[WIP] Add a warning to Topology.from_pdb if the stereo of the molecule in the PDB is different from the substructure template or unique mol #1583
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j-wags
commented
Apr 17, 2023
j-wags
commented
- Tag issue being addressed
- Add tests
- Update docstrings/documentation, if applicable
- Lint codebase
- Update changelog
j-wags
commented
Apr 21, 2023
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| # TODO: This is most likely wrong. This will copy over CW/CCW tags but there's no | ||
| # checking that the substituent order in the molecule and substructure are the same, | ||
| # so this is basically random assignment. Thankfully Molecule.from_polymer_pdb and | ||
| # Topology.from_pdb both overwrite this assignment based on 3D coordinates. The only | ||
| # way I can currently think of doing this right would be to arbitrarily assign CW, | ||
| # then try to run a strict substructure match on it, and if that fails then assign | ||
| # CCW. This would be monstrously inefficient and all it would let us do is compare | ||
| # the substructure stereo to 3D stereo, which is of dubious value anyway. |
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Big blocker here, this basically summarizes it. This will need a lot more work and I don't think it's worth holding up the release for.
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