Well you can just zero all the counts,
for (IAtom atom : mol.atoms())
atom.setImplicitHydrogenCount(0);
but you can still store contracted forms in mol2 so it's not a general
solution,
John
Regards,
John W May
john.wilkinson...@gmail.com
On 22 June 2016 at 11:20, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> Yes, that's right. They are there in the mol2 file.
>
> Strange that you need to "add" them again!
>
> Tim
>
> On 22/06/2016 11:10, John M wrote:
>
> Or actually if the hydrogens are explicit in the input they are preserved.
> Looking this up briefly looks to be the case.
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 22 June 2016 at 10:52, John M <john.wilkinson...@gmail.com> wrote:
>
>> 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>
>> 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>
>>> 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>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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