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)
# 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(
charge_type.upper()))
print("RRMS: {0:.5f}".format(equiv_charge_rrms))
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(
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)
charge_type, ext)
esp_cube = cube_helpers.Cube(path + molecule_name + '_esp.cub')
ed_cube = cube_helpers.Cube(path + molecule_name + '_den.cub')
molecule = esp_cube.molecule
isoval = 0.01
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]
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(
charge_type.upper()))
print("RRMS: {0:.5f}".format(equiv_charge_rrms))
for atom in g.molecule:
@staticmethod
def get_meshgrid(xlim1, xlim2, sampling_num):
charges1 = linspace(xlim1[0], xlim1[1], num=sampling_num)
charges2 = linspace(xlim2[0], xlim2[1], num=sampling_num)
return meshgrid(charges1, charges2)
# CALCULATIONS COMMON TO 1 AND 2D VARIATIONS
if True:
os.mkdir(output_path)
os.mkdir(resp_output_path)
levels = [1, 5, 10, 20, 30, 50, 100]
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)
# Equivalence alternative charge as well (i.e. unrest RESP on its own grid)
alt_esp_equiv_molecule = resp.run_resp(path,
resp_output_path + 'alt_unrest',
resp_type='unrest',
esp_fn=alt_esp_fn,
check_ivary=False)
charges.update_with_charges(esp_charge_type, log_fn, g.molecule)
# This should actually be called esp_charge_rms
charge_rms, charge_rrms = rms_and_rep(g.field, g.molecule,
esp_charge_type)[:2]
resp_rms, resp_rrms = rms_and_rep(g.field, esp_equiv_molecule, 'resp')[:2]
# Note that, crucially, the equivalenced alternative charges are evaluated
# on the same grid as the original charges, i.e. `g.field`
"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)
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(molecule,
args.input_charge_type,
args.respin_location,
respin1_fn="",
respin2_fn="")
# Check equivalence information from respin:
_check_ivary(True, molecule, ivary_list)