On 2012-10-07 22:53, Reinis Danne wrote: > On Sun, Oct 07, 2012 at 10:06:57PM +0200, David van der Spoel wrote: >> On 2012-10-07 21:28, Reinis Danne wrote: >>> On Sun, Oct 07, 2012 at 08:32:53PM +0200, David van der Spoel wrote: >>>> On 2012-10-07 18:35, Reinis Danne wrote: >>>>> On Sun, Oct 07, 2012 at 11:20:16AM +0200, David van der Spoel wrote: >>>>>> >>>>>> 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 >>> >>> Which version of Open Babel are you using? I can't reproduce >>> this with trunk (which is basically soon to be released 2.3.2). >> >> [artemisia:Liquids/DATABASE] % babel -version >> No output file or format spec! >> Open Babel 2.3.1 -- Oct 4 2012 -- 19:42:21 >> >> This is built on a Mac in case that matters, but I get the same on a >> Linux x86_64 box with a freshly compiled 2.3.1. > > Maybe the issue is that it is 2.3.1. Altough I gouldnt find in > commit log what might have changed to affect this. Could you try > SVN checkout for 2-3-x branch? > http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/branches/openbabel-2-3-x/ > > I guess something like this would fetch it: > svn co > https://openbabel.svn.sourceforge.net/svnroot/openbabel/branches/openbabel-2-3-x > > Unfortunately that doesn't help. I fetched the code and installed it:
% which babel /Users/spoel/ob23x/bin//babel [artemisia:~/tmp] % babel -version No output file or format spec! Open Babel 2.3.2 -- Oct 8 2012 -- 09:44:21 % babel -ig03 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 1 molecule converted 1 info messages 16 audit log messages % babel -ipdb 1-butyl-3-methylimidazolium.pdb -oinchi InChI=1S/C8H15N2/c1-3-4-5-10-7-6-9(2)8-10/h6-8H,3-5H2,1-2H3/q+1 1 molecule converted 14 audit log messages Other clues? > Reinis > -- 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
