Hi Noel, Greg, I agree with Noel that the method for making a set of wedge bonds stay exactly where they were in the MolFile should be a lot more explicit.
We managed to get the bonds to stay for most use cases by setting the _drawingBondsWedged property in the input molfile and turning off kekulization. This is not documented in the python docs from what I can see. This code is in our fork of chembl beaker here: https://github.com/thesgc/chembl_beaker/blob/master/chembl_beaker/beaker/core_apps/rasterImages/impl.py#L15 As Noel says there are certain molecules (perhaps if RDKit does not understand the stereochemistry) for which the wedge directions get reversed. We have had users who are looking to depict strained aromatics using wedges and this issue could easily get in the way. Cheers, Andrew Stretton Developer (ChemBioHub) University of Oxford [email protected] Old Road Campus Research Building | Roosevelt Drive | Headington | Oxford | OX3 7DQ ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
