Hi Dmitri, Two things: there was a typo in the function name that Ling Chan provided-I assume it should be Chiral in the middle, not Chrial. That might help you. Also, the atoms in a molecule should have the property _CIPRank set, you might be able to do something with that.
Regards, Dave On Saturday, 10 September 2016, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: > On 09/09/2016 10:42 PM, Ling Chan wrote: > > If your file has 3D coordinates, AssignAtomChrialTagsFromStructure may > help > > you. > > Maybe, if I wasn't getting > > rdkit.Chem.rdmolops.AssignAtomChrialTagsFromStructure( self._mol ) > AttributeError: 'module' object has no attribute > 'AssignAtomChrialTagsFromStructure' > > -- same when calling from rdkit.Chem without rdmolops. > (centos 7, python2-rdkit-2016.03.1-1.el7.centos.x86_64, > rdkit-2016.03.1-1.el7.centos.x86_64) > > >> the MOL reader perceives chirality based on the bond stereo field of the > >> bond block. Instead the atom stereo parity value of the atom block is > read > >> and stored in the "molParity" atom property, but it is ignored for the > >> purpose of chirality perception, as per the MOL file specs: > >> > >> http://c4.cabrillo.edu/404/ctfile.pdf (see in particular Figure 4) > >> > >> Therefore, if the MOL file lacks the bond stereo information chirality > >> won't be set. > > GetProp( "molParity" ) does work, thank you, but as I understand it's > based on atom ordering in the CTAB and not on CIP rules. So it's just as > good as OB's stereo "feature" for my purposes: either way I'd have to > roll my own CIP ordering code to arrive at R/S. > > Thanks. > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > >
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