#!/usr/bin/env python
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"""This script calculates the precision score for a contact prediction
when compared against contacts extracted from a protein structure.
"""
__author__ = "Felix Simkovic"
__date__ = "21 Nov 2016"
__version__ = "0.13.3"
import argparse
import conkit.command_line
import conkit.io
logger = None
[docs]def main():
parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
"-c",
dest="pdbchain",
default=None,
help="PDB chain to use [default: first in file]. "
"Inter-molecular predictions use two letter "
"convention, i.e AD for contacts between A and D.",
)
parser.add_argument("-d", dest="dtn", default=5, type=int, help="Minimum sequence separation [default: 5]")
parser.add_argument(
"-f",
dest="dfactor",
default=1.0,
type=float,
help="number of contacts to include relative to sequence length [default: 1.0]",
)
parser.add_argument("pdbfile")
parser.add_argument("pdbformat", choices=['pdb', 'mmcif'])
parser.add_argument("seqfile")
parser.add_argument("seqformat")
parser.add_argument("confile")
parser.add_argument("conformat")
args = parser.parse_args()
global logger
logger = conkit.command_line.setup_logging(level="info")
if args.pdbchain:
pdb = conkit.io.read(args.pdbfile, args.pdbformat)[args.pdbchain]
else:
pdb = conkit.io.read(args.pdbfile, args.pdbformat)[0]
seq = conkit.io.read(args.seqfile, args.seqformat)[0]
pdb.sequence = seq
pdb.set_sequence_register()
pdb = pdb.as_contactmap()
con = conkit.io.read(args.confile, args.conformat)[0]
con.sequence = seq
con.set_sequence_register()
if args.conformat in conkit.io.DISTANCE_FILE_PARSERS:
con = con.as_contactmap()
logger.info("Min sequence separation for contacting residues: %d", args.dtn)
logger.info("Contact list cutoff factor: %f * L", args.dfactor)
con.remove_neighbors(min_distance=args.dtn, inplace=True)
ncontacts = int(seq.seq_len * args.dfactor)
con.sort("raw_score", reverse=True, inplace=True)
con_sliced = con[:ncontacts]
con_matched = con_sliced.match(pdb)
precision = con_matched.precision
logger.info("Precision score: %f", precision)
if __name__ == "__main__":
import sys
import traceback
try:
main()
sys.exit(0)
except Exception as e:
if not isinstance(e, SystemExit):
msg = "".join(traceback.format_exception(*sys.exc_info()))
logger.critical(msg)
sys.exit(1)
