diff --git a/openfold/np/residue_constants.py b/openfold/np/residue_constants.py index dcb0c6ed..a3b2cf39 100644 --- a/openfold/np/residue_constants.py +++ b/openfold/np/residue_constants.py @@ -29,9 +29,9 @@ # Distance from one CA to next CA [trans configuration: omega = 180]. ca_ca = 3.80209737096 -# Format: The list for each AA type contains chi1, chi2, chi3, chi4 in +# Format: The list for each AA type contains chi1, chi2, chi3, and chi4 in # this order (or a relevant subset from chi1 onwards). ALA and GLY don't have -# chi angles so their chi angle lists are empty. +# chi angles, so their chi angle lists are empty. chi_angles_atoms = { "ALA": [], # Chi5 in arginine is always 0 +- 5 degrees, so ignore it. @@ -137,8 +137,8 @@ # 3: 'psi-group', # 4,5,6,7: 'chi1,2,3,4-group' # The atom positions are relative to the axis-end-atom of the corresponding -# rotation axis. The x-axis is in direction of the rotation axis, and the y-axis -# is defined such that the dihedral-angle-definiting atom (the last entry in +# rotation axis. The x-axis is in the direction of the rotation axis, and the y-axis +# is defined such that the dihedral-angle-defining atom (the last entry in # chi_angles_atoms above) is in the xy-plane (with a positive y-coordinate). # format: [atomname, group_idx, rel_position] rigid_group_atom_positions = { @@ -408,10 +408,10 @@ # Due to symmetries in the amino acids the naming of atoms is ambiguous in # 4 of the 20 amino acids. # (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 +# in LEU, VAL, and ARG can be resolved by using the 3d constellations of # the 'ambiguous' atoms and their neighbours) -# 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. +# For LEU, VAL, and ARG, no ambiguities exist when the prediction outputs are chi angles instead of the location of individual atoms. +# For the rest (i.e., ASP and others), when you rotate the bond by 180 degrees, you get the same configuration due to symmetry. residue_atom_renaming_swaps = { "ASP": {"OD1": "OD2"}, @@ -955,8 +955,8 @@ def sequence_to_onehot( # NB: restype_3to1 differs from Bio.PDB.protein_letters_3to1 by being a simple # 1-to-1 mapping of 3 letter names to one letter names. The latter contains -# many more, and less common, three letter names as keys and maps many of these -# to the same one letter name (including 'X' and 'U' which we don't use here). +# many more, and less common, three-letter names as keys and maps many of these +# to the same one-letter name (including 'X' and 'U' which we don't use here). restype_3to1 = {v: k for k, v in restype_1to3.items()} # Define a restype name for all unknown residues. @@ -967,10 +967,10 @@ def sequence_to_onehot( # The mapping here uses hhblits convention, so that B is mapped to D, J and O -# are mapped to X, U is mapped to C, and Z is mapped to E. Other than that the +# are mapped to X, U is mapped to C, and Z is mapped to E. Other than that, the # remaining 20 amino acids are kept in alphabetical order. # There are 2 non-amino acid codes, X (representing any amino acid) and -# "-" representing a missing amino acid in an alignment. The id for these +# "-" representing a missing amino acid in an alignment. The ID for these # codes is put at the end (20 and 21) so that they can easily be ignored if # desired. HHBLITS_AA_TO_ID = { @@ -1220,7 +1220,7 @@ def _make_rigid_group_constants(): def make_atom14_dists_bounds( overlap_tolerance=1.5, bond_length_tolerance_factor=15 ): - """compute upper and lower bounds for bonds to assess violations.""" + """Compute upper and lower bounds for bonds to assess violations.""" restype_atom14_bond_lower_bound = np.zeros([21, 14, 14], np.float32) restype_atom14_bond_upper_bound = np.zeros([21, 14, 14], np.float32) restype_atom14_bond_stddev = np.zeros([21, 14, 14], np.float32)