Re: [Rdkit-discuss] SDF and FindMolChiralCenters()

[Dimitri M. <dm...@bm...>]

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