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,
default=[-0.0045, 0.011])
diff_field = difference(g.field, rep_esp_field)
error_color_span = check_color_span(diff_field.values,
error_color_span,
default=[-0.0012, 0.019])
graphs.plot_points(
g.field, 2, title=calc, molecule=g.molecule,
plane_eqn=graphs.plane_through_atoms(g.molecule, 1, 2, 3),
dist_thresh=0.5, axes_limits=[(-5, 5)]*2, color_span=color_span,
save_to=path + calc[-6:] + '_V.pdf')
graphs.plot_points(
diff_field, 2, title=calc + " Errors", molecule=g.molecule,
plane_eqn=graphs.plane_through_atoms(g.molecule, 1, 2, 3),
dist_thresh=0.5, axes_limits=[(-5, 5)]*2,
color_span=error_color_span, save_to=path + calc[-6:] + '_E.pdf')
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)
# Write cube
diff.write_cube(charge_dir + '/diff.cub', molecule, charge_type)
# and with elements within the ED isosurface excluded
diff_filtered = copy.deepcopy(diff)
diff_filtered.check_nans = False
_dist, diff_filtered.values = filter_by_dist(exclusion_dist, dist, diff)
diff_filtered.write_cube(charge_dir + '/diff_filtered-iso_' + str(isoval) +
'.cub', molecule, charge_type)
rep_filtered = copy.deepcopy(rep)
rep_filtered.check_nans = False
_dist, rep_filtered.values = filter_by_dist(exclusion_dist, dist, rep)
rms_val, rrms_val = rms_and_rrms(esp_cube.field, rep_filtered,
ignore_nans=True)
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,
default=[-0.0045, 0.011])
diff_field = difference(g.field, rep_esp_field)
error_color_span = check_color_span(diff_field.values,
error_color_span,
default=[-0.0012, 0.019])
graphs.plot_points(
g.field, 2, title=calc, molecule=g.molecule,
plane_eqn=graphs.plane_through_atoms(g.molecule, 1, 2, 3),
dist_thresh=0.5, axes_limits=[(-5, 5)]*2, color_span=color_span,
save_to=path + calc[-6:] + '_V.pdf')
graphs.plot_points(
diff_field, 2, title=calc + " Errors", molecule=g.molecule,
plane_eqn=graphs.plane_through_atoms(g.molecule, 1, 2, 3),
dist_thresh=0.5, axes_limits=[(-5, 5)]*2,
color_span=error_color_span, save_to=path + calc[-6:] + '_E.pdf')
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'
]
for charge_type in all_charges:
print('\n', charge_type.upper())
for atom in molecule:
atom.print_with_charge(charge_type)
sys.stdout.flush()
rep = calc_grid_field(molecule, esp_cube.field.grid, 'rep_esp',
[charge_type])[0]
# Change details of calculating difference here (absolute, relative)
diff = difference(esp_cube.field, rep)
# Write cube
diff.write_cube(output_path + charge_type + '_diff.cub', molecule,
charge_type)
# and with elements within the ED isosurface excluded
diff_filtered = copy.deepcopy(diff)
diff_filtered.check_nans = False
_dist, diff_filtered.values = filter_by_dist(exclusion_dist, dist, diff)
diff_filtered.write_cube(
output_path + charge_type + '_diff_filtered-iso_' + str(isoval) +
'.cub', molecule, charge_type)
ed_cube, isoval, excl_dist = args.exclude
ed_cube = Cube(ed_cube)
isoval = float(isoval)
excl_dist = float(excl_dist)
elif filetype == '.esp':
esp_file1 = resp_helpers.G09_esp(args.field1)
esp_file2 = resp_helpers.G09_esp(args.field2)
# TODO: Molecules not cross-checked. They should be because .esp files in
# Antechamber format produced by repESP will have no identitity info. This
# is fine for now for the difference (actual - reproduced), because actual
# will be Gaussian .esp but not the other way round.
molecule = esp_file1.molecule
field1 = esp_file1.field
field2 = esp_file2.field
diff = difference(field1, field2, relative=args.relative,
absolute=args.absolute)
if filetype == '.cub':
if args.exclude:
diff.check_nans = False
dist = ed_cube.field.distance_transform(isoval)
assign_val = 0 if args.exclusion_as_zero else None
_dist, diff.values = filter_by_dist(excl_dist, dist, diff,
assign_val=assign_val)
diff.write_cube(args.output + '.cub', molecule)
elif filetype == '.esp':
diff.write_to_file(args.output + '.esp', molecule)