(CC'ing the list as I hadn't in my original reply)
Dear Janusz,
this is what I would do:
>>> from rdkit import Chem
>>> mol = Chem.MolFromSmiles('SSC')
>>> print Chem.MolToSmiles(mol)
CSS
>>> print Chem.MolToSmiles(mol, allHsExplicit=True)
[CH3][S][SH]
>>> a = mol.GetAtomWithIdx(1)
>>> print (a.GetTotalValence())
2
>>> desiredValence = 4
>>> a.SetNumExplicitHs(desiredValence - a.GetTotalValence())
>>> a.UpdatePropertyCache()
>>> print (a.GetTotalValence())
4
>>> print Chem.MolToSmiles(mol, allHsExplicit=True)
[CH3][SH2][SH]
Cheers,
p.
> On 06/20/17 15:37, Janusz Petkowski wrote:
> Dear RDKit Community,
>
> I have a quick question regarding a possibility of setting valence of an atom
> in rdkit.
>
> Let's say that I have a molecule like this (smiles notation): PPC or SSC and
> I would like to change the valence of one or more S or P atoms from default
> II for S or III for P to let's say SIV or SVI and PV. As a result I would
> like to have the following molecules (as an example): [H][SH3](C)[SH5],
> [H][SH2]SC, [H][SH3](C)[SH3] or [H][PH3]PC, [H][PH3][PH3]C
>
> Is it possible to output such molecules using SSC or PPC molecules as inputs,
> using one of rdkit methods (modules)?
>
> Thank you very much for your help,
>
> Best regards,
>
> Dr Janusz Petkowski
> Research Fellow at MIT EAPS
> Tel: +1 (617) 258 - 6910
>
>
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