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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