Thanks for that example Nick. We can't handle this automatically since there are multiple interpretations of what the chiral flag means, but I think some relatively straightforward post-processing can do what you're looking for. https://gist.github.com/greglandrum/f85097a8489ba4a5825b0981b1fd2408
If people think it's useful, this is something which we could add to the RDKit itself. -greg On Wed, Jan 31, 2024 at 2:53 PM Tomkinson, Nicholas < nick.tomkin...@astrazeneca.com> wrote: > Hi Greg – sure. So - > > > > > > If I have a V2000 with or without the chiral flag: > > > > > > ACCLDraw01312413482D > > > > 8 8 0 0 1 0 0 0 0 0999 V2000 > > 4.6334 -6.5969 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > 5.6563 -6.0064 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 > > 6.6791 -6.5969 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 > > 6.6791 -7.7781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > 5.6563 -8.3686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > 4.6334 -7.7781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 > > 5.6563 -4.8257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > 3.6109 -8.3684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > 1 2 1 0 0 0 0 > > 3 2 1 0 0 0 0 > > 4 3 1 0 0 0 0 > > 5 4 1 0 0 0 0 > > 1 6 1 0 0 0 0 > > 6 5 1 0 0 0 0 > > 2 7 1 1 0 0 0 > > 6 8 1 1 0 0 0 > > M END > > > > > > ACCLDraw01312413492D > > > > 8 8 0 0 0 0 0 0 0 0999 V2000 > > 4.6334 -6.5969 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > 5.6563 -6.0064 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 > > 6.6791 -6.5969 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 > > 6.6791 -7.7781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > 5.6563 -8.3686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > 4.6334 -7.7781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 > > 5.6563 -4.8257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > 3.6109 -8.3684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > 1 2 1 0 0 0 0 > > 3 2 1 0 0 0 0 > > 4 3 1 0 0 0 0 > > 5 4 1 0 0 0 0 > > 1 6 1 0 0 0 0 > > 6 5 1 0 0 0 0 > > 2 7 1 1 0 0 0 > > 6 8 1 1 0 0 0 > > M END > > > > > > I’d expect the enhanced collections to be output in V3000 format. In this > case the chiral flag is also set but that’s not a biggy for me. (I wish the > chiral flag didn’t exist in V3000.) > > > > > > ACCLDraw01312413472D > > > > 0 0 0 0 0 999 V3000 > > M V30 BEGIN CTAB > > M V30 COUNTS 8 8 0 0 1 > > M V30 BEGIN ATOM > > M V30 1 C 4.6334 -6.5969 0 0 > > M V30 2 C 5.6563 -6.0064 0 0 CFG=2 > > M V30 3 N 6.6791 -6.5969 0 0 CFG=3 > > M V30 4 C 6.6791 -7.7781 0 0 > > M V30 5 C 5.6563 -8.3686 0 0 > > M V30 6 C 4.6334 -7.7781 0 0 CFG=1 > > M V30 7 C 5.6563 -4.8257 0 0 > > M V30 8 C 3.6109 -8.3684 0 0 > > M V30 END ATOM > > M V30 BEGIN BOND > > M V30 1 1 1 2 > > M V30 2 1 3 2 > > M V30 3 1 4 3 > > M V30 4 1 5 4 > > M V30 5 1 1 6 > > M V30 6 1 6 5 > > M V30 7 1 2 7 CFG=1 > > M V30 8 1 6 8 CFG=1 > > M V30 END BOND > > M V30 BEGIN COLLECTION > > M V30 MDLV30/STEABS ATOMS=(2 2 6) > > M V30 END COLLECTION > > M V30 END CTAB > > M END > > > > > > ACCLDraw01312413492D > > > > 0 0 0 0 0 999 V3000 > > M V30 BEGIN CTAB > > M V30 COUNTS 8 8 0 0 0 > > M V30 BEGIN ATOM > > M V30 1 C 4.6334 -6.5969 0 0 > > M V30 2 C 5.6563 -6.0064 0 0 CFG=2 > > M V30 3 N 6.6791 -6.5969 0 0 CFG=3 > > M V30 4 C 6.6791 -7.7781 0 0 > > M V30 5 C 5.6563 -8.3686 0 0 > > M V30 6 C 4.6334 -7.7781 0 0 CFG=1 > > M V30 7 C 5.6563 -4.8257 0 0 > > M V30 8 C 3.6109 -8.3684 0 0 > > M V30 END ATOM > > M V30 BEGIN BOND > > M V30 1 1 1 2 > > M V30 2 1 3 2 > > M V30 3 1 4 3 > > M V30 4 1 5 4 > > M V30 5 1 1 6 > > M V30 6 1 6 5 > > M V30 7 1 2 7 CFG=1 > > M V30 8 1 6 8 CFG=1 > > M V30 END BOND > > M V30 BEGIN COLLECTION > > M V30 MDLV30/STERAC1 ATOMS=(2 6 2) > > M V30 END COLLECTION > > M V30 END CTAB > > M END > > > > Cheers > > > > Nick > > > > > > > > *From:* Greg Landrum <greg.land...@gmail.com> > *Sent:* Wednesday, January 31, 2024 1:45 PM > *To:* Tomkinson, Nicholas <nick.tomkin...@astrazeneca.com> > *Cc:* rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] V2000 to V3000 enhanced stereo question > > > > Hi Nick, > > > > Can you provide an example of exactly what you would like to have happen? > > > > -greg > > > > > > On Tue, Jan 30, 2024 at 5:46 PM Tomkinson, Nicholas < > nick.tomkin...@astrazeneca.com> wrote: > > I am trying to convert a simple V2000 molfile with or without the chiral > flag into a V3000 molfile but this does not create an enhanced stereo > collection in the V3000 molfile. This is a requirement for another > application that does not handle V2000/V3000 mixtures well. Is there anyway > of forcing the writing of the enhanced collection in this context? > > > > Thanks > > > > Nick > > > ------------------------------ > > AstraZeneca UK Limited is a company incorporated in England and Wales with > registered number:03674842 and its registered office at 1 Francis Crick > Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0AA. > > This e-mail and its attachments are intended for the above named recipient > only and may contain confidential and privileged information. If they have > come to you in error, you must not copy or show them to anyone; instead, > please reply to this e-mail, highlighting the error to the sender and then > immediately delete the message. 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