You'll have to be a bit more specific and provide a minimal test case that illustrates which exactly is the problem. Otherwise, the only answer is that you should take a look at pdbformat.cpp and see what the reader does.
- Noel On 10 April 2015 at 21:29, Stefano Forli <fo...@scripps.edu> wrote: > Hi, > > I'm having a few problems in creating molecules from scratch in Python (see > attached code) > My code creates a molecule by creating atoms from coordinates, elements and > bonds. > The main issue is that I get different atom types than I would get by > parsing a simple PDB created with same coordinates and elements (but no > bonds). > > Is there any other step to do other than BeginModify()/EndModify() to be > applied to the molecule to achieve the same results I would get by reading a > file? > > Thanks! > > S > > > -- > Stefano Forli, PhD > > Staff Scientist > Molecular Graphics Laboratory > Dept. of Integrative Structural > and Computational Biology, MB-112F > 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/ > > ------------------------------------------------------------------------------ > BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT > Develop your own process in accordance with the BPMN 2 standard > Learn Process modeling best practices with Bonita BPM through live exercises > http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ > source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
