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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