active-passive-to-ambig.py

#!/usr/bin/env python

"""
Python script to convert a list of active and passive residues into 
ambiguous interaction restraints for HADDOCK
"""

import os, sys, time
import subprocess
import tempfile

def active_passive_to_ambig(active1, passive1, active2, passive2, 
        segid1='A', segid2='B'):
    """Convert active and passive residues to Ambiguous Interaction Restraints

    Parameters
    ----------
    active1 : list
        List of active residue numbers of the first segid

    passive1 : list
        List of passive residue numbers of the first segid

    active2 : list
        List of active residue numbers of the second segid
    
    active2 : list
        List of passive residue numbers of the second segid

    segid1 : string
        Segid to use for the first model

    segid2 : string
        Segid to use for the second model

    """

    all1 = active1 + passive1
    all2 = active2 + passive2

    for resi1 in active1:
        print('assign (resi {:d} and segid {:s})'.format(resi1, segid1))
        print('(')
        lines = []
        c = 0
        for resi2 in all2:
            print('       (resi {:d} and segid {:s})'.format(resi2, segid2))
            c += 1
            if c != len(all2):
                print('        or')
#        for line in lines:
#            print(line)

        print(') 2.0 2.0 0.0\n')
            
    for resi2 in active2:
        print('assign (resi {:d} and segid {:s})'.format(resi2, segid2))
        print('(\n')
        lines = []
        c = 0
        for resi1 in all1:
            print('       (resi {:d} and segid {:s})'.format(resi1, segid1))
            c += 1
            if c != len(all1):
                print('        or\n')
#        for line in lines:
#            print(line)

        print(') 2.0 2.0 0.0\n')

def main():
    import sys
    if len(sys.argv) != 3:
        print '\nUsage:\n     python active-passive_to_ambig.py <active-passive-file1> <active-passive-file2>\n\n' +\
              'where <active-passive-file> is a file consisting of two space-delimited lines with\n' +\
              'the first line active residues numbers and the second line passive residue numbers\n'
        sys.exit()

    active1, passive1 = [[int(x) for x in line.split()] for line in open(sys.argv[1])]
    active2, passive2 = [[int(x) for x in line.split()] for line in open(sys.argv[2])]
    active_passive_to_ambig(active1, passive1, active2, passive2)


if __name__ == '__main__':
    main()