Hi Out of curiosity how are you planning to do the conformational search? Most tools I'm aware of would be expected to treat double bonds appropriately Chris > > Today's Topics: > > 1. Re: Conversion SMILES to XYZ (Volker Settels) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Sep 2017 12:35:29 +0000 > From: Volker Settels <volker.sett...@basf.com> > To: Geoffrey Hutchison <geoff.hutchi...@gmail.com> > Cc: "openbabel-disc...@lists.sf.net" <openbabel-disc...@lists.sf.net> > Subject: Re: [Open Babel] Conversion SMILES to XYZ > Message-ID: > > <vi1pr0402mb27523438d5b755f03678107fe8...@vi1pr0402mb2752.eurprd04.prod.outlook.com> > > Content-Type: text/plain; charset="utf-8" > > Hi Geoff, > > Thanks a lot for your help! > > I checked a couple of xyz files generated from SMILES. In these files, the > hydrogens are always listed after the ?heavy? atoms. If the ?heavy? atoms > always are listed in the same order than in the SMILES, counting characters > to find double bonds could work. What would you think? > > My task is to perform a conformational search for a list of molecules. For > this reason, I have to identify double bonds, which should be excluded from > conformational search due to fixed stereochemistry (?\? or ?/? in SMILES). > Assuming the following SMILES: > > CC\=\CCN=CC > > I have to think about a routine which gives me the atoms involved only in the > first double bond of the SMILES above. After transforming the SMILES into a > format including the 3D structure, I still have to gather the information > about double bonds with specified stereochemistry. Is this possible in the > sdf format? I am not used to this format. > > Best wishes > > Volker > > Von: Geoffrey Hutchison [mailto:geoff.hutchi...@gmail.com] > Gesendet: Dienstag, 12. September 2017 22:04 > An: Volker Settels <volker.sett...@basf.com> > Cc: openbabel-disc...@lists.sf.net > Betreff: Re: [Open Babel] Conversion SMILES to XYZ > > That likely won't work, because in general the SMILES doesn't include > hydrogens. > > If you want to follow double-bonds, I recommend converting to a file format > with bonding information, e.g., SDF. > > Best regards, > -Geoff > > > this is a question regarding the conversion of SMILES to xyz. I have to > identify atoms in the generated xyz file, which are involved in double bonds > with fixed stereochemistry according to the SMILES. A fast solution would be > just to count atoms until ?/? or ?\? is found in the SMILES. But this is only > possible, if it is ensured that in every case the order of atoms within the > xyz file is identical to the one in the SMILE string. Is this the case? > Thanks a lot for your help! > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > ------------------------------ > > End of OpenBabel-discuss Digest, Vol 136, Issue 6 > *************************************************
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