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9ae74ae | 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 | #!/usr/bin/env python3
"""Unified PDB-directory inference entry point for dl_binder_design."""
from __future__ import annotations
import argparse
import json
import subprocess
import sys
from pathlib import Path
ROOT = Path(__file__).resolve().parents[1]
CONFIG_PATH = ROOT / "conf" / "config.json"
MPNN_SCRIPT = ROOT / "model" / "mpnn_fr" / "dl_interface_design.py"
AF2_SCRIPT = ROOT / "model" / "af2_initial_guess" / "predict.py"
def load_config() -> dict:
with CONFIG_PATH.open(encoding="utf-8") as handle:
return json.load(handle)
def package_path(value: str) -> Path:
path = Path(value).expanduser()
return path if path.is_absolute() else ROOT / path
def require_file(path: Path, label: str) -> None:
if not path.is_file() or path.stat().st_size == 0:
raise SystemExit(f"Missing {label}: {path}")
def run(command: list[str]) -> None:
print("Running:", " ".join(command), flush=True)
subprocess.run(command, cwd=ROOT, check=True)
def run_mpnn(args: argparse.Namespace, config: dict, output_dir: Path) -> Path:
checkpoint = package_path(args.mpnn_checkpoint)
require_file(checkpoint, "ProteinMPNN checkpoint")
require_file(
ROOT / "model" / "mpnn_fr" / "ProteinMPNN" / "protein_mpnn_utils.py",
"ProteinMPNN source file",
)
output_dir.mkdir(parents=True, exist_ok=True)
command = [
sys.executable,
str(MPNN_SCRIPT),
"-pdbdir",
str(package_path(args.input_dir)),
"-outpdbdir",
str(output_dir),
"-checkpoint_name",
str(output_dir.parent / f"{output_dir.name}.checkpoint"),
"-checkpoint_path",
str(checkpoint),
"-relax_cycles",
str(args.relax_cycles),
"-seqs_per_struct",
str(args.seqs_per_struct),
]
if args.runlist:
command.extend(["-runlist", str(package_path(args.runlist))])
if args.debug:
command.append("-debug")
run(command)
return output_dir
def run_af2(args: argparse.Namespace, input_dir: Path, output_dir: Path) -> None:
require_file(
ROOT / "weight" / "AlphaFold2" / "params" / "params_model_1_ptm.npz",
"AlphaFold2 model_1_ptm parameters",
)
output_dir.mkdir(parents=True, exist_ok=True)
command = [
sys.executable,
str(AF2_SCRIPT),
"-pdbdir",
str(input_dir),
"-outpdbdir",
str(output_dir),
"-checkpoint_name",
str(output_dir.parent / f"{output_dir.name}.checkpoint"),
"-scorefilename",
str(output_dir.parent / f"{output_dir.name}.sc"),
"-recycle",
str(args.recycle),
]
if args.runlist:
command.extend(["-runlist", str(package_path(args.runlist))])
if args.debug:
command.append("-debug")
run(command)
def add_shared_arguments(parser: argparse.ArgumentParser, config: dict) -> None:
parser.add_argument("--input-dir", default=config["sample_input_dir"])
parser.add_argument("--output-dir", default=config["output_dir"])
parser.add_argument("--runlist", default="")
parser.add_argument("--debug", action="store_true")
def main() -> None:
config = load_config()
parser = argparse.ArgumentParser(description=__doc__)
subparsers = parser.add_subparsers(dest="stage", required=True)
mpnn = subparsers.add_parser("mpnn", help="run ProteinMPNN with optional FastRelax")
add_shared_arguments(mpnn, config)
mpnn.add_argument("--mpnn-checkpoint", default=config["proteinmpnn_checkpoint"])
mpnn.add_argument("--relax-cycles", type=int, default=config["relax_cycles"])
mpnn.add_argument("--seqs-per-struct", type=int, default=config["seqs_per_struct"])
af2 = subparsers.add_parser("af2", help="run AlphaFold2 initial-guess prediction")
add_shared_arguments(af2, config)
af2.add_argument("--recycle", type=int, default=config["recycle"])
pipeline = subparsers.add_parser("pipeline", help="run ProteinMPNN/FastRelax then AF2")
add_shared_arguments(pipeline, config)
pipeline.add_argument("--mpnn-checkpoint", default=config["proteinmpnn_checkpoint"])
pipeline.add_argument("--relax-cycles", type=int, default=config["relax_cycles"])
pipeline.add_argument("--seqs-per-struct", type=int, default=config["seqs_per_struct"])
pipeline.add_argument("--recycle", type=int, default=config["recycle"])
args = parser.parse_args()
base_output = package_path(args.output_dir)
if args.stage == "mpnn":
run_mpnn(args, config, base_output)
elif args.stage == "af2":
run_af2(args, package_path(args.input_dir), base_output)
else:
mpnn_output = run_mpnn(args, config, base_output / "mpnn")
# ProteinMPNN changes output tags, so an input-stage runlist cannot be
# reused for the AF2 stage. AF2 processes all structures just produced.
args.runlist = ""
run_af2(args, mpnn_output, base_output / "af2")
if __name__ == "__main__":
main()
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