def __init__(self, verbose=None):
self.verbose = verbose
self.dpo = DockingParameters()
# @@ ASSUMPTIONS: WCG conventions for dpf and gpf names @@
# @@ 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)
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
def setup(self, dpffile):
self.dpffile = dpffile
self.dpo = DockingParameters()
self.dpo.read(dpffile)
