if not ligand_filename:
print('gpf4_to_gpf3: ligand_filename must be specified.')
usage()
sys.exit()
if not receptor_filename:
receptor_filename = gpf4_stem + '.pdbqs'
print("gpf4_to_gpf3: using default receptor_filename:", receptor_filename)
if not gpf4_filename:
print('gpf4_to_gpf3: no gpf4_filename specified using GridParameter defaults')
#what about nucleic acids???
GPO3 = GridParameters()
GPO3.read4(gpf4_filename)
GPO3.read(gpf4_filename)
if verbose: print('read ', gpf4_filename)
#have to set the ligand_types
GPO3.set_ligand(ligand_filename)
#build an autogrid3 'types' string from autogrid4 ligand_types
GPO3.set_ligand_types3(GPO3['ligand_types']['value'])
if verbose: print('set ligand to ', ligand_filename)
GPO3.set_receptor(receptor_filename)
if verbose: print('set receptor to ', receptor_filename)
if outputfilename is None:
outputfilename = gpf4_stem + '_3.gpf'
GPO3.write(outputfilename, grid_parameter_list)
if verbose:
print("wrote ", outputfilename, ' using:')
for p in grid_parameter_list:
print(p)
sys.exit()
if not ligand_filename:
print 'gpf3_to_gpf4: ligand_filename must be specified.'
usage()
sys.exit()
if not receptor_filename:
receptor_filename = gpf3_stem + '.pdbqt'
print "gpf3_to_gpf4: using default receptor_filename:", receptor_filename
if not gpf3_filename:
print 'gpf3_to_gpf4: no gpf3_filename specified using GridParameter defaults'
#what about nucleic acids???
GPO4 = GridParameters()
if gpf3_filename:
GPO4.read(gpf3_filename)
if verbose: print 'read ', gpf3_filename
else:
if verbose: print 'using gpo defaults'
GPO4.set_ligand4(ligand_filename)
if verbose: print 'set ligand to ', ligand_filename
GPO4.set_receptor4(receptor_filename)
if verbose: print 'set receptor to ', receptor_filename
if outputfilename is None:
outputfilename = gpf3_stem + '_4.gpf'
GPO4.write4(outputfilename, grid_parameter_list4)
if verbose:
print "wrote ", outputfilename, ' using:'
for p in grid_parameter_list4:
print p
# 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'))
# At this point, we have pathnames and filenames for all the
# input and output files, start reading them
######################################################################
# the ligand from the dpf
dpf_ligand = Read(ligand_pathname)[0]
class LibraryGpfWriter:
def __init__(self, gpffile, extension='pdbq', err_file="write_lib_gpf_errors",
prefix='',alltypes=None, extratypes_dict={}, verbose=0):
self.verbose = verbose
if verbose: print("self.verbose = ", verbose)
self.extratypes_dict = extratypes_dict
self.setup(gpffile)
self.alltypes = alltypes
if self.alltypes is None:
self.alltypes = self.gettypes(extension)
self.prefix = prefix
#real element, Rii, epsii
#eg {X:['Cl', 4.09, .02345]}
#WHAT errors should be captured
#self.error_file = open(err_file, 'w')
def setup(self,gpffile):
self.gpffile = gpffile
self.gpo = GridParameters()
self.gpo.read(gpffile)
if len(self.extratypes_dict):
print("update each type in extratypes here")
#????RENAME extratype in receptor and write new output file here?
def set_receptor(self, receptor_filename):
self.gpo.set_receptor(receptor_filename)
ty
def gettypes(self, extension, name=''):
typeDict = {}
key = name + '*.' + extension
ligandfilenames = glob.glob(key)
if self.verbose:
print("processing ", len(ligandfilenames), " files matching ", key)
for ligand_file in ligandfilenames:
m = Read(ligand_file)[0]
for a in m.allAtoms:
typeDict[a.autodock_element] = 1
del(m)
alltypes = list(typeDict.keys())
return alltypes
def write(self, gpo):
#set types in groups of 6 + write
outputlist = []
number_of_files = len(self.alltypes)/6 + 1
ctr = 0
last = 6
for i in range(number_of_files):
if i == number_of_files-1:
current_types = self.alltypes[ctr*6:]
elif last>len(self.alltypes):
current_types = self.alltypes[ctr*6:]
else:
current_types = self.alltypes[ctr*6:last]
gpo['types']['value'] = string.join(current_types,'')
if not gpo.receptor_stem:
gpo.receptor_stem = os.path.splitext(gpo['receptor']['value'])[0]
outputfilename = self.prefix + gpo.receptor_stem + '_'+ str(ctr) + '_library.gpf'
gpo.write(outputfilename, grid_parameter_list)
ctr = ctr + 1
last = last + 6
outputlist.append(outputfilename)
return outputlist
# 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'))
# At this point, we have pathnames and filenames for all the
# input and output files, start reading them
######################################################################
# the ligand from the dpf
dpf_ligand = Read(ligand_pathname)[0]
if not ligand_filename:
print 'gpf3_to_gpf4: ligand_filename must be specified.'
usage()
sys.exit()
if not receptor_filename:
receptor_filename = gpf3_stem + '.pdbqt'
print "gpf3_to_gpf4: using default receptor_filename:", receptor_filename
if not gpf3_filename:
print 'gpf3_to_gpf4: no gpf3_filename specified using GridParameter defaults'
#what about nucleic acids???
GPO4 = GridParameters()
if gpf3_filename:
GPO4.read(gpf3_filename)
if verbose: print 'read ', gpf3_filename
else:
if verbose: print 'using gpo defaults'
GPO4.set_ligand4(ligand_filename)
if verbose: print 'set ligand to ', ligand_filename
GPO4.set_receptor4(receptor_filename)
if verbose: print 'set receptor to ', receptor_filename
if outputfilename is None:
outputfilename = gpf3_stem + '_4.gpf'
GPO4.write4(outputfilename, grid_parameter_list4)
if verbose:
print "wrote ", outputfilename, ' using:'
for p in grid_parameter_list4:
print p
if not ligand_filename:
print 'gpf4_to_gpf3: ligand_filename must be specified.'
usage()
sys.exit()
if not receptor_filename:
receptor_filename = gpf4_stem + '.pdbqs'
print "gpf4_to_gpf3: using default receptor_filename:", receptor_filename
if not gpf4_filename:
print 'gpf4_to_gpf3: no gpf4_filename specified using GridParameter defaults'
#what about nucleic acids???
GPO3 = GridParameters()
GPO3.read4(gpf4_filename)
GPO3.read(gpf4_filename)
if verbose: print 'read ', gpf4_filename
#have to set the ligand_types
GPO3.set_ligand(ligand_filename)
#build an autogrid3 'types' string from autogrid4 ligand_types
GPO3.set_ligand_types3(GPO3['ligand_types']['value'])
if verbose: print 'set ligand to ', ligand_filename
GPO3.set_receptor(receptor_filename)
if verbose: print 'set receptor to ', receptor_filename
if outputfilename is None:
outputfilename = gpf4_stem + '_3.gpf'
GPO3.write(outputfilename, grid_parameter_list)
if verbose:
print "wrote ", outputfilename, ' using:'
for p in grid_parameter_list:
print p
class LibraryGpfWriter:
def __init__(self, gpffile, extension='pdbq', err_file="write_lib_gpf_errors",
prefix='',alltypes=None, extratypes_dict={}, verbose=0):
self.verbose = verbose
if verbose: print "self.verbose = ", verbose
self.extratypes_dict = extratypes_dict
self.setup(gpffile)
self.alltypes = alltypes
if self.alltypes is None:
self.alltypes = self.gettypes(extension)
self.prefix = prefix
#real element, Rii, epsii
#eg {X:['Cl', 4.09, .02345]}
#WHAT errors should be captured
#self.error_file = open(err_file, 'w')
def setup(self,gpffile):
self.gpffile = gpffile
self.gpo = GridParameters()
self.gpo.read(gpffile)
if len(self.extratypes_dict):
print "update each type in extratypes here"
#????RENAME extratype in receptor and write new output file here?
def set_receptor(self, receptor_filename):
self.gpo.set_receptor(receptor_filename)
ty
def gettypes(self, extension, name=''):
typeDict = {}
key = name + '*.' + extension
ligandfilenames = glob.glob(key)
if self.verbose:
print "processing ", len(ligandfilenames), " files matching ", key
for ligand_file in ligandfilenames:
m = Read(ligand_file)[0]
for a in m.allAtoms:
typeDict[a.autodock_element] = 1
del(m)
alltypes = typeDict.keys()
return alltypes
def write(self, gpo):
#set types in groups of 6 + write
outputlist = []
number_of_files = len(self.alltypes)/6 + 1
ctr = 0
last = 6
for i in range(number_of_files):
if i == number_of_files-1:
current_types = self.alltypes[ctr*6:]
elif last>len(self.alltypes):
current_types = self.alltypes[ctr*6:]
else:
current_types = self.alltypes[ctr*6:last]
gpo['types']['value'] = string.join(current_types,'')
if not gpo.receptor_stem:
gpo.receptor_stem = os.path.splitext(gpo['receptor']['value'])[0]
outputfilename = self.prefix + gpo.receptor_stem + '_'+ str(ctr) + '_library.gpf'
gpo.write(outputfilename, grid_parameter_list)
ctr = ctr + 1
last = last + 6
outputlist.append(outputfilename)
return outputlist