Apologies, it was attached in the e-mail before last but had an identifier name (SOXGES.search2.cif) and so may have caused confusion. I've attached it again in this e-mail.
As a general question, is it possible to convert coordinates to smiles that will always preserve the elements present (but may not get the bonding correct)? Best wishes, Scott On 4 December 2012 16:54, Chris Morley <c.mor...@gaseq.co.uk> wrote: > Your problem is the incorrect conversion of a cif file, but you haven't > shown one yet. (Not that I know much about cif files, but others may.) > Conversions in OB go through an internal data structure, OBMol. It sound > like the problem is in the cif to OBMol part, not in the OBMol to SMILES. > > Chris > > On 04/12/2012 15:34, Scott McKechnie wrote: > > Thanks Chris for the helpful comments. Sorry to keep on but I'm still > > left with the problem on going from cif to smiles where the original > > number of elements is not conserved. What I want is to be able to > > reliably represent the original cif molecule as a smiles string and from > > there recreate the molecule with gen3d. The problem at the moment is > > that the number of H atoms is changing. Any work around for this? > > > > On 4 December 2012 15:05, Chris Morley <c.mor...@gaseq.co.uk > > <mailto:c.mor...@gaseq.co.uk>> wrote: > > > > Scott > > > > Your "correct smiles" is not right. The sum of the bond orders to the > > charged nitrogen should be 4, and is only 3 (it has no H attached). > The > > correct SMILES is in my post below. Even with it, the round trip via > > xyz: > > > > obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1" -oxyz --gen3D > > | obabel -ixyz -osmi --append formula > > 1 molecule converted > > C(=O)(O)C[C@@H](C(=O)[O])N1CNC=C1 C7H8N2O4 > > 1 molecule converted > > > > gives a di-radical rather than a zwitterion because xyz does not > > represent charges (or even bonds) and so OpenBabel didn't get any > hints. > > xyz format is poor choice of format for general use. The round trip > > works ok with formats like mol or cml. > > > > Chris > > > > On 04/12/2012 10:51, Scott McKechnie wrote: > > > Hi Chris, > > > > > > Thanks for your reply and apologies for the delayed response. > > Converting > > > the cif to xyz and viewing the molecule shows the correct > > structure but > > > converting the xyz file to smi and then generating coordinates and > > > viewing shows the addition of a H atom. > > > > > > The correct smiles is: C(=O)(O)C[C@@H](C(=O)[O-])[N]1C=C[N+]=C1 > > > The other smiles is: C(=O)([C@@H](CC(=O)O)N1C=CNC1)O > > > > > > One strange feature is that there doesn't appear to be a double > bond > > > between the N atom in the ring and the C atom, leaving the C atom > > with > > > only three bonds. The smiles conversion seems to want to add a H > > here to > > > get the correct bonding. > > > > > > Similarly for an ion, using smiles conversion results in the > > addition of > > > H's. > > > > > > I've attached the cif file. > > > > > > Many thanks, > > > > > > Scott > > > > > > > > > On 30 November 2012 14:53, Chris Morley <c.mor...@gaseq.co.uk > > <mailto:c.mor...@gaseq.co.uk> > > > <mailto:c.mor...@gaseq.co.uk <mailto:c.mor...@gaseq.co.uk>>> > wrote: > > > > > > On 30/11/2012 12:03, scott_m wrote: > > > > Dear all, > > > > > > > > The conversion of > > (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate > > > from a > > > > .cif file to .smi and subsequent generation of coordinates > > from > > > the .smi > > > > file results in the addition of an extra H to one of the > > ring C > > > atoms. The > > > > original cif formula is C7H8N2O4 but this changes to > C7H9N2O4, > > > which is no > > > > longer a zwitterion. > > > > > > > > I also noticed that converting an ion to smi and then from > > smi to xyz > > > > resulted in the addition of hydrogen atoms. Can this be > > avoided? > > > > > > > > Is the smi conversion of ions and zwitterions known to > cause > > > problems? > > > > > > Getting added hydrogens right is a recurrent issue. However > the > > > conversion from SMILES to xyz (and other formats) seems ok. > > Your problem > > > may be in the conversion of the cif file, but you will need > > to append it > > > for somebody (probably not me) to debug. > > > > > > obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1 > > > (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate" -oxyz > --gen3D > > > --title "" > > > --append formula > > > 21 > > > C7H8N2O4 > > > C 2.45602 0.70570 1.56344 > > > O 3.44592 0.48586 2.25208 > > > O 1.43656 1.46670 2.00415 > > > C 2.26356 0.11437 0.19030 > > > C 3.14546 0.74947 -0.88078 > > > H 2.84831 0.31396 -1.84634 > > > C 2.83038 2.27406 -0.99631 > > > O 1.67090 2.60592 -0.61087 > > > O 3.79441 2.97728 -1.40748 > > > N 4.60137 0.42805 -0.71225 > > > C 5.35900 0.94762 0.25841 > > > N 6.58789 0.46124 0.10334 > > > H 7.33992 0.61660 0.75954 > > > C 6.69161 -0.15933 -1.12882 > > > C 5.43119 -0.14873 -1.66026 > > > H 0.84536 1.76580 1.27272 > > > H 1.20439 0.19509 -0.08254 > > > H 2.46795 -0.95767 0.27113 > > > H 5.04774 1.61643 1.05753 > > > H 7.65241 -0.48371 -1.46628 > > > H 5.01646 -0.45579 -2.60586 > > > 1 molecule converted > > > > > > Chris > > > > > > > > > ------------------------------------------------------------------------------ > > > Keep yourself connected to Go Parallel: > > > TUNE You got it built. Now make it sing. Tune shows you how. > > > http://goparallel.sourceforge.net > > > _______________________________________________ > > > OpenBabel-discuss mailing list > > > OpenBabel-discuss@lists.sourceforge.net > > <mailto:OpenBabel-discuss@lists.sourceforge.net> > > > <mailto:OpenBabel-discuss@lists.sourceforge.net > > <mailto:OpenBabel-discuss@lists.sourceforge.net>> > > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > > > > > > > > > > ------------------------------------------------------------------------------ > > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > > Remotely access PCs and mobile devices and provide instant support > > Improve your efficiency, and focus on delivering more value-add > services > > Discover what IT Professionals Know. Rescue delivers > > http://p.sf.net/sfu/logmein_12329d2d > > _______________________________________________ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > <mailto:OpenBabel-discuss@lists.sourceforge.net> > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > > > > > > > > ------------------------------------------------------------------------------ > > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > > Remotely access PCs and mobile devices and provide instant support > > Improve your efficiency, and focus on delivering more value-add services > > Discover what IT Professionals Know. Rescue delivers > > http://p.sf.net/sfu/logmein_12329d2d > > > > > > > > _______________________________________________ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > > > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add services > Discover what IT Professionals Know. Rescue delivers > http://p.sf.net/sfu/logmein_12329d2d > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > >
SOXGES.search2.cif
Description: Binary data
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