usage()
sys.exit()
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:')
if o in ('-h', '--'):
usage()
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:
#
# 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
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")
