Re: [Rdkit-discuss] (no subject)
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Re: [Rdkit-discuss] (no subject)
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From: <che...@gm...> - 2014-05-28 15:19:58
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<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div> <div>Dear Toby,</div> <div> </div> <div>exactly what I was looking for, thanks a lot!</div> <div> </div> <div>RDKit and its community rock!</div> <div> </div> <div> <div name="quote" style="margin:10px 5px 5px 10px; padding: 10px 0 10px 10px; border-left:2px solid #C3D9E5; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"> <div style="margin:0 0 10px 0;"><b>Gesendet:</b> Mittwoch, 28. Mai 2014 um 15:45 Uhr<br/> <b>Von:</b> "Toby Wright" <tob...@in...><br/> <b>An:</b> che...@gm...<br/> <b>Cc:</b> "RDKit Discuss" <rdk...@li...><br/> <b>Betreff:</b> Re: [Rdkit-discuss] (no subject)</div> <div name="quoted-content"> <div> <div> <div> <div> <div> <div> <div>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:<br/> <br/> mol = Chem.MolFromSmiles('FC(Cl)Br')<br/> chiralCentres = Chem.FindMolChiralCenters(mol, includeUnassigned=True)<br/> if chiralCentres:<br/> chiral = Chem.Mol(mol)<br/> firstCentre = chiralCentres[0][0]<br/> chiral.GetAtomWithIdx(firstCentre).SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW)<br/> print Chem.MolToSmiles(chiral, isomericSmiles=True)<br/> chiral.GetAtomWithIdx(firstCentre).SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW)<br/> print Chem.MolToSmiles(chiral, isomericSmiles=True)<br/> <br/> F[C@@H](Cl)Br<br/> F[C@H](Cl)Br<br/> </div> </div> </div> How to extend this to molecules with multiple chiral centres is left as an exercise for the reader ;)<br/> </div> Yours,<br/> </div> Toby Wright<br/> <br/> --</div> <div>InhibOx Ltd</div> </div> <div class="gmail_extra"> <div class="gmail_quote">On 28 May 2014 13:27, <span><<a href="che...@gm..." target="_parent">che...@gm...</a>></span> wrote: <blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex;border-left: 1.0px rgb(204,204,204) solid;padding-left: 1.0ex;"> <div> <div style="font-family: Verdana;font-size: 12.0px;"> <div>Hi RDKitters,</div> <div> </div> <div>I am preparing a set of compounds for a virtual screening.</div> <div>While the majority are achiral compounds, there are also some racemic structures in the dataset.</div> <div>For the virtual screen, I would like to enumerate the enantiomers from these racemates, e.g. from</div> <div> <div>"CC1CCCCN1" -> ["C[C@H]1CCCCN1", "C[C@@H]1CCCCN1"]</div> <div> </div> <div>Is this somehow possible with RDKit?</div> <div> </div> <div>Many thanks in advance.</div> <div>Axel (<a href="http://www.aviru.de" target="_blank">www.aviru.de</a>)</div> </div> </div> </div> <br/> ------------------------------------------------------------------------------<br/> Time is money. Stop wasting it! Get your web API in 5 minutes.<br/> <a href="http://www.restlet.com/download" target="_blank">www.restlet.com/download</a><br/> <a href="http://p.sf.net/sfu/restlet" target="_blank">http://p.sf.net/sfu/restlet</a><br/> _______________________________________________<br/> Rdkit-discuss mailing list<br/> <a href="Rdk...@li..." target="_parent">Rdk...@li...</a><br/> <a href="https://lists.sourceforge.net/lists/listinfo/rdkit-discuss" target="_blank">https://lists.sourceforge.net/lists/listinfo/rdkit-discuss</a><br/> </blockquote> </div> </div> </div> </div> </div> </div></div></body></html> |
