Hmm,
That shouldn't be the case - if you use the ImplicitHydrogenAdder, this
would only be if you then 'convertImplicitToExplicit'.
John
Regards,
John W May
john.wilkinson...@gmail.com
On 22 June 2016 at 10:41, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> 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
>
> On 22 June 2016 at 09:55, Tim Dudgeon <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
>>
>> On 21 June 2016 at 17:22, Tim Dudgeon < <tdudgeon...@gmail.com>
>> 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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