Hi,
Few months back Greg has added CanonicalRankAtoms to rdkit.Chem after my
similar question.
http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolfiles-module.html#CanonicalRankAtoms
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-03-10 13:18 GMT+01:00 Michal Krompiec <michal.kromp...@gmail.com>:
> Thanks a lot, this is exactly what I wanted.
> Best regards,
> Michal
>
> On 10 March 2016 at 12:13, Brian Kelley <fustiga...@gmail.com> wrote:
>
>> The canonicalizer doesn't treat hydrogens any differently than any other
>> atom, but they have to be in the graph. If you are starting from smiles,
>> simply add explicit hydrogens, python example below:
>>
>> >>> from rdkit import Chem
>>
>> >>> m = Chem.MolFromSmiles("CC")
>>
>> >>> mh = Chem.AddHs(m)
>>
>> >>> Chem.MolToSmiles(mh)
>>
>> '[H]C([H])([H])C([H])([H])[H]'
>>
>> >>> order = eval(mh.GetProp("_smilesAtomOutputOrder"))
>>
>> # safer non eval version...
>>
>> >>> order = mh.GetPropsAsDict(includePrivate=True,
>>
>>
>> includeComputed=True)['_smilesAtomOutputOrder']
>>
>> >>> list(order)
>>
>> [2,0,3,4,1,5,6,7]
>>
>> >>>
>>
>> Not that the output order is from the context of the output smiles
>> string, i.e. order[0] is the index of the original atom index that was the
>> outputs first atom and so on. I.e. order[output_atom_idx] = input_atom_idx
>>
>> On Thu, Mar 10, 2016 at 6:27 AM, Michal Krompiec <
>> michal.kromp...@gmail.com> wrote:
>>
>>> Hello,
>>> I need a "canonical" method for generating atom indices for a given
>>> molecule (with 3D coordinates, so the input is e.g. a mol file), for a
>>> molecular descriptor which should be invariant with respect to atom
>>> indexing. As I understand, canonical SMILES will give the same atom indices
>>> for non-hydrogen atoms, but is there a way in RDKit to generate unique
>>> indices for hydrogens as well?
>>> Best regards,
>>> Michal
>>>
>>>
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>>
>
>
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