I've filed a bug at https://sourceforge.net/p/openbabel/bugs/847/. It should be fairly easy to copy the residue info to the separated molecules; I've just done this for stereo info.
Please note for future reference that openbabel-scripting is obsolete. Please send emails to openbabel-discuss instead. - Noel On 8 November 2012 12:37, Stefan Henrich <[email protected]> wrote: > Hi Noel, > > Thank you for the fast answer. Actually, OBMol can be split into separated > OBMol objects but the order of residues of a protein will be mixed up at > least if unknown residue names are present or the protein is disconnected. > Furthermore, for ligands the residue name, residue numbering and the atom > names will not be copied to the new OBMol object. It seems that 'Separate' > just copy atoms from one OBMol to a new ones. > > Best, > Stefan > > > > > On 11/07/2012 04:16 PM, Noel O'Boyle wrote: >> >> Does OBMol::Separate work for this? See the API at >> >> http://openbabel.org/api/2.3/classOpenBabel_1_1OBMol.shtml#a1e5c6955a32c0ec2317a8de12ab7ba5a >> >> - Noel >> >> On 7 November 2012 13:53, Stefan Henrich <[email protected]> wrote: >>> >>> Hi OpenBabel users, >>> >>> Is there an easy way to read a complex structure as a molecule using >>> openbabel (python-API) and to split it afterwards into different >>> molecules (e.g., protein, ligand, cofactor,...) to handle/write it as >>> different objects? Here, it would be helpful not loosing information >>> like residue names what happens if you just copy atoms to a new molecule >>> object. >>> Thank you for your help! >>> >>> Best, >>> Stefan >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> LogMeIn Central: Instant, anywhere, Remote PC access and management. >>> Stay in control, update software, and manage PCs from one command center >>> Diagnose problems and improve visibility into emerging IT issues >>> Automate, monitor and manage. Do more in less time with Central >>> http://p.sf.net/sfu/logmein12331_d2d >>> _______________________________________________ >>> OpenBabel-scripting mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > > > -- > Dr. Stefan Henrich > Research Associate > > HITS gGmbH Schloss-Wolfsbrunnenweg 35 > 69118 Heidelberg > Germany > > phone: +49 6221 533 223 > fax: +49 6221 533 298 > email:[email protected] > http://www.h-its.org > > Amtsgericht Mannheim / HRB 337446 > Managing Directors: > Dr. h. c. Dr.-Ing. E. h. Klaus Tschira > Prof. Dr.-Ing. Andreas Reuter > ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ OpenBabel-scripting mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
