Your usage of babel --filter is correct, however it won't work on a PDB file as the entire PDB file is regarded by OpenBabel as a single "Molecule". It's a good idea though, and maybe something we should think about implementing. Feel free to file a feature request at http://sourceforge.net/tracker/?atid=428743&group_id=40728&func=browse
You didn't attach the PDB file so I can't test this, but you might want to try the --separate option to split the PDB into disconnected fragments. - Noel 2009/11/20 Jack Shultz <j...@drugdiscoveryathome.com>: > Trying to filter a PDB file starting with this compound > > COMPND omega_1 > HETATM 1 C1 UNL 1 1.852 -3.133 1.682 1.00 0.00 C > HETATM 2 C2 UNL 1 0.996 -2.034 1.424 1.00 0.00 C > HETATM 3 C3 UNL 1 2.869 -2.681 2.494 1.00 0.00 C > > I tried it two ways > > [boinc...@vps Ambinter_LL_3D_1-1]$ babel -ipdb Ambinter_LL.pdb -opdb > omega_1.pdb --filter "COMPND='omega_1'" > 0 molecules converted > 52 info messages 12 audit log messages > [boinc...@vps Ambinter_LL_3D_1-1]$ babel -ipdb Ambinter_LL.pdb -opdb > omega_1.pdb --filter "title='omega_1'" > 0 molecules converted > 52 info messages 12 audit log messages > > > > -- > Jack > > http://drugdiscoveryathome.com > http://hydrogenathome.org > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
