Hi Janusz,
AddHs has a parameter "onlyOnAtoms" which takes a list of indices of atoms
to include. [http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolops-
module.html#AddHs]
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-01-20 23:21 GMT+01:00 Janusz Petkowski <jjpet...@mit.edu>:
> Dear RDKit Community,
>
> By default H atoms are not explicit in the molecular graph and because of
> that the substructure matching is ignoring them when searching for
> substructures. It is possible to use Chem.AddHs(mol) to add explicit
> hydrogens to all atoms in the molecule and then perform substructure
> matching but is it possible, in RDkit, to add explicit hydrogens
> specifically to atoms of choice instead to all of them?
>
> So let's say if I do:
>
> m1 = Chem.MolFromSmiles('C=C')
> m1_H = Chem.AddHs(m1)
> print m1_H.GetNumAtoms()
> print Chem.MolToSmiles(m1_H)
>
> The result is:
>
> >>> 6
> >>> [H]C([H])=C([H])[H]
>
> What if I would like to add only one (1) explicit hydrogen atom to a
> specific non-hydrogen atom (let's say m1.GetAtomWithIdx(0). In that case I
> would want to have:
>
> print m1_H.GetNumAtoms()
> print Chem.MolToSmiles(m1_H)
>
> >>> 3
> >>> [H]C=C
>
> I tried to use the following method: m1.GetAtomWithIdx(0).SetNumExplicitHs(1)
> which correctly adds an explicit H to C=C molecule but somehow I cannot
> convert it to smiles with this one additional explicit H added or
> subsequently use for substructure matching.
>
> At the end I would like to do a substructure matching where the following
> query structures:
>
>
> [H]C=C or [H]C=CC match the following molecule:
> [H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
>
> but at the same time those query structures: [H]C=C([H])[H] or
> [H]C([H])=CC do not match [H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
>
> PS. Of course, the structure [H]C([H])=C([H])[H] converted from C=C using
> Chem.AddHs(mol) will not be matched onto
> [H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
> which is correct.
>
> Thank you very much for your help,
>
> Best regards,
>
> Janusz Petkowski
>
>
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