Embedding molecules using convenience_structures.pdb_to_mol does not seem to work properly. Specified coordinates are ignored, and are not fixed.
Currently, this code works by creating an RDKit EmbedParams struct and adding a coordMap argument. Replacing the EmbedMolecule call with the alternative function signature (using arguments vs supplying a struct) enables fixed coords, but I'm unsure of the implications for coordinate generation - can ETKDGv2 still be used?
This may be an upstream bug in RDKit.
Embedding molecules using
convenience_structures.pdb_to_moldoes not seem to work properly. Specified coordinates are ignored, and are not fixed.Currently, this code works by creating an RDKit
EmbedParamsstruct and adding acoordMapargument. Replacing theEmbedMoleculecall with the alternative function signature (using arguments vs supplying a struct) enables fixed coords, but I'm unsure of the implications for coordinate generation - can ETKDGv2 still be used?