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More angles support

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This commit is contained in:
Kevin Wu
2022-09-07 16:49:14 -07:00
parent d915c46cba
commit ea66a91c91
1 changed files with 19 additions and 4 deletions
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23
protdiff/angles_and_coords.py
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@@ -179,15 +179,26 @@ def canonical_distances_and_dihedrals(
# Get any additional angles
non_dihedral_angles = [a for a in angles if a not in calc_angles]
# Gets the N - CA - C for eacch residue
# Gets the N - CA - C for each residue
# https://www.biotite-python.org/apidoc/biotite.structure.filter_backbone.html
backbone_atoms = source_struct[struc.filter_backbone(source_struct)]
for a in non_dihedral_angles:
if a == "tau":
if a == "tau" or a == "N:CA:C":
# tau = N - CA - C internal angles
idx = np.array(
[list(range(i, i + 3)) for i in range(0, len(backbone_atoms), 3)]
)
elif a == "CA:C:1N": # Same as C-N angle in nerf
# This measures an angle between two residues. Due to the way we build
# proteins out later, we do not need to meas
idx = np.array(
[(i + 1, i + 2, i + 3) for i in range(0, len(backbone_atoms) - 3, 3)]
+ [(0, 0, 0)]
)
elif a == "C:1N:1CA":
idx = np.array(
[(i + 2, i + 3, i + 4) for i in range(0, len(backbone_atoms) - 3, 3)] + [(0, 0, 0)]
)
else:
raise ValueError(f"Unrecognized angle: {a}")
calc_angles[a] = struc.index_angle(backbone_atoms, indices=idx)
@@ -292,8 +303,12 @@ def create_new_chain_nerf(
if a in required_dihedrals:
continue
assert a in dists_and_angles
if a == "tau":
if a == "tau" or a == "N:CA:C":
nerf_build_kwargs["bond_angle_ca_c"] = dists_and_angles[a]
elif a == "CA:C:1N":
nerf_build_kwargs['bond_angle_c_n'] = dists_and_angles[a]
elif a == "C:1N:1CA":
nerf_build_kwargs['bond_angle_n_ca'] = dists_and_angles[a]
else:
raise ValueError(f"Unrecognized angle: {a}")
@@ -304,7 +319,7 @@ def create_new_chain_nerf(
elif d == "N:CA":
nerf_build_kwargs["bond_len_n_ca"] = dists_and_angles[d]
elif d == "CA:C":
nerf_build_kwargs['bond_len_ca_c'] = dists_and_angles[d]
nerf_build_kwargs["bond_len_ca_c"] = dists_and_angles[d]
else:
raise ValueError(f"Unrecognized distance: {d}")