parser.add_argument("-o",
"--output",
help="output file name",
default='resp_charges.txt')
args = parser.parse_args()
if args.save_resp_to is None:
save_resp_to = "resp_temp_dir-dont_remove/"
else:
save_resp_to = args.save_resp_to + "/"
if os.path.exists(args.output):
raise FileExistsError("Output file exists: " + args.output)
if os.path.exists(save_resp_to):
raise FileExistsError("Output directory exists: " + save_resp_to)
molecule = run_resp(args.respin_location,
save_resp_to,
resp_type='two_stage',
esp_fn=args.esp_filename)
if args.save_resp_to is None:
shutil.rmtree(save_resp_to)
print("\nThe molecule with RESP charges is:")
for atom in molecule:
atom.print_with_charge('resp')
charges.dump_charges_to_qout(molecule, "resp", args.output)
raise FileExistsError("Output file exists: " + args.output)
if os.path.exists(save_resp_to):
raise FileExistsError("Output directory exists: " + save_resp_to)
input_type = charges_parser.input_type(args.input_charge_type)
respin1, respin2 = _get_input_files(args.respin_location, respin1_fn="",
respin2_fn="")
# Note: the molecule is taken from one of the respin files...
molecule = _read_respin(respin1)[-1]
# ... but this will throw an error if the molecule in log is not the same one
charges._get_charges(args.input_charge_type, args.input_charge_file,
input_type, molecule)
if args.dump_raw:
charges.dump_charges_to_qout(molecule, args.input_charge_type, args.dump_raw)
import sys
sys.exit(0)
if args.esp_file is not None:
try:
averaged_molecule = run_resp(
args.respin_location, save_resp_to, resp_type='unrest',
check_ivary=True, esp_fn=args.esp_file)
except Exception as e:
shutil.rmtree(save_resp_to)
raise e
if args.save_resp_to is None:
shutil.rmtree(save_resp_to)
else:
averaged_charges, ivary_list = equivalence(
"if all charges are to be scaled.",
metavar="SAVE_RESP_TO")
parser.add_argument("-o", "--output",
help="output file name",
default='resp_charges.txt')
args = parser.parse_args()
if args.save_resp_to is None:
save_resp_to = "resp_temp_dir-dont_remove/"
else:
save_resp_to = args.save_resp_to + "/"
if os.path.exists(args.output):
raise FileExistsError("Output file exists: " + args.output)
if os.path.exists(save_resp_to):
raise FileExistsError("Output directory exists: " + save_resp_to)
molecule = run_resp(args.respin_location, save_resp_to, resp_type='two_stage',
esp_fn=args.esp_filename)
if args.save_resp_to is None:
shutil.rmtree(save_resp_to)
print("\nThe molecule with RESP charges is:")
for atom in molecule:
atom.print_with_charge('resp')
charges.dump_charges_to_qout(molecule, "resp", args.output)
except Exception as e:
shutil.rmtree(save_resp_to)
raise e
print("\nOptimizing fit quality...")
if args.scale_all:
regular_args = (start_charges, molecule, esp_file.field)
reg_min_ratio, reg_min_ratio_rrms, compr_charges = minimize_ratio(
'regular', ratio_values, result, regular_args)
else:
func_args = (start_charges, esp_file.field, args.respin_location,
min_resp_calc_dir, args.esp_filename, True)
try:
min_ratio, min_ratio_rrms, compr_charges = minimize_ratio(
'heavy', ratio_values, result, func_args)
except Exception as e:
shutil.rmtree(save_resp_to)
raise e
shutil.rmtree(min_resp_calc_dir)
if not args.scale_all and args.save_resp_to is None:
shutil.rmtree(save_resp_to)
# TODO: plotting requires information about other charges. This would make this
# script much bigger or require input from other scripts.
charges._update_molecule_with_charges(molecule, compr_charges, "compr")
for atom in molecule:
atom.print_with_charge("compr")
charges.dump_charges_to_qout(molecule, "compr", args.output)
except Exception as e:
shutil.rmtree(save_resp_to)
raise e
print("\nOptimizing fit quality...")
if args.scale_all:
regular_args = (start_charges, molecule, esp_file.field)
reg_min_ratio, reg_min_ratio_rrms, compr_charges = minimize_ratio(
'regular', ratio_values, result, regular_args)
else:
func_args = (start_charges, esp_file.field, args.respin_location,
min_resp_calc_dir, args.esp_filename, True)
try:
min_ratio, min_ratio_rrms, compr_charges = minimize_ratio(
'heavy', ratio_values, result, func_args)
except Exception as e:
shutil.rmtree(save_resp_to)
raise e
shutil.rmtree(min_resp_calc_dir)
if not args.scale_all and args.save_resp_to is None:
shutil.rmtree(save_resp_to)
# TODO: plotting requires information about other charges. This would make this
# script much bigger or require input from other scripts.
charges._update_molecule_with_charges(molecule, compr_charges, "compr")
for atom in molecule:
atom.print_with_charge("compr")
charges.dump_charges_to_qout(molecule, "compr", args.output)
if os.path.exists(save_resp_to):
raise FileExistsError("Output directory exists: " + save_resp_to)
input_type = charges_parser.input_type(args.input_charge_type)
respin1, respin2 = _get_input_files(args.respin_location,
respin1_fn="",
respin2_fn="")
# Note: the molecule is taken from one of the respin files...
molecule = _read_respin(respin1)[-1]
# ... but this will throw an error if the molecule in log is not the same one
charges._get_charges(args.input_charge_type, args.input_charge_file,
input_type, molecule)
if args.dump_raw:
charges.dump_charges_to_qout(molecule, args.input_charge_type,
args.dump_raw)
import sys
sys.exit(0)
if args.esp_file is not None:
try:
averaged_molecule = run_resp(args.respin_location,
save_resp_to,
resp_type='unrest',
check_ivary=True,
esp_fn=args.esp_file)
except Exception as e:
shutil.rmtree(save_resp_to)
raise e
if args.save_resp_to is None:
shutil.rmtree(save_resp_to)
