.venv_haddock/lib/python3.12/site-packages/prodigy_prot/cli.py

"""
Binding affinity predictor based on Intermolecular Contacts (ICs).
"""

import argparse
import logging
import sys
from argparse import RawTextHelpFormatter
from pathlib import Path

from Bio.PDB.Structure import Structure

from prodigy_prot.modules.parsers import (get_parser, parse_structure,
                                          validate_structure)
from prodigy_prot.modules.prodigy import Prodigy

# setup logging
logging.basicConfig(level=logging.INFO, stream=sys.stdout, format="%(message)s")
log = logging.getLogger("Prodigy")


ap = argparse.ArgumentParser(description=__doc__, formatter_class=RawTextHelpFormatter)
ap.add_argument(
    "input_path",
    help="Path to either: \n- Structure in PDB or mmCIF format\n- Directory containing structure files",
)
ap.add_argument(
    "--distance-cutoff",
    type=float,
    default=5.5,
    help="Distance cutoff to calculate ICs",
)
ap.add_argument(
    "--acc-threshold",
    type=float,
    default=0.05,
    help="Accessibility threshold for BSA analysis",
)
ap.add_argument(
    "--temperature",
    type=float,
    default=25.0,
    help="Temperature (C) for Kd prediction",
)
ap.add_argument("--contact_list", action="store_true", help="Output a list of contacts")
ap.add_argument(
    "--pymol_selection",
    action="store_true",
    help="Output a script to highlight the interface (pymol)",
)
ap.add_argument(
    "-q",
    "--quiet",
    action="store_true",
    help="Outputs only the predicted affinity value",
)
_co_help = """
By default, all intermolecular contacts are taken into consideration,
a molecule being defined as an isolated group of amino acids sharing
a common chain identifier. In specific cases, for example
antibody-antigen complexes, some chains should be considered as a
single molecule.

Use the --selection option to provide collections of chains that should
be considered for the calculation. Separate by a space the chains that
are to be considered _different_ molecules. Use commas to include multiple
chains as part of a single group:

--selection A B => Contacts calculated (only) between chains A and B.
--selection A,B C => Contacts calculated (only) between \
    chains A and C; and B and C.
--selection A B C => Contacts calculated (only) between \
    chains A and B; B and C; and A and C.
"""
sel_opt = ap.add_argument_group("Selection Options", description=_co_help)
sel_opt.add_argument("--selection", nargs="+", metavar=("A B", "A,B C"))


def main():
    args = ap.parse_args()
    log.setLevel(logging.ERROR if args.quiet else logging.INFO)

    struct_path = Path(args.input_path)

    input_list = []
    if struct_path.is_file():
        input_list.append(struct_path)

    elif struct_path.is_dir():
        for input_f in struct_path.glob("*"):
            if Path(input_f).suffix in [".pdb", ".cif", ".ent"]:
                input_list.append(input_f)

    elif not struct_path.exists():
        log.error(f"File {struct_path} does not exist")
        sys.exit(1)

    else:
        log.error(f"Input path {struct_path} is neither a valid file nor a directory")
        sys.exit(1)

    for input_f in input_list:
        structure, n_chains, n_res = parse_structure(str(input_f))

        if len(input_list) > 1:
            log.info("#" * 42)

        log.info(
            "[+] Parsed structure file {0} ({1} chains, {2} residues)".format(
                structure.id, n_chains, n_res
            )
        )
        prodigy = Prodigy(structure, args.selection, args.temperature)
        prodigy.predict(
            distance_cutoff=args.distance_cutoff, acc_threshold=args.acc_threshold
        )
        prodigy.print_prediction(quiet=args.quiet)

        if args.contact_list:
            prodigy.print_contacts(outfile=str(struct_path.with_suffix(".ic")))

        if args.pymol_selection:
            prodigy.print_pymol_script(outfile=str(struct_path.with_suffix(".pml")))


if __name__ == "__main__":
    sys.exit(main())