def __init__(self, discretization, atom_discretization):
# step 1
self.discretization = discretization
self.atom_discretization = atom_discretization
self.grid = np.zeros(self.discretization.d, dtype=np.int64)
# step 2
atomstogrid(self.grid, self.atom_discretization.discrete_positions,
self.atom_discretization.atoms.radii_as_indices,
self.atom_discretization.sorted_discrete_radii,
[(0, 0, 0)] +
self.discretization.combined_translation_vectors,
self.discretization.grid)
# step 3
result = start_split_and_merge_pipeline(
self.grid, self.discretization.grid,
self.atom_discretization.discrete_positions,
self.discretization.combined_translation_vectors,
self.discretization.get_translation_vector, ObjectType.DOMAIN)
self.centers, translated_areas, non_translated_areas, self.surface_point_list, self.cyclic_area_indices = result
print_message("Number of domains:", len(self.centers))
self.domain_volumes = []
self.critical_domains = [
] # count of very small domains -> domains that can disappear on cutoff radius changes
for domain_index in range(len(self.centers)):
current_cell_sum = (self.grid == -(domain_index + 1)).sum()
if current_cell_sum == 1:
self.critical_domains.append(domain_index)
domain_volume = current_cell_sum * (self.discretization.s_step**3)
self.domain_volumes.append(domain_volume)
self.characteristic_radii = [(0.75 * volume / PI)**(1.0 / 3.0)
for volume in self.domain_volumes]
if translated_areas:
gyration_tensor_parameters = tuple(
calculate_gyration_tensor_parameters(area)
for area in translated_areas)
(self.mass_centers, self.squared_gyration_radii,
self.asphericities, self.acylindricities,
self.anisotropies) = zip(*gyration_tensor_parameters)
self.mass_centers = [
self.discretization.discrete_to_continuous(
point, result_inside_volume=True)
for point in self.mass_centers
]
self.squared_gyration_radii = [
self.discretization.discrete_to_continuous(value,
unit_exponent=2)
for value in self.squared_gyration_radii
]
else:
(self.mass_centers, self.squared_gyration_radii,
self.asphericities, self.acylindricities,
self.anisotropies) = 5 * ([], )
self.triangles()
def __init__(self, discretization, atom_discretization):
# step 1
self.discretization = discretization
self.atom_discretization = atom_discretization
self.grid = np.zeros(self.discretization.d, dtype=np.int64)
# step 2
atomstogrid(self.grid,
self.atom_discretization.discrete_positions,
self.atom_discretization.atoms.radii_as_indices,
self.atom_discretization.sorted_discrete_radii,
[(0, 0, 0)] + self.discretization.combined_translation_vectors,
self.discretization.grid)
# step 3
result = start_split_and_merge_pipeline(self.grid,
self.discretization.grid,
self.atom_discretization.discrete_positions,
self.discretization.combined_translation_vectors,
self.discretization.get_translation_vector,
ObjectType.DOMAIN)
self.centers, translated_areas, non_translated_areas, self.surface_point_list, self.cyclic_area_indices = result
print_message("Number of domains:", len(self.centers))
self.domain_volumes = []
self.critical_domains = [] # count of very small domains -> domains that can disappear on cutoff radius changes
for domain_index in range(len(self.centers)):
current_cell_sum = (self.grid == -(domain_index + 1)).sum()
if current_cell_sum == 1:
self.critical_domains.append(domain_index)
domain_volume = current_cell_sum * (self.discretization.s_step ** 3)
self.domain_volumes.append(domain_volume)
self.characteristic_radii = [(0.75 * volume / PI)**(1.0/3.0) for volume in self.domain_volumes]
if translated_areas:
gyration_tensor_parameters = tuple(calculate_gyration_tensor_parameters(area) for area in translated_areas)
(self.mass_centers, self.squared_gyration_radii, self.asphericities,
self.acylindricities, self.anisotropies) = zip(*gyration_tensor_parameters)
self.mass_centers = [self.discretization.discrete_to_continuous(point, result_inside_volume=True)
for point in self.mass_centers]
self.squared_gyration_radii = [self.discretization.discrete_to_continuous(value, unit_exponent=2)
for value in self.squared_gyration_radii]
else:
(self.mass_centers, self.squared_gyration_radii, self.asphericities,
self.acylindricities, self.anisotropies) = 5*([], )
self.triangles()
def __init__(self,
domain_calculation,
use_surface_points=True,
gyration_tensor_parameters=False):
self.domain_calculation = domain_calculation
if use_surface_points:
self.grid = self.domain_calculation.grid
num_surface_points = sum(
map(len, self.domain_calculation.surface_point_list))
print_message("Number of surface points:", num_surface_points)
else:
self.grid = None
self.sg_cube_size = self.domain_calculation.atom_discretization.sorted_discrete_radii[
0]
if use_surface_points:
domain_seed_point_lists = self.domain_calculation.surface_point_list
else:
domain_seed_point_lists = [
[center] for center in self.domain_calculation.centers
]
discretization = self.domain_calculation.discretization
atom_discretization = self.domain_calculation.atom_discretization
# steps 1 to 5
self.grid3 = mark_cavities(
self.grid, discretization.grid, discretization.d,
self.sg_cube_size, atom_discretization.discrete_positions,
[(0, 0, 0)] + discretization.combined_translation_vectors,
domain_seed_point_lists, use_surface_points)
if gyration_tensor_parameters:
result = start_split_and_merge_pipeline(
self.grid3, discretization.grid,
atom_discretization.discrete_positions,
discretization.combined_translation_vectors,
discretization.get_translation_vector, ObjectType.CAVITY)
translated_areas, non_translated_areas, cyclic_area_indices = result
num_domains = len(self.domain_calculation.centers)
grid_volume = (discretization.grid == 0).sum()
self.cavity_volumes = []
for domain_index in range(num_domains):
self.cavity_volumes.append(
1.0 * (self.grid3 == -(domain_index + 1)).sum() *
(discretization.s_step**3))
self.characteristic_radii = [(0.75 * volume / PI)**(1.0 / 3.0)
for volume in self.cavity_volumes]
# step 6
intersection_table = cavity_intersections(self.grid3, num_domains)
multicavities = []
cavity_to_neighbors = num_domains * [None]
for domain in range(num_domains):
current_neighbors = set([domain])
for neighbor in range(num_domains):
if intersection_table[domain][neighbor] == 1:
current_neighbors.add(neighbor)
for multicavity in multicavities[:]:
if any([
neighbor in multicavity
for neighbor in current_neighbors
]):
current_neighbors = current_neighbors | multicavity
multicavities.remove(multicavity)
multicavities.append(current_neighbors)
for neighbor in current_neighbors:
cavity_to_neighbors[neighbor] = current_neighbors
self.multicavities = multicavities
self.multicavity_volumes = []
for multicavity in multicavities:
self.multicavity_volumes.append(
sum(self.cavity_volumes[cavity_index]
for cavity_index in multicavity))
print_message("Multicavity volumes:", self.multicavity_volumes)
if gyration_tensor_parameters:
def key_func(cavity_index):
cavity_area = non_translated_areas[cavity_index]
a_single_cavity_index = -self.grid3[cavity_area[0]] - 1
max_neighbor_index = max(
cavity_to_neighbors[a_single_cavity_index])
return max_neighbor_index
sorted_area_indices = sorted(range(len(self.multicavities)),
key=key_func)
sorted_translated_areas = [
translated_areas[i] for i in sorted_area_indices
]
sorted_cyclic_area_indices = [
i for i, index in enumerate(sorted_area_indices)
if index in cyclic_area_indices
]
self.cyclic_area_indices = sorted_cyclic_area_indices
if sorted_translated_areas:
gyration_tensor_parameters = tuple(
calculate_gyration_tensor_parameters(area)
for area in sorted_translated_areas)
(self.mass_centers, self.squared_gyration_radii,
self.asphericities, self.acylindricities,
self.anisotropies) = zip(*gyration_tensor_parameters)
self.mass_centers = [
discretization.discrete_to_continuous(
point, result_inside_volume=True)
for point in self.mass_centers
]
self.squared_gyration_radii = [
discretization.discrete_to_continuous(value,
unit_exponent=2)
for value in self.squared_gyration_radii
]
else:
(self.mass_centers, self.squared_gyration_radii,
self.asphericities, self.acylindricities,
self.anisotropies) = 5 * ([], )
self.triangles()
def __init__(self, domain_calculation, use_surface_points=True, gyration_tensor_parameters=False):
self.domain_calculation = domain_calculation
if use_surface_points:
self.grid = self.domain_calculation.grid
num_surface_points = sum(map(len, self.domain_calculation.surface_point_list))
print_message("Number of surface points:", num_surface_points)
else:
self.grid = None
self.sg_cube_size = self.domain_calculation.atom_discretization.sorted_discrete_radii[0]
if use_surface_points:
domain_seed_point_lists = self.domain_calculation.surface_point_list
else:
domain_seed_point_lists = [[center] for center in self.domain_calculation.centers]
discretization = self.domain_calculation.discretization
atom_discretization = self.domain_calculation.atom_discretization
# steps 1 to 5
self.grid3 = mark_cavities(self.grid,
discretization.grid,
discretization.d,
self.sg_cube_size,
atom_discretization.discrete_positions,
[(0, 0, 0)] + discretization.combined_translation_vectors,
domain_seed_point_lists,
use_surface_points)
if gyration_tensor_parameters:
result = start_split_and_merge_pipeline(self.grid3,
discretization.grid,
atom_discretization.discrete_positions,
discretization.combined_translation_vectors,
discretization.get_translation_vector,
ObjectType.CAVITY)
translated_areas, non_translated_areas, cyclic_area_indices = result
num_domains = len(self.domain_calculation.centers)
grid_volume = (discretization.grid == 0).sum()
self.cavity_volumes = []
for domain_index in range(num_domains):
self.cavity_volumes.append(1.0 * (self.grid3 == -(domain_index + 1)).sum() * (discretization.s_step ** 3))
self.characteristic_radii = [(0.75 * volume / PI)**(1.0/3.0) for volume in self.cavity_volumes]
# step 6
intersection_table = cavity_intersections(self.grid3, num_domains)
multicavities = []
cavity_to_neighbors = num_domains * [None]
for domain in range(num_domains):
current_neighbors = set([domain])
for neighbor in range(num_domains):
if intersection_table[domain][neighbor] == 1:
current_neighbors.add(neighbor)
for multicavity in multicavities[:]:
if any([neighbor in multicavity for neighbor in current_neighbors]):
current_neighbors = current_neighbors | multicavity
multicavities.remove(multicavity)
multicavities.append(current_neighbors)
for neighbor in current_neighbors:
cavity_to_neighbors[neighbor] = current_neighbors
self.multicavities = multicavities
self.multicavity_volumes = []
for multicavity in multicavities:
self.multicavity_volumes.append(sum(self.cavity_volumes[cavity_index] for cavity_index in multicavity))
print_message("Multicavity volumes:", self.multicavity_volumes)
if gyration_tensor_parameters:
def key_func(cavity_index):
cavity_area = non_translated_areas[cavity_index]
a_single_cavity_index = -self.grid3[cavity_area[0]] - 1
max_neighbor_index = max(cavity_to_neighbors[a_single_cavity_index])
return max_neighbor_index
sorted_area_indices = sorted(range(len(self.multicavities)), key=key_func)
sorted_translated_areas = [translated_areas[i] for i in sorted_area_indices]
sorted_cyclic_area_indices = [i for i, index in enumerate(sorted_area_indices)
if index in cyclic_area_indices]
self.cyclic_area_indices = sorted_cyclic_area_indices
if sorted_translated_areas:
gyration_tensor_parameters = tuple(calculate_gyration_tensor_parameters(area)
for area in sorted_translated_areas)
(self.mass_centers, self.squared_gyration_radii, self.asphericities,
self.acylindricities, self.anisotropies) = zip(*gyration_tensor_parameters)
self.mass_centers = [discretization.discrete_to_continuous(point, result_inside_volume=True)
for point in self.mass_centers]
self.squared_gyration_radii = [discretization.discrete_to_continuous(value, unit_exponent=2)
for value in self.squared_gyration_radii]
else:
(self.mass_centers, self.squared_gyration_radii, self.asphericities,
self.acylindricities, self.anisotropies) = 5*([], )
self.triangles()
