def test_example08(self):
nice_measures = [[1.976, 3.699], [6.955, 0.602]]
molecules, options = classic_inputs.read_old_input(
'data/shape/example08.dat')
central_atom = options['%central_atom']
reference_polyhedron = []
if options['%labels'] != 0:
for number in options['%labels']:
if int(number) == 0:
for ref in file_io.get_geometry_from_file_ref(
'data/shape/example08.ref', read_multiple=True):
reference_polyhedron.append(ref)
else:
reference_polyhedron.append(
shape.tools.get_shape_label(int(number),
options['%n_atoms']))
results = [[
shape.Shape(molecule).measure(reference_polyhedron[0],
central_atom=central_atom)
for molecule in molecules
],
[
shape.Shape(molecule).measure(reference_polyhedron[1],
central_atom=central_atom)
for molecule in molecules
]]
calculated_results = np.column_stack((results[0], results[1]))
self.assertTrue(
np.allclose(nice_measures, calculated_results, atol=1e-2))
def test_example05(self):
nice_gen_coord = [84., 84., 25.4, 79.1, 23.7, 25., 54.6]
nice_measures = [[12.011, 0.954], [12.012, 0.957], [1.142, 11.245],
[10.707, 1.236], [0.993, 12.826], [1.105, 11.783],
[5.203, 5.085]]
nice_dev_path = [7.2, 7.2, 6.5, 5.5, 10.6, 8.1, 8.6]
nice_path_coordinates = np.array([[0., 16.737], [0.035, 15.355],
[0.144, 14.002], [0.329, 12.681],
[0.593, 11.398], [0.94, 10.158],
[1.371, 8.966], [1.89, 7.828],
[2.497, 6.748], [3.195, 5.732],
[3.984, 4.785], [4.865, 3.911],
[5.837, 3.116], [6.901, 2.403],
[8.055, 1.777], [9.298, 1.241],
[10.626, 0.798], [12.038, 0.45],
[13.53, 0.201], [15.097, 0.05],
[16.737, 0.]])
molecules, options = classic_inputs.read_old_input(
'data/shape/example05.dat')
reference_polyhedron = []
for number in options['%labels']:
reference_polyhedron.append(
shape.tools.get_shape_label(int(number), options['%n_atoms']))
results = [[
shape.Shape(molecule).measure(
reference_polyhedron[0], central_atom=options['%central_atom'])
for molecule in molecules
],
[
shape.Shape(molecule).measure(
reference_polyhedron[1],
central_atom=options['%central_atom'])
for molecule in molecules
]]
dev_path = [
molecule.get_path_deviation(reference_polyhedron[0],
reference_polyhedron[1],
central_atom=options['%central_atom'])
for molecule in molecules
]
gen_coord = [
molecule.get_generalized_coordinate(
reference_polyhedron[0],
reference_polyhedron[1],
central_atom=options['%central_atom'])
for molecule in molecules
]
map = maps.get_shape_map(reference_polyhedron[0],
reference_polyhedron[1],
num_points=20)
self.assertTrue(np.allclose(nice_gen_coord, gen_coord, atol=1e-1))
calculated_results = np.column_stack((results[0], results[1]))
self.assertTrue(
np.allclose(nice_measures, calculated_results, atol=1e-1))
self.assertTrue(np.allclose(nice_dev_path, dev_path, atol=1e-1))
self.assertTrue(
np.allclose(nice_path_coordinates.T, map[:2], atol=1e-1))
def test_example02(self):
nice_measures = [[5.271, 36.847], [5.184, 36.789], [5.047, 36.698],
[5.234, 36.822], [5.1, 36.733]]
molecules, options = classic_inputs.read_old_input(
'data/shape/example02.dat')
reference_polyhedron = []
for number in options['%labels']:
reference_polyhedron.append(
shape.tools.get_shape_label(int(number), options['%n_atoms']))
results = [[
shape.Shape(molecule).measure(reference_polyhedron[0],
options['%central_atom'])
for molecule in molecules
],
[
shape.Shape(molecule).measure(reference_polyhedron[1],
options['%central_atom'])
for molecule in molecules
]]
calculated_results = np.column_stack((results[0], results[1]))
self.assertTrue(
np.allclose(nice_measures, calculated_results, atol=1e-3))
def test_example01(self):
molecules, options = classic_inputs.read_old_input(
'data/shape/example01.dat')
reference_polyhedron = []
for number in options['%labels']:
reference_polyhedron.append(
shape.tools.get_shape_label(int(number), options['%n_atoms']))
results = [[
shape.Shape(molecule).measure(
reference_polyhedron[0], central_atom=options['%central_atom'])
for molecule in molecules
],
[
shape.Shape(molecule).measure(
reference_polyhedron[1],
central_atom=options['%central_atom'])
for molecule in molecules
]]
calculated_results = np.column_stack((results[0], results[1]))
nice_measures = [[31.375, 0.97], [33.44, 0.16]]
self.assertTrue(
np.allclose(nice_measures, calculated_results, atol=1e-3))
def __init__(self,
positions,
symbols=(),
name='',
connectivity=None,
connectivity_thresh=1.2):
# self._central_atom = None
self._symbols = []
self._positions = []
self._atom_groups = list(symbols)
self._name = name
# TODO: This is a mess!
for symbol in symbols:
try:
int(symbol)
self._symbols.append(
tools.atomic_number_to_element(int(symbol)))
except (ValueError, TypeError):
self._symbols.append(symbol.capitalize())
for ida, a in enumerate(symbol):
try:
int(a)
self._symbols[-1] = self._symbols[-1][:ida]
break
except (ValueError, TypeError, IndexError):
pass
try:
float(positions[0])
for symbol in positions:
self._positions.append(float(symbol))
self._positions = list(chunks(self._positions, 3))
except (ValueError, TypeError, IndexError):
for symbol in positions:
self._positions.append([float(j) for j in symbol])
self._positions = np.array(self._positions)
if connectivity is None:
self._connectivity = generate_connectivity_from_geometry(
self, thresh=connectivity_thresh)
else:
self._connectivity = connectivity
self._shape = shape.Shape(self)
self._symmetry = Symmetry(self)
def execute(self):
if self.filename is None:
self.results.setPlainText('WARNING. No input file selected')
self.results.repaint()
# print('WARNING. No input file selected, choose one before running')
else:
# if self.directory is None:
text = "SHAPE's measure " + self.label + "\n"
for geometry in self.geometries:
text += '{:10} {:10.3f}'.format(
geometry.name,
shape.Shape(geometry).measure(self.label,
self.central_atom)) + '\n'
self.results.setPlainText(text)
self.results.repaint()
self.save_button.setEnabled(True)
fragments_list = file_io.get_geometry_from_file_cor(
'../old_examples/coord.cor', read_multiple=True)
# Call shape as method of Geometry class
print_shape_data(geometries_list)
print_shape_data(fragments_list)
# Check multiple calls of shape one calculatioin
methane = geometries_list[0]
for i in range(100):
measure = methane.get_shape_measure('SP-4', central_atom=1)
print('final measure: {}'.format(measure))
# Call shape as method of Shape class (semi function call)
print('measure:', shape.Shape(methane).measure('SP-4', central_atom=1))
print('structure:\n', shape.Shape(methane).structure('SP-4', central_atom=1))
# test symgroup
print('\nSYMMETRY' '\n--------')
geometries_list = file_io.get_geometry_from_file_pdb(
'../old_examples/methane.pdb', read_multiple=True)
print('measure C3: {} '.format(geometries_list[0].get_symmetry_measure('c3')))
# Check multiple calls of symgroup one calculatioin
for i in range(100):
measure = methane.get_symmetry_measure('C3', central_atom=1)
print('measure: {:^10.3f} '.format(measure))
print('measure: {:^10.3f} '.format(
def test_example04(self):
nice_measures = [[31.375, 0.97], [33.44, 0.16]]
nice_structures = [[2.63702000e+00, 9.00254000e+00, 1.50230800e+01],
[4.04611899e+00, 8.76816018e+00, 1.39529277e+01],
[2.90730181e+00, 8.13748396e+00, 1.65607229e+01],
[1.17328859e+00, 8.36062228e+00, 1.42286293e+01],
[2.42137060e+00, 1.07438936e+01, 1.53500401e+01],
[-3.47837193e-17, -9.20929468e-18, 2.51183874e-17],
[3.77908106e-01, 9.50150647e-01, -8.46343078e-01],
[-3.77908106e-01, -9.50150647e-01, 8.46343078e-01],
[-1.14966271e+00, 6.33326997e-01, 1.97661211e-01],
[1.14966271e+00, -6.33326997e-01, -1.97661211e-01],
[2.63702000e+00, 9.00254000e+00, 1.50230800e+01],
[3.76728743e+00, 7.46687014e+00, 1.40425715e+01],
[4.02414490e+00, 8.97967996e+00, 1.66578721e+01],
[1.24989510e+00, 9.02540004e+00, 1.33882879e+01],
[1.50675257e+00, 1.05382099e+01, 1.60035885e+01],
[9.74091060e-17, 1.01739088e-17, -5.98080786e-17],
[5.66862241e-01, 1.42522607e+00, -1.26951447e+00],
[-5.66862241e-01, -1.42522607e+00, 1.26951447e+00],
[-1.72449417e+00, 9.49990377e-01, 2.96491640e-01],
[1.72449417e+00, -9.49990377e-01, -2.96491640e-01]]
molecules, options = classic_inputs.read_old_input(
'data/shape/example04.dat')
reference_polyhedron = []
for number in options['%labels']:
reference_polyhedron.append(
shape.tools.get_shape_label(int(number), options['%n_atoms']))
results = [[
shape.Shape(molecule).structure(
reference_polyhedron[0], central_atom=options['%central_atom'])
for molecule in molecules
]]
calculated_results = np.concatenate((results[0][0], results[0][1]))
results.append([
shape.Shape(molecule).structure(
reference_polyhedron[1], central_atom=options['%central_atom'])
for molecule in molecules
])
calculated_results = np.concatenate(
(calculated_results, np.concatenate(
(results[1][0], results[1][1]))))
results = []
results.append([
shape.Shape(molecule).measure(
reference_polyhedron[0], central_atom=options['%central_atom'])
for molecule in molecules
])
results.append([
shape.Shape(molecule).measure(
reference_polyhedron[1], central_atom=options['%central_atom'])
for molecule in molecules
])
calculated_results = [
calculated_results,
np.column_stack((results[0], results[1]))
]
self.assertTrue(
np.allclose(nice_structures, calculated_results[0], atol=1e-3))
self.assertTrue(
np.allclose(nice_measures, calculated_results[1], atol=1e-3))