out = new ByteArrayOutputStream()
> def writer = new SMILESWriter(out)
> writer.writeAtomContainer(mol)
> println new String(out.toByteArray())
>
> The file appears to be a valid mol2 format file, but when I try to write
> it out as smiles it blows up with:
>
> java.lang.NullPointerException: One or more atoms had an undefined number
> of implicit hydrogens
> at
> com.google.common.base.Preconditions.checkNotNull(Preconditions.java:229)
> at org.openscience.cdk.smiles.CDKToBeam.toBeamAtom(CDKToBeam.java:195)
> at org.openscience.cdk.smiles.CDKToBeam.toBeamGraph(CDKToBeam.java:145)
> at
> org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:369)
> at
> org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:325)
> at
> org.openscience.cdk.io.SMILESWriter.writeAtomContainer(SMILESWriter.java:179)
>
> What am I missing?
>
> Tim
>
>
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