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> 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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