>
> That doesn't help. They are not implicit hydrogens, they are real
> (explicit) ones.
> So presumably they would need to be deleted and then implicit ones adding
> back?
?
See back a couple of mails: suppressHydrogens
<http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.html#suppressHydrogens(org.openscience.cdk.interfaces.IAtomContainer)>
.
J
Regards,
John W May
john.wilkinson...@gmail.com
On 22 June 2016 at 12:07, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> That doesn't help. They are not implicit hydrogens, they are real
> (explicit) ones.
> So presumably they would need to be deleted and then implicit ones adding
> back?
>
> Tim
>
> On 22/06/2016 11:42, John M wrote:
>
> 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>
>> 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>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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