Re: [Rdkit-discuss] (no subject)

[Toby W. <tob...@in...>]

Looking around I see references to a method called
Chem.AssignAtomChiralcodes that I couldn't get working so the following
method might not be ideal, but it seems to work:

mol = Chem.MolFromSmiles('FC(Cl)Br')
chiralCentres = Chem.FindMolChiralCenters(mol, includeUnassigned=True)
if chiralCentres:
     chiral = Chem.Mol(mol)
     firstCentre = chiralCentres[0][0]

chiral.GetAtomWithIdx(firstCentre).SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW)
     print Chem.MolToSmiles(chiral, isomericSmiles=True)

chiral.GetAtomWithIdx(firstCentre).SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW)
     print Chem.MolToSmiles(chiral, isomericSmiles=True)

F[C@@H](Cl)Br
F[C@H](Cl)Br

How to extend this to molecules with multiple chiral centres is left as an
exercise for the reader ;)

Yours,

Toby Wright

--
InhibOx Ltd


On 28 May 2014 13:27, <che...@gm...> wrote:

> Hi RDKitters,
>
> I am preparing a set of compounds for a virtual screening.
> While the majority are achiral compounds, there are also some racemic
> structures in the dataset.
> For the virtual screen, I would like to enumerate the enantiomers from
> these racemates, e.g. from
>  "CC1CCCCN1" -> ["C[C@H]1CCCCN1", "C[C@@H]1CCCCN1"]
>
> Is this somehow possible with RDKit?
>
> Many thanks in advance.
> Axel (www.aviru.de)
>
>
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