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#!/usr/bin/env pythonsh
#
#
#
# $Header: /mnt/raid/services/cvs/python/packages/share1.5/AutoDockTools/Utilities24/prepare_gpf4.py,v 1.18 2011/06/14 17:25:51 rhuey Exp $
#
import string
import os.path
import glob
from MolKit import Read
from AutoDockTools.GridParameters import GridParameters, grid_parameter_list4
from AutoDockTools.GridParameters import GridParameter4FileMaker
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
def usage():
print "Usage: prepare_gpf4.py -l pdbqt_file -r pdbqt_file "
print " -l ligand_filename"
print " -r receptor_filename"
print
print "Optional parameters:"
print " [-i reference_gpf_filename]"
print " [-o output_gpf_filename]"
print " [-x flexres_filename]"
print " [-p parameter=newvalue. For example: -p ligand_types='HD,Br,A,C,OA' or p npts='60,60,66' or gridcenter='2.5,6.5,-7.5']"
print " [-d directory of ligands to use to set types]"
print " [-y boolean to center grids on center of ligand]"
print " [-n boolean to NOT size_box_to_include_ligand]"
print " [-I increment npts in all 3 dimensions by this integer]"
print " [-v]"
print
print "Prepare a grid parameter file (GPF) for AutoDock4."
print
print " The GPF will by default be <receptor>.gpf. This"
print "may be overridden using the -o flag."
if __name__ == '__main__':
import getopt
import sys
try:
opt_list, args = getopt.getopt(sys.argv[1:], 'vl:r:i:x:o:p:d:ynI:')
except getopt.GetoptError, msg:
print 'prepare_gpf4.py: %s' % msg
usage()
sys.exit(2)
receptor_filename = ligand_filename = None
list_filename = gpf_filename = gpf_filename = None
output_gpf_filename = None
flexres_filename = None
directory = None
parameters = []
verbose = None
center_on_ligand = False
size_box_to_include_ligand = True
npts_increment = 0
ligand_types_defined = False
for o, a in opt_list:
if o in ('-v', '--v'):
verbose = 1
if o in ('-l', '--l'):
ligand_filename = a
if verbose: print 'ligand_filename=', ligand_filename
if o in ('-r', '--r'):
receptor_filename = a
if verbose: print 'receptor_filename=', receptor_filename
if o in ('-i', '--i'):
gpf_filename = a
if verbose: print 'reference_gpf_filename=', gpf_filename
if o in ('-x', '--x'):
flexres_filename = a
if verbose: print 'flexres_filename=', flexres_filename
if o in ('-o', '--o'):
output_gpf_filename = a
if verbose: print 'output_gpf_filename=', output_gpf_filename
if o in ('-p', '--p'):
parameters.append(a)
if a.split('=')[0]=="ligand_types": ligand_types_defined = True
if verbose: print 'parameters=', parameters
if o in ('-d', '--d'):
directory = a
if verbose: print 'directory=', directory
if o in ('-y', '--y'):
center_on_ligand = True
if verbose: print 'set center_on_ligand to ', center_on_ligand
if o in ('-n', '--n'):
size_box_to_include_ligand = False
if verbose: print 'set size_box_to_include_ligand to ', size_box_to_include_ligand
if o in ('-I', '--I'):
npts_increment = int(a)
if verbose: print 'set npts_increment to ', npts_increment
if o in ('-h', '--'):
usage()
sys.exit()
if (not receptor_filename) or (ligand_filename is None and directory is None and ligand_types_defined is False):
print "prepare_gpf4.py: ligand and receptor filenames"
print " must be specified."
usage()
sys.exit()
gpfm = GridParameter4FileMaker(size_box_to_include_ligand=size_box_to_include_ligand,verbose=verbose)
if gpf_filename is not None:
gpfm.read_reference(gpf_filename)
if ligand_filename is not None:
gpfm.set_ligand(ligand_filename)
gpfm.set_receptor(receptor_filename)
if directory is not None:
gpfm.set_types_from_directory(directory)
if flexres_filename is not None:
flexmol = Read(flexres_filename)[0]
flexres_types = flexmol.allAtoms.autodock_element
lig_types = gpfm.gpo['ligand_types']['value'].split()
all_types = lig_types
for t in flexres_types:
if t not in all_types:
all_types.append(t)
all_types_string = all_types[0]
if len(all_types)>1:
for t in all_types[1:]:
all_types_string = all_types_string + " " + t
gpfm.gpo['ligand_types']['value'] = all_types_string
for param_str in parameters:
if param_str.find("parameter_file")>-1:
parameters.append("custom_parameter_file=1")
break
for p in parameters:
key,newvalue = string.split(p, '=')
if key=='gridcenter' and newvalue.find(',')>-1:
newvalue = newvalue.split(',')
newvalue = string.join(newvalue)
kw = {key:newvalue}
apply(gpfm.set_grid_parameters, (), kw)
#gpfm.set_grid_parameters(spacing=1.0)
if center_on_ligand is True:
gpfm.gpo['gridcenterAuto']['value'] = 0
cenx,ceny,cenz = gpfm.ligand.getCenter()
gpfm.gpo['gridcenter']['value'] = "%.3f %.3f %.3f" %(cenx,ceny,cenz)
if npts_increment:
orig_npts = gpfm.gpo['npts']['value'] #[40,40,40]
if verbose: print "before increment npts=", orig_npts
for ind in range(3):
gpfm.gpo['npts']['value'][ind] += npts_increment
if verbose: print "after increment npts =", gpfm.gpo['npts']['value']
gpfm.write_gpf(output_gpf_filename)
#prepare_gpf4.py -l 1ebg_lig.pdbqt -r 1ebg_rec.pdbqt -p spacing=0.4 -p ligand_types="HD,Br,A,C,OA" -p npts="60,60,60" -i ref.gpf -o testing.gpf
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