Fix issue #392 #393
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Fix issue #392 #393
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Also note that I chose not to use direct conversion, since it appears to be less reliable if the molecule wasn't loaded from SDF, PDB, or Mol2, i.e. whatever RDKit does to fix things when going from those formats seems to more reliably recover the formal charge than converting directly when that info isn't present, e.g. if you went from a molecule loaded from AMBER files. |
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Feb 19, 2025
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This PR fixes #392 by improving the robustness of the internal formal charge calculation within the
Parameterssub-module. Now we preferentially use the format the the original molecule was loaded from, either PDB or SDF, or try both if none are present in the file formats list. This means that we can still get a result if the PDB conversion doesn't work, etc.Note that I haven't been provided with the problem file in this case, so haven't added an additional test. All existing tests pass.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]