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add comment about the interpretation of ambiguous atoms #314

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May 17, 2023
Merged

add comment about the interpretation of ambiguous atoms #314

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4 changes: 3 additions & 1 deletion openfold/np/residue_constants.py
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Expand Up @@ -410,7 +410,9 @@
# (The LDDT paper lists 7 amino acids as ambiguous, but the naming ambiguities
# in LEU, VAL and ARG can be resolved by using the 3d constellations of
# the 'ambiguous' atoms and their neighbours)
# TODO: ^ interpret this
# Because for LEU, VAL and ARG, no ambiguous exist when the prediction output is chi angle instead of the location of individual atoms.
# For the rest, ASP and others, when you rotate the bond 180 degree, you get the same configuraiton due to symmetry.

residue_atom_renaming_swaps = {
"ASP": {"OD1": "OD2"},
"GLU": {"OE1": "OE2"},
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