The bit I didn't like was when I added the implicit hydrogens and then
exported to smiles then the smiles contains all those hydrogens (as
Explicit/Expanded/Sprouted in your terminology). So to me it looks like
it added explicit hydrogens.
Tim
On 22/06/2016 10:08, John M wrote:
Sorry could be my bad wording, there are really three 'levels' of
hydrogens representation. This isn't that confusing but the
terminology is often misnamed in toolkits/formats. Even there where i
said explicit I should have said labelled or something similar:
Implicit/Undefined -> defined by valence rules -> CCO
Labelled/Contracted/Suppressed -> explicitly stated in format ->
[CH3][CH2][OH]
Explicit/Expanded/Sprouted -> explicit nodes ->
C][H])([H])([H])C([H])([H])O[H]
When CDK says 'ImplicitHydrogenAdder' it's not adding implicit
hydrogens per say but rather taken a molecule with some unknown
hydrogen counts (implicit) it sets the value of these explicitly. They
are still contracted on the parent atoms. You can take always expand
these and make them explicit nodes in the graph if so desired
(AtomContainerManipulator.convertImplicitHydrogensToExplicit) or
something similar. The reverse is 'suppressExplicitHydrogens', also
for legacy reason 'removeExplicitHydrogens' but doesn't actually
remove them so the 'suppress' name is preffered.
John
Regards,
John W May
john.wilkinson...@gmail.com <mailto:john.wilkinson...@gmail.com>
On 22 June 2016 at 09:55, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
John
Thanks for that. Adding implicit hydrogens does indeed resolve the
problem.
But does this mean that for formats like this you MUST add
IMPLICIT hydrogens everywhere (there's no way for them to be
explicit)? That's ugly!
Tim
On 21/06/2016 19:04, John M wrote:
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 <mailto:john.wilkinson...@gmail.com>
On 21 June 2016 at 17:22, Tim Dudgeon <tdudgeon...@gmail.com
<mailto: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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