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"""Constants associated with side chains."""
from collections.abc import Mapping, Sequence
import itertools
# Format: The list for each AA type contains chi1, chi2, chi3, 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_ATOMS: Mapping[str, Sequence[tuple[str, ...]]] = {
'ALA': [],
# Chi5 in arginine is always 0 +- 5 degrees, so ignore it.
'ARG': [
('N', 'CA', 'CB', 'CG'),
('CA', 'CB', 'CG', 'CD'),
('CB', 'CG', 'CD', 'NE'),
('CG', 'CD', 'NE', 'CZ'),
],
'ASN': [('N', 'CA', 'CB', 'CG'), ('CA', 'CB', 'CG', 'OD1')],
'ASP': [('N', 'CA', 'CB', 'CG'), ('CA', 'CB', 'CG', 'OD1')],
'CYS': [('N', 'CA', 'CB', 'SG')],
'GLN': [
('N', 'CA', 'CB', 'CG'),
('CA', 'CB', 'CG', 'CD'),
('CB', 'CG', 'CD', 'OE1'),
],
'GLU': [
('N', 'CA', 'CB', 'CG'),
('CA', 'CB', 'CG', 'CD'),
('CB', 'CG', 'CD', 'OE1'),
],
'GLY': [],
'HIS': [('N', 'CA', 'CB', 'CG'), ('CA', 'CB', 'CG', 'ND1')],
'ILE': [('N', 'CA', 'CB', 'CG1'), ('CA', 'CB', 'CG1', 'CD1')],
'LEU': [('N', 'CA', 'CB', 'CG'), ('CA', 'CB', 'CG', 'CD1')],
'LYS': [
('N', 'CA', 'CB', 'CG'),
('CA', 'CB', 'CG', 'CD'),
('CB', 'CG', 'CD', 'CE'),
('CG', 'CD', 'CE', 'NZ'),
],
'MET': [
('N', 'CA', 'CB', 'CG'),
('CA', 'CB', 'CG', 'SD'),
('CB', 'CG', 'SD', 'CE'),
],
'PHE': [('N', 'CA', 'CB', 'CG'), ('CA', 'CB', 'CG', 'CD1')],
'PRO': [('N', 'CA', 'CB', 'CG'), ('CA', 'CB', 'CG', 'CD')],
'SER': [('N', 'CA', 'CB', 'OG')],
'THR': [('N', 'CA', 'CB', 'OG1')],
'TRP': [('N', 'CA', 'CB', 'CG'), ('CA', 'CB', 'CG', 'CD1')],
'TYR': [('N', 'CA', 'CB', 'CG'), ('CA', 'CB', 'CG', 'CD1')],
'VAL': [('N', 'CA', 'CB', 'CG1')],
}
CHI_GROUPS_FOR_ATOM = {}
for res_name, chi_angle_atoms_for_res in CHI_ANGLES_ATOMS.items():
for chi_group_i, chi_group in enumerate(chi_angle_atoms_for_res):
for atom_i, atom in enumerate(chi_group):
CHI_GROUPS_FOR_ATOM.setdefault((res_name, atom), []).append(
(chi_group_i, atom_i)
)
# Mapping from (residue_name, atom_name) pairs to the atom's chi group index
# and atom index within that group.
CHI_GROUPS_FOR_ATOM: Mapping[tuple[str, str], Sequence[tuple[int, int]]] = (
CHI_GROUPS_FOR_ATOM
)
MAX_NUM_CHI_ANGLES: int = 4
ATOMS_PER_CHI_ANGLE: int = 4
# A list of atoms for each AA type that are involved in chi angle calculations.
CHI_ATOM_SETS: Mapping[str, set[str]] = {
residue_name: set(itertools.chain(*atoms))
for residue_name, atoms in CHI_ANGLES_ATOMS.items()
}
# If chi angles given in fixed-length array, this matrix determines how to mask
# them for each AA type. The order is as per restype_order (see below).
CHI_ANGLES_MASK: Sequence[Sequence[float]] = (
(0.0, 0.0, 0.0, 0.0), # ALA
(1.0, 1.0, 1.0, 1.0), # ARG
(1.0, 1.0, 0.0, 0.0), # ASN
(1.0, 1.0, 0.0, 0.0), # ASP
(1.0, 0.0, 0.0, 0.0), # CYS
(1.0, 1.0, 1.0, 0.0), # GLN
(1.0, 1.0, 1.0, 0.0), # GLU
(0.0, 0.0, 0.0, 0.0), # GLY
(1.0, 1.0, 0.0, 0.0), # HIS
(1.0, 1.0, 0.0, 0.0), # ILE
(1.0, 1.0, 0.0, 0.0), # LEU
(1.0, 1.0, 1.0, 1.0), # LYS
(1.0, 1.0, 1.0, 0.0), # MET
(1.0, 1.0, 0.0, 0.0), # PHE
(1.0, 1.0, 0.0, 0.0), # PRO
(1.0, 0.0, 0.0, 0.0), # SER
(1.0, 0.0, 0.0, 0.0), # THR
(1.0, 1.0, 0.0, 0.0), # TRP
(1.0, 1.0, 0.0, 0.0), # TYR
(1.0, 0.0, 0.0, 0.0), # VAL
)
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