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prepare_dpf4.py
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#!/usr/bin/env python
#
#
#
# $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/Utilities24/prepare_dpf4.py,v 1.16 2011/11/30 18:02:01 rhuey Exp $
#
import string
import os.path
from MolKit import Read
from AutoDockTools.DockingParameters import DockingParameters, DockingParameter4FileMaker, genetic_algorithm_list, \
genetic_algorithm_local_search_list4, local_search_list4,\
simulated_annealing_list4
def usage():
print "Usage: prepare_dpf4.py -l pdbqt_file -r pdbqt_file"
print " -l ligand_filename"
print " -r receptor_filename"
print
print "Optional parameters:"
print " [-o output dpf_filename]"
print " [-i template dpf_filename]"
print " [-x flexres_filename]"
print " [-p parameter_name=new_value]"
print " [-k list of parameters to write]"
print " [-e write epdb dpf ]"
print " [-v] verbose output"
print " [-L] use local search parameters"
print " [-S] use simulated annealing search parameters"
print " [-s] seed population using ligand's present conformation"
print
print "Prepare a docking parameter file (DPF) for AutoDock4."
print
print " The DPF will by default be <ligand>_<receptor>.dpf. 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:], 'sLShvl:r:i:o:x:p:k:e')
except getopt.GetoptError, msg:
print 'prepare_dpf4.py: %s' % msg
usage()
sys.exit(2)
receptor_filename = ligand_filename = None
dpf_filename = None
template_filename = None
flexres_filename = None
parameters = []
parameter_list = genetic_algorithm_local_search_list4
pop_seed = False
verbose = None
epdb_output = False
for o, a in opt_list:
if verbose: print "o=", o, ' a=', a
if o in ('-v', '--v'):
verbose = 1
if verbose: print 'verbose output'
if o in ('-l', '--l'): #ligand filename
ligand_filename = a
if verbose: print 'ligand_filename =', ligand_filename
if o in ('-r', '--r'): #receptor filename
receptor_filename = a
if verbose: print 'receptor_filename =', receptor_filename
if o in ('-x', '--x'): #flexres_filename
flexres_filename = a
if verbose: print 'flexres_filename =', flexres_filename
if o in ('-i', '--i'): #input reference
template_filename = a
if verbose: print 'template_filename =', template_filename
if o in ('-o', '--o'): #output filename
dpf_filename = a
if verbose: print 'output dpf_filename =', dpf_filename
if o in ('-p', '--p'): #parameter
parameters.append(a)
#print 'parameters =', parameters
if verbose: print 'parameters =', parameters
if o in ('-e', '--e'):
epdb_output = True
if verbose: print 'output epdb file'
parameter_list = epdb_list4_2
if o in ('-k', '--k'): #parameter_list_to_write
parameter_list = a
if verbose: print 'parameter_list =', parameter_list
if o in ('-L', '--L'): #parameter_list_to_write
local_search = 1
parameter_list = local_search_list4
if verbose: print 'parameter_list =', parameter_list
if o in ('-S', '--S'): #parameter_list_to_write
parameter_list = simulated_annealing_list4
if verbose: print 'parameter_list =', parameter_list
if o in ('-h', '--'):
usage()
sys.exit()
if o in ('-s'):
pop_seed = True
if (not receptor_filename) or (not ligand_filename):
print "prepare_dpf4.py: ligand and receptor filenames"
print " must be specified."
usage()
sys.exit()
#9/2011: fixing local_search bugs:
# specifically:
# 1. quaternion0 0 0 0 0
# 2. dihe0 0 0 0 0 0 <one per rotatable bond>
# 3. about == tran0
# 4. remove tstep qstep and dstep
# 5. remove ls_search_freq
local_search = parameter_list==local_search_list4
dm = DockingParameter4FileMaker(verbose=verbose)
if template_filename is not None: #setup values by reading dpf
dm.dpo.read(template_filename)
dm.set_ligand(ligand_filename)
dm.set_receptor(receptor_filename)
if flexres_filename is not None:
flexmol = Read(flexres_filename)[0]
flexres_types = flexmol.allAtoms.autodock_element
lig_types = dm.dpo['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
if verbose: print "adding ", t, " to all_types->", all_types_string
dm.dpo['ligand_types']['value'] = all_types_string
dm.dpo['flexres']['value'] = flexres_filename
dm.dpo['flexres_flag']['value'] = True
#dm.set_docking_parameters( ga_num_evals=1750000,ga_pop_size=150, ga_run=20, rmstol=2.0)
kw = {}
for p in parameters:
key,newvalue = string.split(p, '=')
#detect string reps of lists: eg "[1.,1.,1.]"
if newvalue[0]=='[':
nv = []
for item in newvalue[1:-1].split(','):
nv.append(float(item))
#print "nv=", nv
newvalue = nv
if key=='epdb_flag':
print "setting epdb_flag to", newvalue
kw['epdb_flag'] = 1
elif key=='set_psw1':
print "setting psw1_flag to", newvalue
kw['set_psw1'] = 1
kw['set_sw1'] = 0
elif key=='set_sw1':
print "setting set_sw1 to", newvalue
kw['set_sw1'] = 1
kw['set_psw1'] = 0
elif key=='include_1_4_interactions_flag':
kw['include_1_4_interactions'] = 1
elif 'flag' in key:
if newvalue in ['1','0']:
newvalue = int(newvalue)
if newvalue =='False':
newvalue = False
if newvalue =='True':
newvalue = True
elif local_search and 'about' in key:
kw['about'] = newvalue
kw['tran0'] = newvalue
else:
kw[key] = newvalue
apply(dm.set_docking_parameters, (), kw)
if key not in parameter_list:
#special hack for output_pop_file
if key=='output_pop_file':
parameter_list.insert(parameter_list.index('set_ga'), key)
else:
parameter_list.append(key)
dm.write_dpf(dpf_filename, parameter_list, pop_seed)
#prepare_dpf4.py -l indinavir.pdbq -r 1hsg.pdbqs -p ga_num_evals=20000000 -p ga_pop_size=150 -p ga_run=17 -i ref.dpf -o testing.dpf