)
parms = {}
parms['simulated_annealing_list4'] = simulated_annealing_list4
parms['genetic_algorithm_list4'] = genetic_algorithm_list4
parms[
'genetic_algorithm_local_search_list4'] = genetic_algorithm_local_search_list4
parms['local_search_list4'] = local_search_list4
#what about nucleic acids???
DPO4 = DockingParameters()
print("default: ligand_types=", DPO4['ligand_types']['value'])
orig_compute_unbound_extended_flag = DPO4['compute_unbound_extended_flag'][
'value']
if dpf3_filename:
DPO4.read(dpf3_filename)
if verbose: print('read ', dpf3_filename)
DPO4['compute_unbound_extended_flag'][
'value'] = orig_compute_unbound_extended_flag
else:
if verbose: print('using dpo defaults')
DPO4.set_ligand(ligand_filename)
DPO4.set_version("4.1")
DPO4['set_sw1']['value'] = 0
DPO4['set_sw1_flag']['value'] = 0
DPO4['set_psw1']['value'] = 1
DPO4['set_psw1_flag']['value'] = 1
res = DPO4.set_ligand_types_from_filename(ligand_filename)
if res == "ERROR": raise Exception('unreadable file' + ligand_filename)
if verbose:
print("ligand_types=", DPO4['ligand_types']['value'])
print "dpf3_to_dpf4: using default receptor_filename:", receptor_filename
if not dpf3_filename:
print 'dpf3_to_dpf4: no dpf3_filename specified using GridParameter defaults'
parms= {}
parms['simulated_annealing_list4'] = simulated_annealing_list4
parms['genetic_algorithm_list4'] = genetic_algorithm_list4
parms['genetic_algorithm_local_search_list4'] = genetic_algorithm_local_search_list4
parms['local_search_list4'] = local_search_list4
#what about nucleic acids???
DPO4 = DockingParameters()
print "default: ligand_types=", DPO4['ligand_types']['value']
orig_compute_unbound_extended_flag = DPO4['compute_unbound_extended_flag']['value']
if dpf3_filename:
DPO4.read(dpf3_filename)
if verbose: print 'read ', dpf3_filename
DPO4['compute_unbound_extended_flag']['value'] = orig_compute_unbound_extended_flag
else:
if verbose: print 'using dpo defaults'
DPO4.set_ligand(ligand_filename)
DPO4.set_version("4.1")
DPO4['set_sw1']['value'] = 0
DPO4['set_sw1_flag']['value'] = 0
DPO4['set_psw1']['value'] = 1
DPO4['set_psw1_flag']['value'] = 1
res = DPO4.set_ligand_types_from_filename(ligand_filename)
if res=="ERROR": raise 'unreadable file', ligand_filename
if verbose:
print "ligand_types=", DPO4['ligand_types']['value']
print 'set ligand to ', ligand_filename
# @@ from docking directory name @@
dpf_pathname = os.path.join(docking_pathname, docking_name) + ".dpf"
dpf_filename = os.path.basename(dpf_pathname)
# remove "faahNNNN_ from docking name
gpf_pathname = os.path.join(docking_pathname, docking_name[9:]) + ".gpf"
gpf_filename = os.path.basename(gpf_pathname)
#
# get filenames from the dpf and gpf
#
from AutoDockTools.DockingParameters import DockingParameters
from AutoDockTools.GridParameters import GridParameters
dpo = DockingParameters()
log.info("reading dpf: %s" % dpf_pathname)
dpo.read(dpf_pathname)
ligand_filename = dpo["move"]["value"]
ligand_pathname = os.path.join(docking_pathname, ligand_filename)
log.info("ligand_filename: %s" % ligand_filename)
log.debug("ligand_pathname: %s" % ligand_pathname)
gpo = GridParameters()
log.info("reading gpf: %s" % gpf_pathname)
gpo.read(gpf_pathname)
receptor_filename = gpo["receptor"]["value"]
receptor_pathname = os.path.join(docking_pathname, receptor_filename)
log.info("receptor_filename: %s" % receptor_filename)
log.debug("receptor_pathname: %s" % receptor_pathname)
# docking log pathnames
dlg_pathname_list = glob.glob(os.path.join(docking_pathname, '*.dlg'))
class LibraryDpfWriter:
def __init__(self, dpffile, extension='pdbq', \
err_file="write_lib_dpf_errors",
prefix='', verbose=0):
self.verbose = verbose
if verbose: print("self.verbose = ", verbose)
self.prefix = prefix
self.setup(dpffile)
self.parm_list_dict = {}
self.parm_list_dict['GALS'] = genetic_algorithm_local_search_list
self.parm_list_dict['GA'] = genetic_algorithm_list
self.parm_list_dict['LS'] = local_search_list
self.parm_list_dict['SA'] = simulated_annealing_list
self.ligandfilenames = []
self.extension = extension
self.error_file = open(err_file, 'w')
def setup(self, dpffile):
self.dpffile = dpffile
self.dpo = DockingParameters()
self.dpo.read(dpffile)
def getligands(self, extension, name=''):
typeDict = {}
key = name + '*.' + extension
self.ligandfilenames = glob.glob(key)
return self.ligandfilenames
def write(self, dpo, style='GALS'):
#one file per ligand
dpffiles = []
receptor_stem = self.dpo.receptor_stem
parm_list = self.parm_list_dict[style]
if not len(self.ligandfilenames):
self.getligands(self.extension)
#print "len(self.ligandfilenames)=", len(self.ligandfilenames)
for ligand_file in self.ligandfilenames:
#get the types
typeDict = {}
m = Read(ligand_file)[0]
for a in m.allAtoms:
typeDict[a.autodock_element] = 1
type_list = list(typeDict.keys())
#check that there is a map for each type
ok = 1
for t in type_list:
mapfile = receptor_stem + '.' + t + '.map'
try:
assert os.path.exists(mapfile)
except:
ok = 0
ostr = ligand_file + " missing map " + t + "\n"
self.error_file.write(ostr)
break #try to continue 'for' statement with next filename
#update dpo with ligand specific values
if not ok:
if self.verbose:
print("problem with ", ligand_file)
continue
types = string.join(type_list,'')
self.dpo['move']['value'] = ligand_file
if self.verbose: print("set types to ", types)
self.dpo['types']['value'] = types
#CAUTION: dpo['torsdof']['value'] is [0,0.3113]
self.dpo['torsdof']['value'][0] = m.TORSDOF
if hasattr(m, 'ndihe'):
ndihe = m.ndihe
elif hasattr(m, 'torscount'):
ndihe = m.torscount
elif hasattr(m, 'torTree'):
ndihe = len(m.torTree.torsionMap)
else:
msg = ligand_file + " is not properly formatted: no torsions!"
raise AttributeError(msg)
self.dpo['ndihe']['value'] = ndihe
outputfilename = self.prefix + m.name + "_" + style + ".dpf"
if self.verbose: print("writing ", outputfilename)
self.dpo.write(outputfilename, parm_list)
dpffiles.append(outputfilename)
return dpffiles
# @@ from docking directory name @@
dpf_pathname = os.path.join(docking_pathname, docking_name) + ".dpf"
dpf_filename = os.path.basename(dpf_pathname)
# remove "faahNNNN_ from docking name
gpf_pathname = os.path.join(docking_pathname, docking_name[9:]) + ".gpf"
gpf_filename = os.path.basename(gpf_pathname)
#
# get filenames from the dpf and gpf
#
from AutoDockTools.DockingParameters import DockingParameters
from AutoDockTools.GridParameters import GridParameters
dpo = DockingParameters()
log.info("reading dpf: %s" % dpf_pathname)
dpo.read(dpf_pathname)
ligand_filename = dpo["move"]["value"]
ligand_pathname = os.path.join(docking_pathname, ligand_filename)
log.info ("ligand_filename: %s" % ligand_filename)
log.debug("ligand_pathname: %s" % ligand_pathname)
gpo = GridParameters()
log.info("reading gpf: %s" % gpf_pathname)
gpo.read(gpf_pathname)
receptor_filename = gpo["receptor"]["value"]
receptor_pathname = os.path.join(docking_pathname, receptor_filename)
log.info ("receptor_filename: %s" % receptor_filename)
log.debug("receptor_pathname: %s" % receptor_pathname)
# docking log pathnames
dlg_pathname_list = glob.glob(os.path.join( docking_pathname, '*.dlg'))
class LibraryDpfWriter:
def __init__(self, dpffile, extension='pdbq', \
err_file="write_lib_dpf_errors",
prefix='', verbose=0):
self.verbose = verbose
if verbose: print "self.verbose = ", verbose
self.prefix = prefix
self.setup(dpffile)
self.parm_list_dict = {}
self.parm_list_dict['GALS'] = genetic_algorithm_local_search_list
self.parm_list_dict['GA'] = genetic_algorithm_list
self.parm_list_dict['LS'] = local_search_list
self.parm_list_dict['SA'] = simulated_annealing_list
self.ligandfilenames = []
self.extension = extension
self.error_file = open(err_file, 'w')
def setup(self, dpffile):
self.dpffile = dpffile
self.dpo = DockingParameters()
self.dpo.read(dpffile)
def getligands(self, extension, name=''):
typeDict = {}
key = name + '*.' + extension
self.ligandfilenames = glob.glob(key)
return self.ligandfilenames
def write(self, dpo, style='GALS'):
#one file per ligand
dpffiles = []
receptor_stem = self.dpo.receptor_stem
parm_list = self.parm_list_dict[style]
if not len(self.ligandfilenames):
self.getligands(self.extension)
#print "len(self.ligandfilenames)=", len(self.ligandfilenames)
for ligand_file in self.ligandfilenames:
#get the types
typeDict = {}
m = Read(ligand_file)[0]
for a in m.allAtoms:
typeDict[a.autodock_element] = 1
type_list = typeDict.keys()
#check that there is a map for each type
ok = 1
for t in type_list:
mapfile = receptor_stem + '.' + t + '.map'
try:
assert os.path.exists(mapfile)
except:
ok = 0
ostr = ligand_file + " missing map " + t + "\n"
self.error_file.write(ostr)
break #try to continue 'for' statement with next filename
#update dpo with ligand specific values
if not ok:
if self.verbose:
print "problem with ", ligand_file
continue
types = string.join(type_list,'')
self.dpo['move']['value'] = ligand_file
if self.verbose: print "set types to ", types
self.dpo['types']['value'] = types
#CAUTION: dpo['torsdof']['value'] is [0,0.3113]
self.dpo['torsdof']['value'][0] = m.TORSDOF
if hasattr(m, 'ndihe'):
ndihe = m.ndihe
elif hasattr(m, 'torscount'):
ndihe = m.torscount
elif hasattr(m, 'torTree'):
ndihe = len(m.torTree.torsionMap)
else:
msg = ligand_file + " is not properly formatted: no torsions!"
raise AttributeError, msg
self.dpo['ndihe']['value'] = ndihe
outputfilename = self.prefix + m.name + "_" + style + ".dpf"
if self.verbose: print "writing ", outputfilename
self.dpo.write(outputfilename, parm_list)
dpffiles.append(outputfilename)
return dpffiles
