Hi, I gave it a shot and I think I got something working for the cases that Chris reported. In the file phmodel.txt I've modified the line at the guanidine/amidine pattern as follows:
#guanidine or amidine TRANSFORM *~[#6^2:1](~[#7:2])(~[#7:3]) >> *~[#6:1](=[#7+1:2])(-[#7:3]) 12.5 # NEW #TRANSFORM [#6^2+0:1](~[N^2])(~[N^2])* >> [#6+:1](~N)(~N)* 12.5 # OLD I believe there's a mistake is the definition of a net charge on the carbon, which is unlikely to be there. Also, the Daylight documentation doens't mention the "^" symbol in the SMARTS, but the source of parsmart.cpp suggests that defines the hybridization (sp2, in the case above). I've left it there and I've set an explicit double bond on one of the nitrogens. If somebody has a more informed opinion on the matter, it's more than welcome, otherwise I'll make a push request on GIT as it is. Best, S On 11/18/2016 04:17 AM, Chris Swain wrote: > Hi, > > Ok, I’ll have a look and see what I can contribute. > > Cheers, > > Chris > >> The (de)protonation rules are stored as a list of transformation using SMARTS >> format in a file called /phmodel.txt/inside the /data/ directory. Such file >> is editable but as Geoff suggested is not trivial to carefully enumerate all >> the potential transformations for many functional groups and substructures >> at different pH. As far as I know currently there is no open source software >> that do that properly, so any advance in this sense will be appreciated by >> the community. >> Gio > > ------------------------------------------------------------------------------ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Stefano Forli, PhD Assistant Professor of ISCB Molecular Graphics Laboratory Dept. of Integrative Structural and Computational Biology, MB-112A The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037-1000, USA. tel: +1 (858)784-2055 fax: +1 (858)784-2860 email: fo...@scripps.edu http://www.scripps.edu/~forli/ ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
