atom.print_with_charge('resp')
print("\nChecking differences between raw and equivalenced charges ...")
print(compare_charges(esp_charge_type, 'resp', g.molecule, esp_equiv_molecule))
start_charges = [atom.charges[charge_type + '_equiv'] for atom in g.molecule]
num = 50
ratio_limits = (0, 1.5)
print("\nEvaluating HEAVY ratios. This may take a while.")
heavy_args = (g.field, path, resp_output_path, esp_fn, False)
heavy_result, indicator_charge, ratio_values = resp.eval_ratios(
'heavy',
ratio_limits,
start_charges,
num,
indicator_label,
heavy_args,
first_verbose=True)
if zero_net_charge:
# Scaling all charges is only possible with neutral molecules as
# otherwise in this case there's no free hydrogens to compensate as in
# the 'heavy_only' version
print("\nEvaluating REGULAR ratios. This may take a while.")
regular_args = (g.molecule, g.field)
# Note that indicator charge and ratio values are re-used from the heavy
# version. This is fine for ratio_values. For indicator_charge it's fine as
# long as the indicator charge is on a heavy atom. TODO
result = resp.eval_ratios('regular',
ratio_limits,
print("RRMS: {0:.5f}".format(resp_charge_rrms))
for atom in esp_equiv_molecule:
atom.print_with_charge('resp')
print("\nChecking differences between raw and equivalenced charges ...")
print(compare_charges(esp_charge_type, 'resp', g.molecule, esp_equiv_molecule))
start_charges = [atom.charges[charge_type + '_equiv'] for atom in g.molecule]
num = 50
ratio_limits = (0, 1.5)
print("\nEvaluating HEAVY ratios. This may take a while.")
heavy_args = (g.field, path, resp_output_path, esp_fn, False)
heavy_result, indicator_charge, ratio_values = resp.eval_ratios(
'heavy', ratio_limits, start_charges, num, indicator_label, heavy_args,
first_verbose=True)
if zero_net_charge:
# Scaling all charges is only possible with neutral molecules as
# otherwise in this case there's no free hydrogens to compensate as in
# the 'heavy_only' version
print("\nEvaluating REGULAR ratios. This may take a while.")
regular_args = (g.molecule, g.field)
# Note that indicator charge and ratio values are re-used from the heavy
# version. This is fine for ratio_values. For indicator_charge it's fine as
# long as the indicator charge is on a heavy atom. TODO
result = resp.eval_ratios('regular', ratio_limits, start_charges, num,
indicator_label, regular_args,
first_verbose=True)[0]
# For now a patch:
args.indicator = 1
input_type = charges_parser.input_type(args.input_charge_type)
charges._get_charges(args.input_charge_type, args.input_charge_file,
input_type, molecule)
start_charges = [atom.charges[args.input_charge_type] for atom in molecule]
print("\nEvaluating ratios...")
if args.scale_all:
regular_args = (molecule, esp_file.field)
result, indicator_charge, ratio_values = eval_ratios('regular',
args.limits,
start_charges,
args.sampling,
args.indicator,
regular_args,
first_verbose=True)
else:
func_args = (esp_file.field, args.respin_location, save_resp_to,
args.esp_filename, False)
try:
result, indicator_charge, ratio_values = eval_ratios(
'heavy',
args.limits,
start_charges,
args.sampling,
args.indicator,
func_args,
first_verbose=True)
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
heavy_min_ratio, heavy_min_ratio_rrms, compr_charges = resp.minimize_ratio(
'heavy', ratio_values, heavy_result, heavy_args)
shutil.rmtree(opt_output_path)
# Presentation: 3D
if False:
fig = plt.figure()
ax = fig.gca(projection='3d')
# raise ValueError("Indicator label {0} requested but the molecule has "
# "only {1} atoms.".format(args.indicator, len(molecule)))
# For now a patch:
args.indicator = 1
input_type = charges_parser.input_type(args.input_charge_type)
charges._get_charges(args.input_charge_type, args.input_charge_file,
input_type, molecule)
start_charges = [atom.charges[args.input_charge_type] for atom in molecule]
print("\nEvaluating ratios...")
if args.scale_all:
regular_args = (molecule, esp_file.field)
result, indicator_charge, ratio_values = eval_ratios(
'regular', args.limits, start_charges, args.sampling, args.indicator,
regular_args, first_verbose=True)
else:
func_args = (esp_file.field, args.respin_location, save_resp_to,
args.esp_filename, False)
try:
result, indicator_charge, ratio_values = eval_ratios(
'heavy', args.limits, start_charges, args.sampling, args.indicator,
func_args, first_verbose=True)
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)
