Hi, I am using WedgeMolBonds() to label converted 3D->2D conformations,
roughly:
// ... read in 3D mol
assignChiralTypesFrom3D(mol);
assignStereochemistry(mol,true,true);
WedgeMolBonds(mol,&mol.getConformer());
compute2DCoords(...)
However, this does not produce an accurate result. In
Hello again!
RDKit nicely provides several functions to accept molecule input under the
FileParsers module. For example, we have MolFileToMol(), MolBlockToMol(),
Mol2FileToMol(), and so forth. Each of these parses the input and then
does various cleanup to generate stereochemistry and such.
In
Thanks for the response, Greg!
When I set cleanIt=false, I get the same results as if I didn't call
assignStereoChemistry() at all. In this case, the fused ring example
(cases 1 and 2 in the GitHub thread) look correct, but, as you noted, the
third case looks wrong.
So I guess the question is,
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