if o in ('-S', '--S'): #parameter_list_to_write
parameter_list = simulated_annealing_list4_1
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_dpf41.py: ligand and receptor filenames"
print " must be specified."
usage()
sys.exit()
dm = DockingParameter42FileMaker(autodock_parameter_version=4.1,
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:]:
if (not receptor_filename) or (not ligand_filename):
print "prepare_dpf42.py: ligand and receptor filenames"
print " must be specified."
usage()
sys.exit()
#11/2011: 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 = local_search_list4_2
#parameter_list =local_search_list4_2
dm = DockingParameter42FileMaker(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:]:
if (not receptor_filename) or (not ligand_filename):
print("prepare_dpf42.py: ligand and receptor filenames")
print(" must be specified.")
usage()
sys.exit()
#11/2011: 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 = local_search_list4_2
#parameter_list =local_search_list4_2
dm = DockingParameter42FileMaker(verbose=verbose, pop_seed=pop_seed)
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:]: