#!/home/jenkins/workspace/ccpem/ccp-em_centos5/devtools/install/devbin/python

__author__ = "Felix Simkovic"
__date__ = "21 Nov 2016"
__version__ = "0.1"

import argparse
import conkit
import logging
import sys

logging.basicConfig(format='%(message)s', level=logging.INFO)


def main():
    text = """
Calculate the contact precision value

File format options are:

    Contact files: [{0}]

"""
    options = sorted(conkit.io.CONTACT_FILE_PARSERS.keys())
    text = text.format(' '.join(options))
    parser = argparse.ArgumentParser(description=text, 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('seqfile')
    parser.add_argument('seqformat')
    parser.add_argument('confile')
    parser.add_argument('conformat')
    args = parser.parse_args()
    
    # Compute all the data
    if args.pdbchain:
        pdb = conkit.io.read(args.pdbfile, 'pdb')[args.pdbchain]
    else:
        pdb = conkit.io.read(args.pdbfile, 'pdb')[0]
    seq = conkit.io.read(args.seqfile, args.seqformat)[0]
    con = conkit.io.read(args.confile, args.conformat)[0]
    
    con.sequence = seq
    con.assign_sequence_register()

    logging.info('Distance to neighbors: {0}'.format(args.dtn))
    con.remove_neighbors(min_distance=args.dtn, inplace=True)

    ncontacts = int(seq.seq_len * args.dfactor)
    logging.info('Number of contacts: {0}'.format(ncontacts))
    con.sort('raw_score', reverse=True, inplace=True)
    con_sliced = con[:ncontacts]
    
    con_matched = con_sliced.match(pdb)
    precision = con_matched.precision
    
    logging.info('Precision score: {0}'.format(precision))


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