Do you want to try writing a patch for the mol2 reader to ignore these? This could be implemented as an option for the mol2 file reader.
- Noel On 8 November 2013 13:08, Maciek Wójcikowski <mac...@wojcikowski.pl> wrote: > Hi, > > Currently I'm working on GOLD docking results, and try to process them > through OB. Unfortunately OB doesn't understand GOLD's explicit lone pair > pseudo atoms (atom type: Lp). For mol2 -> mol2 conversion it changes it to > Xx type atoms, for sdf (sdf defines them as * type) -> mol2 they are changed > as dummy atoms (Du). There is probably no way to remove them at conversion, > unless I didn't found one, but maybe it should be fixed? From brief code > analysis the lone pairs are defined implicitly, but maybe OB should also > understand explicit representations as valid, or at least recognise Lp/*, as > in mol2/sdf, atom types and ignore them. > > ---- > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > ------------------------------------------------------------------------------ > November Webinars for C, C++, Fortran Developers > Accelerate application performance with scalable programming models. Explore > techniques for threading, error checking, porting, and tuning. Get the most > from the latest Intel processors and coprocessors. See abstracts and > register > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
