"""haddock3-re score subcommand."""
import json
from pathlib import Path
import sys
from haddock import log
from haddock.core.defaults import INTERACTIVE_RE_SUFFIX
from haddock.core.typing import Union
from haddock.libs.libinteractive import handle_ss_file, handle_clt_file
from haddock.libs.libplots import read_capri_table
[docs]def add_rescore_arguments(rescore_subcommand):
"""Add arguments to the score subcommand."""
rescore_subcommand.add_argument(
"capri_dir",
help="The caprieval directory to rescore.",
)
rescore_subcommand.add_argument(
"-e",
"--w_elec",
help="weight of the electrostatic component.",
required=False,
type=float,
)
rescore_subcommand.add_argument(
"-w",
"--w_vdw",
help="weight of the van-der-Waals component.",
required=False,
type=float,
)
rescore_subcommand.add_argument(
"-d",
"--w_desolv",
help="weight of the desolvation component.",
required=False,
type=float,
)
rescore_subcommand.add_argument(
"-b",
"--w_bsa",
help="weight of the BSA component.",
required=False,
type=float,
)
rescore_subcommand.add_argument(
"-a",
"--w_air",
help="weight of the AIR component.",
required=False,
type=float,
)
return rescore_subcommand
ANA_FOLDER = "interactive" # name of the analysis folder
[docs]def rescore(
capri_dir: Union[str, Path],
w_elec: Union[bool, float] = None,
w_vdw: Union[bool, float] = None,
w_desolv: Union[bool, float] = None,
w_bsa: Union[bool, float] = None,
w_air: Union[bool, float] = None,
) -> Path:
"""Rescore the CAPRI models."""
log.info(f"Rescoring {capri_dir}")
# load the scoring pars via json
weights_filename = Path(capri_dir, "weights_params.json")
if not weights_filename.exists():
log.error(f"weights file {weights_filename} not found. Exiting.")
sys.exit(1)
scoring_pars = json.load(open(weights_filename, "r"))
log.info(f"Previous scoring parameters: {scoring_pars}")
if w_elec is not None:
scoring_pars.update({"w_elec": w_elec})
if w_vdw is not None:
scoring_pars.update({"w_vdw": w_vdw})
if w_desolv is not None:
scoring_pars.update({"w_desolv": w_desolv})
if w_bsa is not None:
scoring_pars.update({"w_bsa": w_bsa})
if w_air is not None:
scoring_pars.update({"w_air": w_air})
log.info(f"Rescoring parameters: {scoring_pars}")
capri_ss = Path(capri_dir, "capri_ss.tsv")
capri_clt = Path(capri_dir, "capri_clt.tsv")
if not capri_ss.exists() or not capri_clt.exists():
log.error("capri_ss.tsv or capri_clt.tsv not found. Exiting.")
sys.exit(1)
# ss file
df_ss = read_capri_table(capri_ss)
# now we want to rewrite the score parameter
new_scores = scoring_pars["w_vdw"] * df_ss["vdw"] + \
scoring_pars["w_elec"] * df_ss["elec"] + \
scoring_pars["w_bsa"] * df_ss["bsa"] + \
scoring_pars["w_desolv"] * df_ss["desolv"] + \
scoring_pars["w_air"] * df_ss["air"]
df_ss["score"] = new_scores
# now we want to write the new capri_ss.tsv file
run_dir = Path(capri_dir).parent
capri_name = Path(capri_dir).name
# create the interactive folder
outdir = Path(run_dir, f"{capri_name}_{INTERACTIVE_RE_SUFFIX}")
outdir.mkdir(exist_ok=True)
# handle ss file first
df_ss, clt_ranks_dict = handle_ss_file(df_ss)
capri_ss_file = Path(outdir, "capri_ss.tsv")
log.info(f"Saving capri_ss file to {capri_ss_file}")
df_ss.to_csv(capri_ss_file, sep="\t", index=False, float_format="%.3f")
df_clt = handle_clt_file(df_ss, clt_ranks_dict)
capri_clt_file = Path(outdir, "capri_clt.tsv")
df_clt.to_csv(
capri_clt_file,
sep="\t",
index=False,
float_format="%.3f",
)
# Write the latest parameters file
# define output fname
rescoring_params_fname = Path(outdir, "weights_params.json")
# write json file
with open(rescoring_params_fname, 'w', encoding='utf-8') as jsonf:
json.dump(
scoring_pars,
jsonf,
indent=4,
)
log.info(f"new rescoring parameters written in: {rescoring_params_fname}")
# return path to the new interactive folder
return outdir