Hi Greg, Thank you for the link! It seems that Huw pasted in the same piece of code as the one you provided. I managed to fix the issue using the above function.
Would it be worthwhile to add it into the Cookbook, if it's a reocurring problem for some? I personally never would've thought to check the Chembl code, and I haven't found anything related on the subject on RDKit sites. Best, Adam Greg Landrum <greg.land...@gmail.com> ezt írta (időpont: 2022. márc. 23., Sze, 17:16): > Hi Adam, > > By default the RDKit picks the locations to do wedging. There's no > built-in function to reapply the wedging from an input mol file (we > probably should add this), but you can find a good one here, as part of the > ChEMBL structure pipeline: > > https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py#L469 > > -greg > > > On Tue, Mar 22, 2022 at 11:01 AM Ádám Baróthi <barothi.a...@gmail.com> > wrote: > >> Hello Everyone, >> >> I'm having some trouble trying to depict molecules the exact same way as >> the input mol block (V2000) was drawn. My main problem is that I've drawn >> in a wedge bond between atoms 1 and 7 (the right hand side of the >> cyclopropyl ring), and RDKit depicts the molecule with a wedge bond between >> atoms 0 and 1 (the left hand side of the cyclohexane ring). >> >> Google colab showing the difference between the structures >> <https://colab.research.google.com/drive/1MAeSpivr4IRfu0T34MmDoaICXSig1aja?usp=sharing> >> >> Is there a way to force the depiction to match the input exactly without >> having to set the bond types manually? >> >> Molecule in question: >> >> ACCLDraw03222210522D >> >> 11 12 0 0 1 0 0 0 0 0999 V2000 >> 15.0356 -8.9726 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 16.0593 -8.3815 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 >> 17.0831 -8.9726 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 17.0831 -10.1547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 16.0593 -10.7457 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 >> 15.0356 -10.1547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 16.0593 -11.9269 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 >> 16.6510 -7.3567 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 >> 15.4680 -7.3567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 17.6738 -6.7662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 18.6967 -7.3567 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 >> 3 4 1 0 0 0 0 >> 4 5 1 0 0 0 0 >> 5 6 1 0 0 0 0 >> 1 6 1 0 0 0 0 >> 5 7 1 1 0 0 0 >> 2 8 1 1 0 0 0 >> 8 9 1 0 0 0 0 >> 2 9 1 0 0 0 0 >> 8 10 1 0 0 0 0 >> 10 11 1 0 0 0 0 >> M END >> >> Best, >> Adam >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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