Rework chirality detection in restype determination for PDB loading#698
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roccomoretti wants to merge 10 commits into
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Rework chirality detection in restype determination for PDB loading#698roccomoretti wants to merge 10 commits into
roccomoretti wants to merge 10 commits into
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It bases its decisions on the type returned by get_representative type, which may be a misnomer. Also, as it stands now, it's superflous to the decide_is_l_aa/decide_is_d_aa/decide_is_known_achiral (None of the types which would trigger d_l_threeletter_codes_are_same_for_aa() are listed in those sets.
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Aside from cosmetic changes in debug-level tracers, the swm_dna_bridge and rna_denovo_dna_bridge integration tests change as the input PDBs type the first nucleotide in the chain as |
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A side quest from PR #687
Currently, we have a rather brittle atom-name-based approach to chirality detection on PDB read-in, which isn't as robust as it could be, in large part due to trying to decide chirality early on. Instead of imposing L/D identity early, we can defer it until later with the atom name matching heuristics. This way, the D & L version of amino acids can co-exist with non-aa residues with the same three letter code (e.g. when we're loading a CCD type with the same three letter code as an unrelated Rosetta residue type), and the ResidueTypeFinder should pick the best match.
I've also reworked the atom name matching heuristics, implementing the previously proposed idea to separate out virtual atom counts from non-virtual counts.