filetype = args.template_file[-4:]
if filetype not in ['.cub', '.esp']:
print("The template file must have the extension .cub or .esp")
sys.exit(1)
if os.path.exists(args.output + filetype):
raise FileExistsError("Output file exists: " + args.output + filetype)
if filetype == '.cub':
template_cube = cube_helpers.Cube(args.template_file)
molecule = template_cube.molecule
elif filetype == '.esp':
esp_file = resp_helpers.G09_esp(args.template_file)
molecule = esp_file.molecule
input_type = charges_parser.input_type(args.input_charge_type)
charges._get_charges(args.input_charge_type, args.input_charge_file,
input_type, molecule)
if filetype == '.cub':
rep_field = calc_grid_field(molecule, template_cube.field.grid, 'rep_esp',
[args.input_charge_type])[0]
rep_field.write_cube(args.output + '.cub', molecule,
args.input_charge_type)
elif filetype == '.esp':
rep_field = calc_non_grid_field(molecule, esp_file.field.points, 'rep_esp',
[args.input_charge_type])[0]
rep_field.write_to_file(args.output + '.esp', molecule)
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)
# 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)
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)
filetype = args.template_file[-4:]
if filetype not in ['.cub', '.esp']:
print("The template file must have the extension .cub or .esp")
sys.exit(1)
if os.path.exists(args.output + filetype):
raise FileExistsError("Output file exists: " + args.output + filetype)
if filetype == '.cub':
template_cube = cube_helpers.Cube(args.template_file)
molecule = template_cube.molecule
elif filetype == '.esp':
esp_file = resp_helpers.G09_esp(args.template_file)
molecule = esp_file.molecule
input_type = charges_parser.input_type(args.input_charge_type)
charges._get_charges(args.input_charge_type, args.input_charge_file,
input_type, molecule)
if filetype == '.cub':
rep_field = calc_grid_field(molecule, template_cube.field.grid, 'rep_esp',
[args.input_charge_type])[0]
rep_field.write_cube(args.output + '.cub', molecule,
args.input_charge_type)
elif filetype == '.esp':
rep_field = calc_non_grid_field(molecule, esp_file.field.points, 'rep_esp',
[args.input_charge_type])[0]
rep_field.write_to_file(args.output + '.esp', molecule)
atom = cube.molecule[0]
grid = cube.field.grid
# Write the field as a new cube
out_cube_path = "tests/temp_test.cub"
while True:
try:
cube.field.write_cube(out_cube_path, cube.molecule, 'cube')
break
except FileExistsError:
os.remove(out_cube_path)
# This is getting complicated so these initialization lines should be a
# separate test. That likely requires a custom test suite so that they're only
# executed once and before the others.
dist_field = calc_grid_field(cube.molecule, grid, 'dist')
repESP_field = calc_grid_field(cube.molecule, grid, 'rep_esp', ['cube'])[0]
# Values calculated with an independent ad-hoc script
dist_result = [
0.1, 0.3, 0.7, 0.316227766, 0.424264068, 0.761577310, 0.608276253,
0.670820393, 0.921954445, 0.223606797, 0.360555127, 0.728010988,
0.374165738, 0.469041575, 0.787400787, 0.640312423, 0.7, 0.943398113,
0.412310562, 0.5, 0.806225774, 0.509901951, 0.583095189, 0.860232526,
0.728010988, 0.781024967, 1.004987562
]
# Values above in Bohr, convert to Angstrom
dist_result = [angstrom_per_bohr * elem for elem in dist_result]
# Isovalue selected so that only two points fall above it
ed_isoval = 7.01e-07
edt_field = cube.field.distance_transform(ed_isoval)
atom = cube.molecule[0]
grid = cube.field.grid
# Write the field as a new cube
out_cube_path = "tests/temp_test.cub"
while True:
try:
cube.field.write_cube(out_cube_path, cube.molecule, 'cube')
break
except FileExistsError:
os.remove(out_cube_path)
# This is getting complicated so these initialization lines should be a
# separate test. That likely requires a custom test suite so that they're only
# executed once and before the others.
dist_field = calc_grid_field(cube.molecule, grid, 'dist')
repESP_field = calc_grid_field(cube.molecule, grid, 'rep_esp', ['cube'])[0]
# Values calculated with an independent ad-hoc script
dist_result = [0.1, 0.3, 0.7, 0.316227766, 0.424264068, 0.761577310,
0.608276253, 0.670820393, 0.921954445, 0.223606797, 0.360555127,
0.728010988, 0.374165738, 0.469041575, 0.787400787, 0.640312423,
0.7, 0.943398113, 0.412310562, 0.5, 0.806225774, 0.509901951,
0.583095189, 0.860232526, 0.728010988, 0.781024967, 1.004987562]
# Values above in Bohr, convert to Angstrom
dist_result = [angstrom_per_bohr*elem for elem in dist_result]
# Isovalue selected so that only two points fall above it
ed_isoval = 7.01e-07
edt_field = cube.field.distance_transform(ed_isoval)
# This was calculated with the aforementioned script as the smaller elements of
# the distance matrices from those two points.
