On 2012-10-07 18:35, Reinis Danne wrote: > On Sun, Oct 07, 2012 at 11:20:16AM +0200, David van der Spoel wrote: >> Hi, >> >> when reading a gaussian output file the total charge is available and >> that could be used to improve the bond order perception, alternatively >> there could be a command line option to tell babel about the total charge. > > This is a known issue with formats which doesn't contain > explicit formal charges. SDF and MOL files should work with > charged heterocycles, and MOL2 format plugin was recently > improved to better handle them. > > I might also look at it since I'm working with related code. > >> >> Related to this it would be great if one could turn off the proton >> generation, since for many ions babel adds a proton where there >> shouldn't be one (e.g. imidazolium and other ionic liquids, organic >> cations). > > It shouldn't add Hs if there are explicit Hs in the structure > already (unless explicitly asked). Do you have a case where it > is not so? > Yes, this happens with gaussian files containing ions (which do have info about the formal charge) but not with the corresponding pdb file.
% wget http://folding.bmc.uu.se/1-butyl-3-methylimidazolium-g4.log.gz % babel -ig98 1-butyl-3-methylimidazolium/1-butyl-3-methylimidazolium-g4.log.gz -oinchi InChI=1S/C8H16N2/c1-3-4-5-10-7-6-9(2)8-10/h6-7H,3-5,8H2,1-2H3 % wget http://folding.bmc.uu.se/1-butyl-3-methylimidazolium.pdb % babel -ipdb 1-butyl-3-methylimidazolium.pdb InChI=1S/C8H15N2/c1-3-4-5-10-7-6-9(2)8-10/h6-8H,3-5H2,1-2H3/q+1 > You have options to add or delete polar/nonpolar Hs, for details > see: > obabel -L ops > e.g., strip all Hs: > obabel input --DeletePolarH --DeleteNonPolarH -O output > I'm aware of these options, but that's not what I need. > > Reinis > > ------------------------------------------------------------------------------ > Don't let slow site performance ruin your business. Deploy New Relic APM > Deploy New Relic app performance management and know exactly > what is happening inside your Ruby, Python, PHP, Java, and .NET app > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > http://p.sf.net/sfu/newrelic-dev2dev > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
