Dear Toby,
exactly what I was looking for, thanks a lot!
RDKit and its community rock!
Gesendet: Mittwoch, 28. Mai 2014 um 15:45 Uhr
Von: "Toby Wright" <toby.wri...@inhibox.com>
An: chemis...@gmx.de
Cc: "RDKit Discuss" <rdkit-discuss@lists.sourceforge.net>
Betreff: Re: [Rdkit-discuss] (no subject)
Von: "Toby Wright" <toby.wri...@inhibox.com>
An: chemis...@gmx.de
Cc: "RDKit Discuss" <rdkit-discuss@lists.sourceforge.net>
Betreff: Re: [Rdkit-discuss] (no subject)
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
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
--
InhibOx Ltd
On 28 May 2014 13:27, <chemis...@gmx.de> 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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