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(
molecule, args.input_charge_type, args.respin_location, respin1_fn="",
respin2_fn="")
# Check equivalence information from respin:
_check_ivary(True, molecule, ivary_list)
# The new molecule and name 'resp' is for consistency with the
# equivalencing code above
averaged_molecule = copy.deepcopy(molecule)
charges._update_molecule_with_charges(averaged_molecule, averaged_charges,
"resp")
message = charges.compare_charges(args.input_charge_type, "resp", molecule,
averaged_molecule, thresh=args.thresh)
thresh_message = " vary by more than the threshold of " + str(args.thresh)
if message:
print("\nThe following charges" + thresh_message)
print(message)
else:
print("\nNo charges" + thresh_message)
charges.dump_charges_to_qout(averaged_molecule, "resp", args.output)
dist = ed_cube.field.distance_transform(isoval)
exclusion_dist = 0
check_ivary = True
for charge_type in ['mk', 'chelpg']:
esp_equiv_molecule = resp.run_resp(path,
output_path + 'unrest_' + charge_type,
resp_type='unrest',
esp_fn=molecule_name + '_' +
charge_type + '.esp',
check_ivary=check_ivary)
check_ivary = False
charges = [atom.charges['resp'] for atom in esp_equiv_molecule]
_update_molecule_with_charges(molecule, charges, charge_type + '_equiv')
pickled_fn = path + "compromise_nbo_and_{0}/molecule.p".format(charge_type)
with open(pickled_fn, "rb") as f:
pickled_mol = pickle.load(f)
charges = [atom.charges[charge_type] for atom in pickled_mol]
_update_molecule_with_charges(molecule, charges, 'compr_' + charge_type)
charges = [atom.charges['nbo_equiv'] for atom in pickled_mol]
_update_molecule_with_charges(molecule, charges, 'nbo_equiv')
all_charges = [
'chelpg_equiv', 'mk_equiv', 'nbo_equiv', 'compr_chelpg', 'compr_mk'
]
log_fn = path + molecule_name + "_" + charge_type + ".log"
esp_log_fn = path + molecule_name + "_" + esp_charge_type + ".log"
g = resp_helpers.G09_esp(path + esp_fn)
# Both the Gaussian ESP fitting methods and other charge assignment methods may
# not yield equivalent charges. As equivalent charges make more sense for force
# field development, they will be used. The ESP charges are equivalenced by
# performing unrestrained RESP, which will be used as a reference for the fit
# minimum. Charges from the other method will be equivalenced manually by my
# averaging function `resp.equivalence`. They will be scaled to obtain
# different ratio charges. All the charges are calculated and printed at the
# start for reference.
update_with_charges(esp_charge_type, esp_log_fn, g.molecule)
update_with_charges(charge_type, log_fn, g.molecule)
equiv_charges = resp.equivalence(g.molecule, charge_type, path)[0]
_update_molecule_with_charges(g.molecule, equiv_charges,
charge_type + '_equiv')
print("\nRunning unrestrained RESP to fit ESP with equivalence:")
esp_equiv_molecule = resp.run_resp(path,
resp_output_path + 'unrest',
resp_type='unrest',
esp_fn=esp_fn)
charge_rrms = rms_and_rep(g.field, g.molecule, charge_type)[1]
equiv_charge_rrms = rms_and_rep(g.field, g.molecule, charge_type + '_equiv')[1]
esp_charge_rrms = rms_and_rep(g.field, g.molecule, esp_charge_type)[1]
resp_charge_rrms = rms_and_rep(g.field, esp_equiv_molecule, 'resp')[1]
print("\nThe molecule with {0} charges:".format(charge_type.upper()))
print("RRMS: {0:.5f}".format(charge_rrms))
for atom in g.molecule:
atom.print_with_charge(charge_type)
log_fn = path + molecule_name + "_" + charge_type + ".log"
esp_log_fn = path + molecule_name + "_" + esp_charge_type + ".log"
g = resp_helpers.G09_esp(path + esp_fn)
# Both the Gaussian ESP fitting methods and other charge assignment methods may
# not yield equivalent charges. As equivalent charges make more sense for force
# field development, they will be used. The ESP charges are equivalenced by
# performing unrestrained RESP, which will be used as a reference for the fit
# minimum. Charges from the other method will be equivalenced manually by my
# averaging function `resp.equivalence`. They will be scaled to obtain
# different ratio charges. All the charges are calculated and printed at the
# start for reference.
update_with_charges(esp_charge_type, esp_log_fn, g.molecule)
update_with_charges(charge_type, log_fn, g.molecule)
equiv_charges = resp.equivalence(g.molecule, charge_type, path)[0]
_update_molecule_with_charges(g.molecule, equiv_charges, charge_type+'_equiv')
print("\nRunning unrestrained RESP to fit ESP with equivalence:")
esp_equiv_molecule = resp.run_resp(
path, resp_output_path + 'unrest', resp_type='unrest', esp_fn=esp_fn)
charge_rrms = rms_and_rep(g.field, g.molecule, charge_type)[1]
equiv_charge_rrms = rms_and_rep(g.field, g.molecule, charge_type + '_equiv')[1]
esp_charge_rrms = rms_and_rep(g.field, g.molecule, esp_charge_type)[1]
resp_charge_rrms = rms_and_rep(g.field, esp_equiv_molecule, 'resp')[1]
print("\nThe molecule with {0} charges:".format(charge_type.upper()))
print("RRMS: {0:.5f}".format(charge_rrms))
for atom in g.molecule:
atom.print_with_charge(charge_type)
print("\nThe molecule with equivalenced {0} charges:".format(
if True:
with open(output_path + "result.p", "rb") as f:
read_result = pickle.load(f)
rel_rrms = [
100 * (elem - read_result.resp_rrms) / read_result.resp_rrms
for elem in read_result.rrms
]
rel_rrms = np.array(rel_rrms)
rel_rrms.resize([read_result.sampling_num, read_result.sampling_num])
# Non-ESP charge and its minimized ratio
charges.update_with_charges(charge_type, charge_log_fn, molecule)
equiv_start_charges = resp.equivalence(molecule, charge_type, path)[0]
charge_type += '_equiv'
charges._update_molecule_with_charges(molecule, equiv_start_charges,
charge_type)
os.mkdir(opt_output_path)
# Scan roughly various ratios to find bracket for minimization
print("\nScanning roughly various ratios. This shouldn't take long.")
heavy_args = (g.field, path, opt_output_path, esp_fn, False)
heavy_result, indicator_charge, ratio_values = resp.eval_ratios(
'heavy', (0, 2),
equiv_start_charges,
10,
vary_label1,
heavy_args,
first_verbose=True)
# Minimization
print("\nStarting minimization of charge ratio.")
heavy_args = (equiv_start_charges, g.field, path, opt_output_path, esp_fn,
True) # True for optimization
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)
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(molecule,
args.input_charge_type,
args.respin_location,
respin1_fn="",
respin2_fn="")
# Check equivalence information from respin:
_check_ivary(True, molecule, ivary_list)
# The new molecule and name 'resp' is for consistency with the
# equivalencing code above
averaged_molecule = copy.deepcopy(molecule)
charges._update_molecule_with_charges(averaged_molecule, averaged_charges,
"resp")
message = charges.compare_charges(args.input_charge_type,
"resp",
molecule,
averaged_molecule,
thresh=args.thresh)
thresh_message = " vary by more than the threshold of " + str(args.thresh)
if message:
print("\nThe following charges" + thresh_message)
print(message)
else:
print("\nNo charges" + thresh_message)
charges.dump_charges_to_qout(averaged_molecule, "resp", args.output)