I think the underlying problem is that the current aromaticity code is optimized for the situation where the location of hydrogens is unknown. This is useful for PDB files, but in the general case, it is solving a more difficult problem than we need to.
I'm not 100% sure of the interaction between the aromaticity code and the implicit valence flags on individual atoms. The question is, is it possible to prevent the hydrogens being moved by the aromaticity code by setting flags in the format reader? - Noel On 5 December 2012 06:51, Miguel Quirós Olozábal <mqui...@ugr.es> wrote: > Hello, I am using openbabel to convert the CIFs of the Crystallography > Open Database to SMILES and subsequently perform substructure searches. > I have pointed out several times in this forum the problems that I am > finding in such conversions and searches, many of them similar to that > your are hinting to. The only suggestion I can offer from my experience > is to use version 2.2.3 instead of current 2.3.1. The former is less > prune to add spurious hydrogens, remove aromaticity when it should not, > etc (it does in many times, however, when metal atoms are involved which > is the case in most COD files). > > Best wishes > Miguel Quirós > > El mar, 04-12-2012 a las 15:34 +0000, Scott McKechnie escribió: >> 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> 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>> 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> >> > >> 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 > > -- > Miguel Quirós Olozábal > Departamento de Química Inorgánica. Facultad de Ciencias. > Universidad de Granada. 18071 Granada. SPAIN. > email: mquiros<at>ugr<dot>es > mquiros<arroba>ugr<punto>es > > > ------------------------------------------------------------------------------ > 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. 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