# color_limit = max(abs(np.nanmin(esp_values)), abs(np.nanmax(esp_values)))
# color_span = [-color_limit, color_limit]
# Note that the y-axis is not set for different charge_types! If this is
# desired behaviour, it could be set in a similar manner here.
for charge_type in charge_types.keys():
charge_dir = output_path + charge_type
# raises OSError if directory exists
os.mkdir(charge_dir)
if charge_types[charge_type][0] in ['.', '_']:
filename = path + molecule_name + charge_types[charge_type]
else:
filename = path + charge_types[charge_type]
update_with_charges(charge_type, filename, molecule)
print("\n{0} charges:".format(charge_type.upper()))
for atom in molecule:
atom.print_with_charge(charge_type)
# The same but to file (would be better with my Tee class from featsel)
with open(charge_dir + '/charges.txt', 'w') as f:
for atom in esp_cube.molecule:
atom.print_with_charge(charge_type, f=f)
# This is costly but was designed to be easy for many charge types, so
# should be moved outside of the loop
rep = calc_grid_field(esp_cube.molecule, esp_cube.field.grid, 'rep_esp',
[charge_type])[0]
# Change details of calculating difference here (absolute, relative)
diff = difference(esp_cube.field, rep)
with open(path + "fit_points.p", 'wb') as f:
pickle.dump([elem.filename for elem in calcs], f)
# PART 2 --- run when the Gaussian calculations have been completed
if False:
with open(path + "fit_points.p", 'rb') as f:
calcs = pickle.load(f)
rms_list = []
charges_dict = {}
color_span = []
error_color_span = []
for calc in calcs:
g = resp_helpers.G09_esp(path + calc + '.esp')
charges.update_with_charges(charge_type, path + calc + '.log',
g.molecule)
with open(path + calc + "-charges.txt", "a") as fc:
for atom in g.molecule:
atom.print_with_charge(charge_type, fc)
if atom.label in charges_dict:
charges_dict[atom.label].append(atom.charges[charge_type])
else:
charges_dict[atom.label] = [atom.charges[charge_type]]
min_rms, min_rrms, rep_esp_field = rms_and_rep(g.field, g.molecule,
charge_type)
rms_list.append(min_rms)
print("\n", min_rms, file=fc)
# Default given as extremal values of methane CHelpG
color_span = check_color_span(g.field.values, color_span,
os.mkdir(resp_output_path)
os.mkdir(min_resp_output_path)
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]
os.mkdir(resp_output_path)
os.mkdir(min_resp_output_path)
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:
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`
alt_resp_rms, alt_resp_rrms = rms_and_rep(g.field, alt_esp_equiv_molecule,
'resp')[:2]
print("\nThe molecule with {0} charges:".format(esp_charge_type.upper()))
print(" RMS: {0:.5f}".format(charge_rms))
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)
with open(path + "fit_points.p", 'wb') as f:
pickle.dump([elem.filename for elem in calcs], f)
# PART 2 --- run when the Gaussian calculations have been completed
if False:
with open(path + "fit_points.p", 'rb') as f:
calcs = pickle.load(f)
rms_list = []
charges_dict = {}
color_span = []
error_color_span = []
for calc in calcs:
g = resp_helpers.G09_esp(path + calc + '.esp')
charges.update_with_charges(charge_type, path + calc + '.log',
g.molecule)
with open(path + calc + "-charges.txt", "a") as fc:
for atom in g.molecule:
atom.print_with_charge(charge_type, fc)
if atom.label in charges_dict:
charges_dict[atom.label].append(atom.charges[charge_type])
else:
charges_dict[atom.label] = [atom.charges[charge_type]]
min_rms, min_rrms, rep_esp_field = rms_and_rep(g.field, g.molecule,
charge_type)
rms_list.append(min_rms)
print("\n", min_rms, file=fc)
# Default given as extremal values of methane CHelpG
color_span = check_color_span(g.field.values, color_span,
# color_limit = max(abs(np.nanmin(esp_values)), abs(np.nanmax(esp_values)))
# color_span = [-color_limit, color_limit]
# Note that the y-axis is not set for different charge_types! If this is
# desired behaviour, it could be set in a similar manner here.
for charge_type in charge_types.keys():
charge_dir = output_path + charge_type
# raises OSError if directory exists
os.mkdir(charge_dir)
if charge_types[charge_type][0] in ['.', '_']:
filename = path + molecule_name + charge_types[charge_type]
else:
filename = path + charge_types[charge_type]
update_with_charges(charge_type, filename, molecule)
print("\n{0} charges:".format(charge_type.upper()))
for atom in molecule:
atom.print_with_charge(charge_type)
# The same but to file (would be better with my Tee class from featsel)
with open(charge_dir + '/charges.txt', 'w') as f:
for atom in esp_cube.molecule:
atom.print_with_charge(charge_type, f=f)
# This is costly but was designed to be easy for many charge types, so
# should be moved outside of the loop
rep = calc_grid_field(esp_cube.molecule, esp_cube.field.grid, 'rep_esp',
[charge_type])[0]
# Change details of calculating difference here (absolute, relative)
diff = difference(esp_cube.field, rep)