sys.exit(1)
if filetype == '.cub':
g = cube_helpers.Cube(args.points_file)
elif filetype == '.esp':
g = resp_helpers.G09_esp(args.points_file)
# TODO: The colour span is calculated based on all values, but if only a slice
# is plotted, the shown points may occupy only a narrow range.
if args.color_range:
color_span = args.color_range
elif args.sym_color_range:
color_limit = max(abs(np.nanmin(g.field.get_values())),
abs(np.nanmax(g.field.get_values())))
color_span = [-color_limit, color_limit]
else:
color_span = [min(g.field.get_values()), max(g.field.get_values())]
if args.slice_atoms:
plane_eqn = graphs.plane_through_atoms(g.molecule, *args.slice_atoms)
else:
plane_eqn = args.slice_eqn
graphs.plot_points(
g.field, args.dimension, molecule=g.molecule,
plane_eqn=plane_eqn,
dist_thresh=args.slice_dist,
axes_limits=[args.limits]*args.dimension,
color_span=color_span,
save_to=args.output)
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')
save_to = path + "RMS.pdf"
calc_plot(calcs, rms_list, charge_type.upper() + " RMS value",
set_lim=True, save_to=save_to)
for atom in g.molecule:
save_to = path + atom.atomic_number + str(atom.label) + "_charge.pdf"
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')
save_to = path + "RMS.pdf"
calc_plot(calcs, rms_list, charge_type.upper() + " RMS value",
set_lim=True, save_to=save_to)
for atom in g.molecule:
save_to = path + atom.identity + str(atom.label) + "_charge.pdf"
