Thanks a lot, this is exactly what I wanted.
Best regards,
Michal
On 10 March 2016 at 12:13, Brian Kelley <[email protected]> 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 <
> [email protected]> 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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