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)
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(
charge_type.upper()))
print("RRMS: {0:.5f}".format(equiv_charge_rrms))
for atom in g.molecule:
atom.print_with_charge(charge_type + '_equiv')
print("\nChecking differences between raw and equivalenced charges ...")
print(compare_charges(charge_type, charge_type + '_equiv', g.molecule))
print("\nThe molecule with {0} charges:".format(esp_charge_type.upper()))
print("RRMS: {0:.5f}".format(esp_charge_rrms))
for atom in g.molecule:
atom.print_with_charge(esp_charge_type)
print(
"\nThe molecule with equivalenced {0} charges (unrestrained RESP):".format(
esp_charge_type.upper()))
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))
print("RRMS: {0:.5f}".format(charge_rrms))
print("RMSV: {0:.5f}".format(charge_rms / charge_rrms))
for atom in g.molecule:
atom.print_with_charge(esp_charge_type)
print("\nThe molecule with equivalenced {0} charges (unrestrained RESP):".
format(esp_charge_type.upper()))
print(" RMS: {0:.5f}".format(resp_rms))
print("RRMS: {0:.5f}".format(resp_rrms))
print("RMSV: {0:.5f}".format(resp_rms / resp_rrms))
for atom in esp_equiv_molecule:
atom.print_with_charge('resp')
print("\nChecking differences between raw and equivalenced charges ...")
print(
charges.compare_charges(esp_charge_type, 'resp', g.molecule,
esp_equiv_molecule))
print("\nThe molecule with equivalenced {0} charges (unrestrained RESP) "
"evaluated on the {1} grid:".format(alt_esp_charge_type.upper(),
esp_charge_type.upper()))
print(" RMS: {0:.5f}".format(alt_resp_rms))
print("RRMS: {0:.5f}".format(alt_resp_rrms))
print("RMSV: {0:.5f}".format(alt_resp_rms / alt_resp_rrms))
print(
"Percentage increase over equivalenced {0} charges: {1:.2f} %".format(
esp_charge_type.upper(),
100 * (alt_resp_rrms - resp_rrms) / resp_rrms))
for atom in alt_esp_equiv_molecule:
atom.print_with_charge('resp')
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(
charge_type.upper()))
print("RRMS: {0:.5f}".format(equiv_charge_rrms))
for atom in g.molecule:
atom.print_with_charge(charge_type + '_equiv')
print("\nChecking differences between raw and equivalenced charges ...")
print(compare_charges(charge_type, charge_type + '_equiv', g.molecule))
print("\nThe molecule with {0} charges:".format(esp_charge_type.upper()))
print("RRMS: {0:.5f}".format(esp_charge_rrms))
for atom in g.molecule:
atom.print_with_charge(esp_charge_type)
print("\nThe molecule with equivalenced {0} charges (unrestrained RESP):"
.format(esp_charge_type.upper()))
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))
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)
