Hi Michael, This is by design: the RDKit picks which bonds are wedged when a CTAB is generated. The wedging information provided in the input CTAB is only used to determine chirality.
-greg On Sun, Aug 19, 2012 at 2:37 AM, Michael Palmer <[email protected]> wrote: > >>>> from rdkit import Chem >>>> block = open('truncated.mol').read() >>>> print block > 16134395 > Marvin 08171214412D > > 9 8 0 0 0 0 999 V2000 > 6.4522 4.5670 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 7.1667 4.9795 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 > 7.8812 4.5670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 7.1667 5.8045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 7.8812 6.2170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 7.8812 7.0420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 8.5956 5.8045 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 8.5956 4.9795 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 7.8812 3.7420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 0 0 0 > 2 3 1 0 0 0 0 > 2 4 1 6 0 0 0 > 4 5 1 0 0 0 0 > 5 6 2 0 0 0 0 > 5 7 1 0 0 0 0 > 3 8 1 0 0 0 0 > 3 9 2 0 0 0 0 > M END > > # input contains stereo bond between atoms 2 and 4 > >>>> m=Chem.MolFromMolBlock(block) >>>> from rdkit.Chem import AllChem >>>> block2 = AllChem.MolToMolBlock(m) >>>> print block2 > 16134395 > RDKit 2D > > 9 8 0 0 0 0 0 0 0 0999 V2000 > 6.4522 4.5670 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 7.1667 4.9795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 7.8812 4.5670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 7.1667 5.8045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 7.8812 6.2170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 7.8812 7.0420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 8.5956 5.8045 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 8.5956 4.9795 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 7.8812 3.7420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 > 2 3 1 6 > 2 4 1 0 > 4 5 1 0 > 5 6 2 0 > 5 7 1 0 > 3 8 1 0 > 3 9 2 0 > M END > > # stereo bond has migrated to atoms 2 and 3 in the output > > > -- > Michael Palmer > University of Waterloo > Waterloo, Canada > science.uwaterloo.ca/~mpalmer > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
