Does anybody have a clue what this flag (noInvalidateMMStereoAndTextType) is doing?
I was using openbabel to minimize a molecule and trying to figure out how it was parameterising some nitrogens (sp2/sp3 for nitrogens is always a problem as they both have 3 bonds) (mmff94). I wrote out the molecule as MOL2 where there is a field for type (some form of potential type). But when displayed in pymol this field was blank. I tracked this down to this flag noInvalidateMMStereoAndTextType - when reading this flag is set to 1 before the call to ObjectMoleculeMOL2SetFormalCharges which sets it back to 0 at end of this routine. Then at end of reading there is a call to ObjectMoleculeInvalidate(I, cRepAll, cRepInvAll, -1); which blanks textType - hence display of null string. I then tried setting text_type in a chempy model and using load_model - from this found that noInvalidateMMStereoAndTextType is set to 0 in CoordSetNew - and again the seemingly obligatory ObjectMoleculeInvalidate(I, cRepAll, cRepInvAll, -1); at end of reading clobbers any input data. For the moment Im setting the flag to 1 in CoordSetNew and commenting assigns to 0 - then input textType fields are displayed. I just cant figure out what this was supposed to be doing - it just doesnt seem right that input data of this type is being clobbered. Thanks for any info David ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
