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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