Hi David, very well analyzed. You are right that noInvalidateMMStereoAndTextType should never be set to 0 in the open-source version, we will fix that.
FYI: The incentive version of PyMOL can use a proprietary Schrödinger library to assign text_type and stereochemistry, in which case that flag is used. Cheers, Thomas On 21 Mar 2014, at 14:04, David Osguthorpe <david.osgutho...@gmail.com> wrote: > 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 -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ 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
