#!/usr/bin/env python
#
# 
#
# $Header: /mnt/raid/services/cvs/python/packages/share1.5/AutoDockTools/Utilities24/write_each_cluster_LE_conf.py,v 1.3 2011/12/27 22:41:53 rhuey Exp $
#
import os, glob

from MolKit import Read
from AutoDockTools.Docking import Docking
from mglutil.math.rmsd import RMSDCalculator
from string import strip




if __name__ == '__main__':
    import sys
    import getopt


    def usage():
        print "Usage: write_largest_cluster_ligand.py "
        print "    This script does the following: "
        print "         (1) read all the files with extension '.dlg' into one Docking"
        print "         (2) compute a clustering at the specified rms tolerance "
        print "         (3) write the ligand with the coordinates of the "
        print "             lowest-energy conformation in each cluster to a separate file" 
        print "    "
        print "    Optional parameters:"
        print "        [-t]    rms_tolerance (default 2.0)"
        print "        [-o pdbqt_filename] (default ligandstem_clust#.pdbqt)"
        print "        [-v]    verbose output"

    # process command arguments
    try:
        opt_list, args = getopt.getopt(sys.argv[1:], 't:o:vh')
    except getopt.GetoptError, msg:
        print 'write_each_cluster_LE_conf.py: %s' %msg
        usage()
        sys.exit(2)

    # initialize required parameters
    # optional parameters
    verbose = None
    #-o outputfilestem
    outputfilestem = None
    #-t rms_tolerance
    rms_tolerance = 2.0

    #'t:o:vh'
    for o, a in opt_list:
        #print "o=", o, " a=", a
        if o in ('-o', '--o'):
            outputfilestem = a
            if verbose: print 'set stem for outputfile to ', a
        if o in ('-t', '--t'):
            rms_tolerance = float(a)
            if verbose: print 'set rms_tolerance to ', a
        if o in ('-v', '--v'):
            verbose = True
            if verbose: print 'set verbose to ', True
        if o in ('-h', '--'):
            usage()
            sys.exit()

    dlg_list = glob.glob('*.dlg')
    d = Docking()
    for dlg in dlg_list: 
        d.readDlg(dlg)
    d.clusterer.rmsTool = RMSDCalculator(d.ligMol.allAtoms.coords[:])
    d.clusterer.make_clustering(rms_tolerance)
    clustering = d.clusterer.clustering_dict[rms_tolerance]
    for clust in clustering:
        clustStr = str(clustering.index(clust))
        if verbose: print "processing clust number ", clustStr
        #update the coordinates to those of conf with lowest energy in current cluster
        d.ch.set_conformation(clust[0])
        parser = d.ligMol.parser
        lines = []
        #have to add newline character to lines read from dlg
        for l in parser.allLines:
            l = strip(l)
            l+= '\n'
            lines.append(l)
        parser.allLines = lines
        coords = d.ligMol.allAtoms.coords
        if outputfilestem is None:
            parser.write_with_new_coords(coords, d.ligMol.name  + "_LE_clust"+clustStr +'.pdbqt') 
        else:
            parser.write_with_new_coords(coords, outputfilestem  + clustStr +'.pdbqt')
        if verbose: print 'wrote %s' %outputfilestem


# To execute this command type:
# write_each_cluster_LE_conf.py  [-t rms_tolerance, -o outputfilestem] -v




