File size: 5,989 Bytes
5631464 | 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 | """LightDock integration sampling module.
For more details about this module, please `refer to the haddock3 user manual
<https://www.bonvinlab.org/haddock3-user-manual/modules/sampling.html#lightdock-module>`_
"""
import shutil
import subprocess
from pathlib import Path
from haddock import log
from haddock.core.defaults import MODULE_DEFAULT_YAML
from haddock.core.typing import Any, FilePath
from haddock.libs import libpdb
from haddock.libs.libio import working_directory
from haddock.libs.libontology import Format, PDBFile
from haddock.libs.libutil import check_subprocess
from haddock.modules import BaseHaddockModule
RECIPE_PATH = Path(__file__).resolve().parent
DEFAULT_CONFIG = Path(RECIPE_PATH, MODULE_DEFAULT_YAML)
class HaddockModule(BaseHaddockModule):
"""HADDOCK3 Lightdock module."""
name = RECIPE_PATH.name
def __init__(
self,
order: int,
path: Path,
*ignore: Any,
initial_params: FilePath = DEFAULT_CONFIG,
**everything: Any,
) -> None:
super().__init__(order, path, initial_params)
@classmethod
def confirm_installation(cls) -> None:
"""Confirm this module is installed."""
check_subprocess('lightdock3.py -h')
def _run(self) -> None:
"""Execute module."""
# Get the models generated in previous step
models: list[PDBFile] = [
p
for p in self.previous_io.output
if p.file_type == Format.PDB
]
# Check if multiple models are provided
if len(models) > 1:
_msg = "Only one model allowed in LightDock sampling module"
self.finish_with_error(_msg)
model = models[0]
# Check if chain IDs are present
_path = Path(model.path, model.file_name)
segids, chains = libpdb.identify_chainseg(_path)
if set(segids) != set(chains):
log.info("No chain IDs found, using segid information")
libpdb.swap_segid_chain(
Path(model.path, model.file_name),
Path(self.path, model.file_name),
)
else:
# Copy original model to this working path
shutil.copyfile(
Path(model.path, model.file_name),
Path(self.path, model.file_name),
)
model_with_chains = self.path / model.file_name
# Split by chain
new_models = libpdb.split_by_chain(model_with_chains)
if model_with_chains in new_models:
self.finish_with_error(f"Input {model_with_chains} cannot be"
" split by chain")
# Receptor and ligand PDB structures
rec_chain = self.params["receptor_chains"][0]
lig_chain = self.params["ligand_chains"][0]
receptor_pdb_file = (f"{Path(model.file_name).stem}_"
f"{rec_chain}.{Format.PDB}")
ligand_pdb_file = (f"{Path(model.file_name).stem}_"
f"{lig_chain}.{Format.PDB}")
# Setup
log.info("Running LightDock setup")
with working_directory(self.path):
swarms = self.params["swarms"]
glowworms = self.params["glowworms"]
noxt = self.params["noxt"]
noh = self.params["noh"]
cmd = (f"lightdock3_setup.py {receptor_pdb_file}"
f" {ligand_pdb_file} -s {swarms} -g {glowworms}")
if noxt:
cmd += " --noxt"
if noh:
cmd += " --noh"
subprocess.call(cmd, shell=True)
# Simulation
log.info("Running LightDock simulation")
with working_directory(self.path):
steps = self.params["steps"]
scoring = self.params["scoring"]
cores = self.params['ncores'] or 1
cmd = f"lightdock3.py setup.json {steps} -c {cores} -s {scoring}"
subprocess.call(cmd, shell=True)
# Clustering
# Ranking
log.info("Generating ranking")
with working_directory(self.path):
steps = self.params["steps"]
swarms = self.params["swarms"]
cmd = f"lgd_rank.py {swarms} {steps}"
subprocess.call(cmd, shell=True)
# Generate top, requires a hack to use original structures (H, OXT,
# etc.)
log.info("Generating top structures")
with working_directory(self.path):
# Save structures, needs error control
shutil.copyfile(
Path(self.path, receptor_pdb_file),
Path(self.path, f"tmp_{receptor_pdb_file}"),
)
shutil.copyfile(
Path(self.path, ligand_pdb_file),
Path(self.path, f"tmp_{ligand_pdb_file}")
)
shutil.copy(
Path(self.path, receptor_pdb_file),
Path(self.path, f"lightdock_{receptor_pdb_file}"),
)
shutil.copy(
Path(self.path, ligand_pdb_file),
Path(self.path, f"lightdock_{ligand_pdb_file}"),
)
# Create top
steps = self.params["steps"]
top = self.params["top"]
cmd = (f"lgd_top.py {receptor_pdb_file} {ligand_pdb_file}"
f" rank_by_scoring.list {top}")
subprocess.call(cmd, shell=True)
# Tidy top files
expected: list[PDBFile] = []
top = self.params["top"]
for i in range(top):
file_name = f"top_{i+1}.{Format.PDB}"
tidy_file_name = f"haddock_top_{i+1}.{Format.PDB}"
libpdb.tidy(self.path / file_name, self.path / tidy_file_name)
expected.append(PDBFile(tidy_file_name,
topology=model.topology,
path=self.path))
self.output_models = models
self.export_io_models()
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