File size: 5,437 Bytes
5e797a4 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 | """Represent an Haddock model."""
from haddock.core.typing import FilePath
class HaddockModel:
"""Represent HADDOCK model."""
def __init__(self, pdb_f: FilePath) -> None:
remarks = self._load_remarks(pdb_f)
self.energies = self._load_energies(remarks)
self.interface_energies = self._load_per_interface_energies(remarks)
@staticmethod
def _load_remarks(pdb_f: FilePath) -> list[str]:
"""Load remark lines from PDB file
Parameters
----------
pdb_f : FilePath
Path to a PDB file
Returns
-------
remarks : list[str]
List of PDB lines containing remarks.
"""
remarks: list[str] = []
with open(pdb_f) as fh:
for line in fh.readlines():
if line.startswith('REMARK'):
remarks.append(line)
return remarks
@staticmethod
def _load_energies(remarks: list[str]) -> dict[str, float]:
"""Load HADDOCK energy terms from PDB remarks.
Parameters
----------
remarks : list[str]
List of PDB lines containing remarks.
Returns
-------
energy_dic : dict[str, float]
Dictionary of energy terms with their values
"""
energy_dic: dict[str, float] = {}
for line in remarks:
# TODO: use regex to do this
if 'energies' in line:
energy_values = map(
float,
line.rstrip().split(':')[-1].split(',')
)
total, bonds, angles, improper, dihe, vdw, elec, air, cdih, coup, rdcs, vean, dani, xpcs, rg = energy_values # noqa: E501
energy_dic['total'] = total
energy_dic['bonds'] = bonds
energy_dic['angles'] = angles
energy_dic['improper'] = improper
energy_dic['dihe'] = dihe
energy_dic['vdw'] = vdw
energy_dic['elec'] = elec
energy_dic['air'] = air
energy_dic['cdih'] = cdih
energy_dic['coup'] = coup
energy_dic['rdcs'] = rdcs
energy_dic['vean'] = vean
energy_dic['dani'] = dani
energy_dic['xpcs'] = xpcs
energy_dic['rg'] = rg
if 'buried surface area' in line:
bsa = float(line.rstrip().split(':')[-1])
energy_dic['bsa'] = bsa
if 'Desolvation energy' in line:
desolv = float(line.rstrip().split(':')[-1])
energy_dic['desolv'] = desolv
if 'Symmetry energy' in line:
sym = float(line.rstrip().split(':')[-1])
energy_dic['sym'] = sym
return energy_dic
@staticmethod
def _load_per_interface_energies(
remarks: list[str],
) -> dict[str, dict[str, float]]:
"""Read a pdb file and parse per interface scores.
Parameters
----------
remarks : list[str]
List of PDB lines containing remarks.
Returns
-------
interfaces_scores : dict[str, dict[str, float]]
Dictionary holding per interfaces scores.
"""
header = None
interfaces_scores: dict[str, dict[str, float]] = {}
for _ in remarks:
if _.startswith("REMARK Interface"):
s_ = _.strip().split()[2:]
# Extract header
if not header:
header = s_
# Extract data
else:
chain1 = s_[header.index("Chain1")]
chain2 = s_[header.index("Chain2")]
haddockscore = float(s_[header.index("HADDOCKscore")])
evdw = float(s_[header.index("Evdw")])
eelec = float(s_[header.index("Eelec")])
edesol = float(s_[header.index("Edesol")])
bsa = float(s_[header.index("BSA")])
# Combine chains together
chains_key = f"{chain1}_{chain2}"
# Hold data
interfaces_scores[chains_key] = {
"HADDOCKscore": haddockscore,
"vdw": evdw,
"elec": eelec,
"desolv": edesol,
"bsa": bsa,
}
return interfaces_scores
def calc_haddock_score(self, **weights: float) -> float:
"""Calculate the haddock score based on the weights and energies."""
return self.calc_score(self.energies, **weights)
@staticmethod
def calc_score(energies: dict[str, float], **weights: float) -> float:
"""Compute sum of weighted energy terms.
Parameters
----------
energies : dict[str, float]
Dict of energy values for each energy term
Returns
-------
weighted_score : float
Sum of weighted energy terms
"""
weighted_score: float = 0.0
for weight_name, weight_value in weights.items():
component_id = weight_name.split("_")[1]
try:
weighted_score += energies[component_id] * weight_value
except KeyError:
continue
return weighted_score
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