def _set_clipping_planes(self):
'''Clipping planes'''
clip_planes = list()
if self._magnetic:
pos = Vector3(-74.9, -99.0, 228.8)
size = Vector3(70.0, 100.0, 70.0)
clip_planes.append([1.0, 0.0, 0.0, -pos.x + size.x])
clip_planes.append([-1.0, 0.0, 0.0, pos.x + size.x])
clip_planes.append([0.0, 1.0, 0.0, -pos.y + size.y])
clip_planes.append([0.0, -1.0, 0.0, pos.y + size.y])
clip_planes.append([0.0, 0.0, 1.0, -pos.z + size.z])
clip_planes.append([0.0, 0.0, -1.0, pos.z + size.z])
else:
clip_planes.append([1.0, 0.0, 0.0, scene_size * 1.5 + 5])
clip_planes.append([-1.0, 0.0, 0.0, scene_size * 1.5 + 5])
clip_planes.append([0.0, 0.0, 1.0, scene_size + 5])
clip_planes.append([0.0, 0.0, -1.0, scene_size + 5])
cps = self._core.get_clip_planes()
ids = list()
if cps:
for cp in cps:
ids.append(cp['id'])
self._core.remove_clip_planes(ids)
for plane in clip_planes:
self._core.add_clip_plane(plane)
def _add_surfactants_a(self, frame):
spa_sequences = [[0, 3750]]
spa_random_seeds = [2]
spa_frames = [
[
Vector3(-400.0, -100.0, 100.0),
Quaternion(-0.095, 0.652, -0.326, 0.677),
Vector3(250.0, -50.0, 100.0),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_SINUSOIDAL
],
]
for surfactant_index in range(len(spa_frames)):
name = 'Surfactant-A ' + str(surfactant_index)
sequence = spa_sequences[surfactant_index]
pos, rot, progress = self._get_transformation(
start_frame=sequence[0],
end_frame=sequence[1],
frame=frame,
data=spa_frames[surfactant_index])
self._log(3, '- ' + name + ' (%.01f pct)' % progress)
self._add_surfactant_a(
name=name,
position=pos,
rotation=rot,
random_seed=spa_random_seeds[surfactant_index])
self._add_glucose_to_surfactant_head(name=name)
def add_cell(bioexplorer, name, size, height, position=Vector3()):
ace2_receptor = Protein(sources=[PDB_FOLDER + '6m18.pdb'],
occurences=20,
position=Vector3(0.0, 6.0, 0.0))
membrane = ParametricMembrane(sources=[
MEMBRANE_FOLDER + 'segA.pdb', MEMBRANE_FOLDER + 'segB.pdb',
MEMBRANE_FOLDER + 'segC.pdb', MEMBRANE_FOLDER + 'segD.pdb'
],
occurences=1200000)
cell = Cell(name=name,
size=size,
shape=bioexplorer.ASSEMBLY_SHAPE_SINUSOIDAL,
membrane=membrane,
receptor=ace2_receptor,
extra_parameters=[height],
random_position_seed=1,
random_position_strength=0.025,
random_rotation_seed=2,
random_rotation_strength=2.0)
bioexplorer.add_cell(cell=cell,
position=position,
representation=PROTEIN_REPRESENTATION)
if ADD_GLYCANS:
bioexplorer.add_multiple_glycans(
representation=PROTEIN_REPRESENTATION,
assembly_name=name,
glycan_type=bioexplorer.NAME_GLYCAN_COMPLEX,
protein_name=bioexplorer.NAME_RECEPTOR,
paths=COMPLEX_PATHS,
indices=[53, 90, 103, 322, 432, 690])
bioexplorer.add_multiple_glycans(
representation=PROTEIN_REPRESENTATION,
assembly_name=name,
glycan_type=bioexplorer.NAME_GLYCAN_HYBRID,
protein_name=bioexplorer.NAME_RECEPTOR,
paths=HYBRID_PATHS,
indices=[546])
indices = [[155, Quaternion(0.707, 0.0, 0.707, 0.0)],
[730, Quaternion(0.707, 0.0, 0.707, 0.0)]]
for index in indices:
o_glycan_name = name + '_' + bioexplorer.NAME_GLYCAN_O_GLYCAN + '_' + str(
index[0])
o_glycan = Sugars(assembly_name=name,
name=o_glycan_name,
source=O_GLYCAN_PATHS[0],
protein_name=name + '_' +
bioexplorer.NAME_RECEPTOR,
representation=PROTEIN_REPRESENTATION,
chain_ids=[2, 4],
site_indices=[index[0]],
rotation=index[1])
bioexplorer.add_sugars(o_glycan)
def test_cell():
resource_folder = 'tests/test_files/'
pdb_folder = resource_folder + 'pdb/'
bio_explorer = BioExplorer('localhost:5000')
bio_explorer.reset()
# Suspend image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=0)
# Proteins
protein_representation = bio_explorer.REPRESENTATION_ATOMS
# Membrane parameters
membrane_size = 800.0
membrane_height = 80
membrane_nb_receptors = 20
membrane_nb_lipids = 1200000
# ACE2 Receptor
ace2_receptor = Protein(sources=[pdb_folder + '6m1d.pdb'],
occurences=membrane_nb_receptors,
position=Vector3(0.0, 6.0, 0.0))
membrane = Membrane(sources=[pdb_folder + 'membrane/popc.pdb'],
occurences=membrane_nb_lipids)
cell = Cell(name='Cell',
size=membrane_size,
shape=bio_explorer.ASSEMBLY_SHAPE_SINUSOIDAL,
membrane=membrane,
receptor=ace2_receptor,
extra_parameters=[membrane_height])
bio_explorer.add_cell(cell=cell,
position=Vector3(4.5, -186, 7.0),
representation=protein_representation,
random_seed=1)
# Set rendering settings
bio_explorer.core_api().set_renderer(
background_color=[96 / 255, 125 / 255, 139 / 255],
current='bio_explorer',
samples_per_pixel=1,
subsampling=4,
max_accum_frames=64)
params = bio_explorer.core_api().BioExplorerRendererParams()
params.shadows = 0.75
params.soft_shadows = 1.0
bio_explorer.core_api().set_renderer_params(params)
# Restore image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=20)
def _add_lymphocyte(self, frame):
if frame < 1400:
'''Lymphocyte is not in the field of view'''
return
'''Protein animation params'''
params = [0, 0, 0.0, frame + 2, 0.2]
clip_planes = [
[1.0, 0.0, 0.0, scene_size * 1.5 + 5],
[-1.0, 0.0, 0.0, scene_size * 1.5 + 5],
[0.0, 0.0, 1.0, scene_size + 5],
[0.0, 0.0, -1.0, scene_size + 5]
]
name = 'Emile'
lymphocyte_sequence = [0, 3750]
lymphocyte_frames = [Vector3(-2500.0, 100.0, 30.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(-830.0, 100.0, 30.0), Quaternion(0.707, 0.707, 0.0, 0.0),
ROTATION_MODE_LINEAR]
protein_sources = [
membrane_folder + 'segA.pdb',
membrane_folder + 'segB.pdb',
membrane_folder + 'segC.pdb',
membrane_folder + 'segD.pdb'
]
mesh_based_membrane = MeshBasedMembrane(
mesh_source=lymphocyte_path, protein_sources=protein_sources,
density=lymphocyte_density, surface_variable_offset=lymphocyte_surface_variable_offset,
assembly_params=params
)
pos, rot, progress = self._get_transformation(
start_frame=lymphocyte_sequence[0], end_frame=lymphocyte_sequence[1],
frame=frame, data=lymphocyte_frames)
self._log(3, '- ' + name + ' (%.01f pct)' % progress)
scale = Vector3(1.0, 1.0, 1.0)
status = self._be.add_mesh_based_membrane(
name, mesh_based_membrane, position=pos,
rotation=rot, scale=scale,
clipping_planes=clip_planes
)
for i in range(len(protein_sources)):
status = self._be.set_protein_color_scheme(
assembly_name=name, name=BioExplorer.NAME_MEMBRANE + '_' + str(i),
color_scheme=BioExplorer.COLOR_SCHEME_CHAINS,
palette_name='OrRd', palette_size=5)
def _add_surfactants_d(self, frame):
spd_sequences = [[0, 3750], [0, 2600], [0, 2600], [0, 3750]]
spd_random_seeds = [1, 1, 1, 2]
spd_flights = [
[Vector3(300, 124.0, 0.0), Quaternion(-0.095, 0.652, -0.326, 0.677),
Vector3(74.0, 24.0, -45.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_SINUSOIDAL],
# SP-D is used for the head focus on 3rd virus spike
[Vector3(-50, 250.0, 20.0), Quaternion(0.087, 0.971, -0.147, -0.161),
Vector3(-11.0, 108.0, 20.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
# SP-D attaching to lymphocyte
[Vector3(-200.0, 100.0, 100.0), Quaternion(0.519, 0.671, 0.528, -0.036),
Vector3(-135.0, 135.0, 140.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
[Vector3(100.0, 0.0, -80.0), Quaternion(-0.095, 0.652, -0.326, 0.677),
Vector3(-260.0, 50.0, 150.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_SINUSOIDAL]
]
for surfactant_index in range(len(spd_sequences)):
name = 'Surfactant-D ' + str(surfactant_index)
sequence = spd_sequences[surfactant_index]
pos, rot, progress = self._get_transformation(
start_frame=sequence[0], end_frame=sequence[1],
frame=frame, data=spd_flights[surfactant_index])
self._log(3, '- ' + name + ' (%.01f pct)' % progress)
self._add_surfactant_d(
name=name, position=pos, rotation=rot,
random_seed=spd_random_seeds[surfactant_index])
def test_immune():
resource_folder = 'tests/test_files/'
pdb_folder = resource_folder + 'pdb/immune/'
bio_explorer = BioExplorer('localhost:5000')
bio_explorer.reset()
print('BioExplorer version ' + bio_explorer.version())
# Suspend image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=0)
# Proteins
lactoferrin_path = pdb_folder + '1b0l.pdb'
defensin_path = pdb_folder + '1ijv.pdb'
# Scene parameters
scene_size = 800
# Lactoferrins
lactoferrins = Protein(sources=[lactoferrin_path],
load_non_polymer_chemicals=True,
occurences=150)
lactoferrins_volume = Volume(name=bio_explorer.NAME_LACTOFERRIN,
size=scene_size,
protein=lactoferrins)
bio_explorer.add_volume(volume=lactoferrins_volume,
representation=bio_explorer.REPRESENTATION_ATOMS,
position=Vector3(0.0, scene_size / 2.0 - 200.0,
0.0))
# Defensins
defensins = Protein(sources=[defensin_path],
load_non_polymer_chemicals=True,
occurences=300)
defensins_volume = Volume(name=bio_explorer.NAME_DEFENSIN,
size=scene_size,
protein=defensins)
bio_explorer.add_volume(volume=defensins_volume,
representation=bio_explorer.REPRESENTATION_ATOMS,
position=Vector3(0.0, scene_size / 2.0 - 200.0,
0.0),
random_seed=3)
# Restore image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=20)
def test_mesh():
resource_folder = 'tests/test_files/'
pdb_folder = resource_folder + 'pdb/'
obj_folder = resource_folder + 'obj/'
bio_explorer = BioExplorer('localhost:5000')
bio_explorer.reset()
print('BioExplorer version ' + bio_explorer.version())
mesh_source = obj_folder + 'suzanne.obj'
scale = Vector3(5, 5, 5)
# Membrane
protein_source = pdb_folder + 'membrane/popc.pdb'
mesh_based_membrane = MeshBasedMembrane(mesh_source=mesh_source,
protein_source=protein_source,
density=5.0,
surface_variable_offset=2.0)
bio_explorer.add_mesh_based_membrane('Mesh',
mesh_based_membrane,
scale=scale)
# Receptors
protein_source = pdb_folder + '6m1d.pdb'
mesh_based_membrane = MeshBasedMembrane(mesh_source=mesh_source,
protein_source=protein_source,
density=0.02,
surface_fixed_offset=5.0)
bio_explorer.add_mesh_based_membrane('Receptors',
mesh_based_membrane,
scale=scale)
def test_glucose():
resource_folder = 'tests/test_files/'
pdb_folder = resource_folder + 'pdb/'
bio_explorer = BioExplorer('localhost:5000')
bio_explorer.reset()
print('BioExplorer version ' + bio_explorer.version())
# Suspend image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=0)
# Proteins
glucose_path = pdb_folder + 'glucose.pdb'
# Scene parameters
scene_size = 800.0
# Glucose
protein = Protein(sources=[glucose_path],
load_non_polymer_chemicals=True,
occurences=120000)
volume = Volume(name=bio_explorer.NAME_GLUCOSE,
size=scene_size,
protein=protein)
bio_explorer.add_volume(volume=volume,
representation=bio_explorer.REPRESENTATION_ATOMS,
position=Vector3(0.0, scene_size / 2.0 - 200.0,
0.0))
# Restore image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=20)
def add_glucose(bioexplorer, size, number):
protein = Protein(sources=[GLUCOSE_PATH],
load_non_polymer_chemicals=True,
occurences=number)
volume = Volume(name=bioexplorer.NAME_GLUCOSE, size=size, protein=protein)
bioexplorer.add_volume(volume=volume,
representation=bioexplorer.REPRESENTATION_ATOMS,
position=Vector3(0.0, size / 2.0 - 200.0, 0.0))
def add_lactoferrins(bioexplorer, size, number):
lactoferrins = Protein(sources=[LACTOFERRINS_PATH],
load_non_polymer_chemicals=True,
occurences=number)
lactoferrins_volume = Volume(name=bioexplorer.NAME_LACTOFERRIN,
size=size,
protein=lactoferrins)
bioexplorer.add_volume(volume=lactoferrins_volume,
representation=bioexplorer.REPRESENTATION_ATOMS,
position=Vector3(0.0, size / 2.0 - 200.0, 0.0))
def add_defensins(bioexplorer, size, number):
defensins = Protein(sources=[DEFENSINS_PATH],
load_non_polymer_chemicals=True,
occurences=number)
defensins_volume = Volume(name=bioexplorer.NAME_DEFENSIN,
size=size,
protein=defensins)
bioexplorer.add_volume(volume=defensins_volume,
representation=bioexplorer.REPRESENTATION_ATOMS,
position=Vector3(0.0, size / 2.0 - 200.0, 0.0))
def _add_glucose(self, frame):
glucose = Protein(
sources=[glucose_path], load_non_polymer_chemicals=True,
occurences=nb_glucoses)
volume = Volume(
name=BioExplorer.NAME_GLUCOSE, size=scene_size, protein=glucose,
random_position_seed=frame + 20, random_position_stength=scene_size / 600.0,
random_rotation_seed=frame + 21, random_rotation_stength=0.3
)
status = self._be.add_volume(
volume=volume, representation=protein_representation,
position=Vector3(0.0, scene_size / 2.0 - 200.0, 0.0),
random_seed=100)
def _add_lactoferrins(self, frame):
lactoferrin = Protein(
sources=[lactoferrin_path], load_non_polymer_chemicals=True,
occurences=nb_lactoferrins)
lactoferrins_volume = Volume(
name=BioExplorer.NAME_LACTOFERRIN, size=scene_size, protein=lactoferrin,
random_position_seed=frame + 30, random_position_stength=scene_size / 400.0,
random_rotation_seed=frame + 31, random_rotation_stength=0.3
)
status = self._be.add_volume(
volume=lactoferrins_volume, representation=protein_representation,
position=Vector3(0.0, scene_size / 2.0 - 200.0, 0.0),
random_seed=101)
def _add_defensins(self, frame):
defensin = Protein(
sources=[defensin_path], load_non_polymer_chemicals=True,
occurences=nb_defensins)
defensins_volume = Volume(
name=BioExplorer.NAME_DEFENSIN, size=scene_size, protein=defensin,
random_position_seed=frame + 40, random_position_stength=scene_size / 400.0,
random_rotation_seed=frame + 41, random_rotation_stength=0.3
)
status = self._be.add_volume(
volume=defensins_volume, representation=protein_representation,
position=Vector3(0.0, scene_size / 2.0 - 200.0, 0.0),
random_seed=102)
def test_surfactant():
resource_folder = 'tests/test_files/'
pdb_folder = resource_folder + 'pdb/surfactant/'
bio_explorer = BioExplorer('localhost:5000')
bio_explorer.reset()
print('BioExplorer version ' + bio_explorer.version())
# Suspend image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=0)
bio_explorer.core_api().set_camera(
orientation=[0.0, 0.0, 0.0, 1.0], position=[0, 0, 200], target=[0, 0, 0])
# Proteins
protein_representation = bio_explorer.REPRESENTATION_ATOMS
head_source = pdb_folder + '1pw9.pdb'
branch_source = pdb_folder + '1k6f.pdb'
# SP-D
surfactant_d = Surfactant(
name='SP-D', surfactant_protein=bio_explorer.SURFACTANT_PROTEIN_D, head_source=head_source,
branch_source=branch_source)
bio_explorer.add_surfactant(
surfactant=surfactant_d, representation=protein_representation, position=Vector3(-50, 0, 0),
random_seed=10)
# SP-A
surfactant_a = Surfactant(
name='SP-A', surfactant_protein=bio_explorer.SURFACTANT_PROTEIN_A, head_source=head_source,
branch_source=branch_source)
bio_explorer.add_surfactant(
surfactant=surfactant_a, representation=protein_representation, position=Vector3(50, 0, 0))
# Restore image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=20)
def _get_transformation(self, start_frame, end_frame, frame, data):
'''Progress'''
progress = (frame - start_frame) * 1.0 / (end_frame - start_frame)
progress = max(0.0, progress)
progress = min(1.0, progress)
'''Position'''
start_pos = data[0].to_list()
end_pos = data[2].to_list()
pos = start_pos
for i in range(3):
pos[i] += (end_pos[i] - start_pos[i]) * progress
'''Rotation'''
start_rot = data[1]
end_rot = data[3]
rot = Quaternion.slerp(start_rot, end_rot, progress)
if data[4] == ROTATION_MODE_SINUSOIDAL:
rot = Quaternion.slerp(start_rot, end_rot,
math.cos((progress - 0.5) * math.pi))
return [Vector3(pos[0], pos[1], pos[2]), rot, progress * 100.0]
def _add_surfactants_d(self, frame):
spd_sequences = [[-1550, 3750], [0, 3750], [0, 3750]]
spd_random_seeds = [1, 2, 6]
spd_flights = [[
Vector3(-340.0, 0.0, -100.0),
Quaternion(-0.095, 0.652, -0.326, 0.677),
Vector3(74.0 + (74.0 + 340), 24.0 + (24.0 - 0.0),
-45.0 + (-45.0 + 100)),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_SINUSOIDAL
],
[
Vector3(-200, 0.0, -200.0),
Quaternion(0.087, 0.971, -0.147, -0.161),
Vector3(304.0, 75.0, -100.0),
Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_SINUSOIDAL
],
[
Vector3(-460.0, 50.0, 0.0),
Quaternion(0.519, 0.671, 0.528, -0.036),
Vector3(160.0, -50.0, -50.0),
Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_SINUSOIDAL
]]
for surfactant_index in range(len(spd_sequences)):
name = 'Surfactant-D ' + str(surfactant_index)
sequence = spd_sequences[surfactant_index]
pos, rot, progress = self._get_transformation(
start_frame=sequence[0],
end_frame=sequence[1],
frame=frame,
data=spd_flights[surfactant_index])
self._log(3, '- ' + name + ' (%.01f pct)' % progress)
self._add_surfactant_d(
name=name,
position=pos,
rotation=rot,
random_seed=spd_random_seeds[surfactant_index])
self._add_glucose_to_surfactant_head(name=name)
def test_vector3_to_list():
try:
vector = Vector3(0, 1, 2)
assert vector.to_list() == [0, 1, 2]
except RuntimeError:
assert True
def test_high_glucose():
try:
# Connect to BioExplorer server
bioexplorer = BioExplorer('localhost:5000')
core = bioexplorer.core_api()
print('BioExplorer version ' + bioexplorer.version())
bioexplorer.reset()
# Suspend image streaming
core.set_application_parameters(image_stream_fps=0)
# Build full model
add_virus(bioexplorer,
name='Coronavirus 1',
position=Vector3(-289.5, -97.0, -97.5),
open_conformation_indices=[1])
add_virus(bioexplorer,
name='Coronavirus 2',
position=Vector3(-79.5, -102.0, 229.5),
open_conformation_indices=[1])
add_virus(bioexplorer,
name='Coronavirus 3',
position=Vector3(296.5, -125.0, 225.5),
open_conformation_indices=[1])
add_virus(bioexplorer,
name='Coronavirus 4',
position=Vector3(4.5, 100.0, 7.5))
add_virus(bioexplorer,
name='Coronavirus 5',
position=Vector3(204.5, -100.0, 27.5),
open_conformation_indices=[1])
add_virus(bioexplorer,
name='Coronavirus 6',
position=Vector3(54.5, -100.0, -257.5),
open_conformation_indices=[1])
add_cell(bioexplorer,
name='Cell 1',
size=CELL_SIZE,
height=CELL_HEIGHT,
position=Vector3(4.5, -186.0, 7.0))
add_surfactant_d(bioexplorer,
name='Surfactant-D 1',
position=Vector3(74.0, 24.0, -45.0),
random_seed=1)
add_surfactant_d(bioexplorer,
name='Surfactant-D 2',
position=Vector3(104.0, 175.0, -89.0),
random_seed=2)
add_surfactant_d(bioexplorer,
name='Surfactant-D 3',
position=Vector3(-260.0, 50.0, 0.0),
random_seed=6)
add_surfactant_a(bioexplorer,
name='Surfactant-A 1',
position=Vector3(-100.0, 150.0, 0.0),
random_seed=2)
add_glucose(bioexplorer, CELL_SIZE, 360000)
add_lactoferrins(bioexplorer, CELL_SIZE, 50)
add_defensins(bioexplorer, CELL_SIZE, 100)
# Apply default materials
bioexplorer.apply_default_color_scheme(bioexplorer.SHADING_MODE_BASIC)
# Set rendering settings
core.set_renderer(background_color=[96 / 255, 125 / 255, 139 / 255],
current='bio_explorer',
samples_per_pixel=1,
subsampling=4,
max_accum_frames=64)
params = core.BioExplorerRendererParams()
params.shadows = 0.75
params.soft_shadows = 1.0
core.set_renderer_params(params)
# Restore image streaming
core.set_application_parameters(image_stream_fps=20)
except Exception as ex:
print(ex)
raise
def _add_viruses(self, frame):
virus_radii = [45.0, 44.0, 45.0, 43.0, 44.0]
virus_sequences = [
[[0, 2599], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6]],
[[0, 2599], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6]],
[[0, 2599], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6]],
[[0, 2999], [3000, 3099], [3100, 3299], [3300, 3750], [1e6, 1e6], [1e6, 1e6]],
[[0, 599], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1600, 3750]],
]
virus_flights_in = [
[Vector3(-35.0, 300.0, -70.0), Quaternion(0.519, 0.671, 0.528, -0.036),
Vector3(-5.0, 45.0, -33.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
[Vector3(153.0, 300.0, -200.0), Quaternion(0.456, 0.129, -0.185, -0.860),
Vector3(73.0, 93.0, -130.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
# Virus used for SP-D zoom
[Vector3(-100.0, 300.0, 20.0), Quaternion(0.087, 0.971, -0.147, -0.161),
Vector3(-79.0, 108.0, 80.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
# Virus getting inside cell
[Vector3(224.9, 300.0, -220.0), Quaternion(-0.095, 0.652, -0.326, 0.677),
Vector3(211.5, -104.9, -339.2), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
# Virus used for detailed view of the Spike
[Vector3(200.0, 20.0, -150.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(200.0, 20.0, -150.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR]
]
virus_flights_out = [
# Unused
[Vector3(-5.0, 45.0, -33.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(-105.0, 45.0, -33.0), Quaternion(0.0, 1.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
# Unused
[Vector3(73.0, 93.0, -130.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(-33.0, 93.0, -130.0), Quaternion(0.0, 0.0, 1.0, 0.0),
ROTATION_MODE_LINEAR],
# Virus used for SP-D zoom
[Vector3(-84.0, 110.0, 75.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(-100.0, -100.0, 51.2), Quaternion(0.087, 0.971, -0.147, -0.161),
ROTATION_MODE_LINEAR],
# Unused
[Vector3(0.0, 0.0, 0.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(0.0, 0.0, 0.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
# Virus used for detailed view of the Spike
[Vector3(200.0, 20.0, -150.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(300.0, -100.0, -100.0), Quaternion(0.456, 0.129, -0.185, -0.860),
ROTATION_MODE_LINEAR]
]
for virus_index in range(len(virus_sequences)):
name = 'Coronavirus ' + str(virus_index)
current_sequence = 0
sequences = virus_sequences[virus_index]
for i in range(len(sequences)):
if frame >= sequences[i][0]:
current_sequence = i
'''Initialize position and rotation to end-of-flight values'''
start_frame = sequences[current_sequence][0]
end_frame = sequences[current_sequence][1]
progress_in_sequence = (frame - start_frame) / (end_frame - start_frame)
morphing_step = 0.0
if current_sequence == 0:
'''Flying'''
pos, rot, progress = self._get_transformation(start_frame, end_frame,
frame, virus_flights_in[virus_index])
self._log(3, '- Virus %d is flying in... (%.01f pct)' % (virus_index, progress))
elif current_sequence == 1:
'''Landing'''
pos = virus_flights_in[virus_index][2]
rot = virus_flights_in[virus_index][3]
pos.y -= landing_distance * progress_in_sequence
self._log(3, '- Virus %d is landing...' % virus_index)
elif current_sequence == 2:
'''Merging into cell'''
pos = virus_flights_in[virus_index][2]
rot = virus_flights_in[virus_index][3]
morphing_step = (frame - start_frame) / (end_frame - start_frame)
pos.y -= landing_distance
self._log(3, '- Virus %d is merging in (%.01f pct)' %
(virus_index, morphing_step * 100.0))
elif current_sequence == 3:
'''Inside cell'''
self._log(3, '- Virus %d is inside cell' % virus_index)
'''Virus is not added to the scene'''
self._be.remove_assembly(name=name)
continue
elif current_sequence == 4:
'''Merging out of cell'''
pos = virus_flights_out[virus_index][0]
rot = virus_flights_out[virus_index][1]
morphing_step = 1.0 - (frame - start_frame) / (end_frame - start_frame)
self._log(3, '- Virus %d is merging out (%.01f pct)' %
(virus_index, morphing_step * 100.0))
else:
'''Flying out'''
pos, rot, progress = self._get_transformation(start_frame, end_frame,
frame, virus_flights_out[virus_index])
self._log(3, '- Virus %d is flying out... (%.01f pct)' % (virus_index, progress))
if False:
self._be.add_sphere(name=name, position=pos, radius=virus_radii[virus_index])
else:
self._be.add_coronavirus(
name=name, resource_folder=resource_folder,
representation=protein_representation, position=pos, rotation=rot,
add_glycans=add_glycans,
assembly_params=[virus_radii[virus_index], 5 * frame + 2 * virus_index,
0.25, frame + 2 * virus_index + 1, 0.1, morphing_step]
)
def _add_cell(self, frame):
name = 'Cell'
nb_receptors = cell_nb_receptors
size = scene_size * 2.0
height = scene_size / 10.0
position = Vector3(4.5, -186.0, 7.0)
random_seed = 10
nb_lipids = cell_nb_lipids
ace2_receptor = Protein(sources=[pdb_folder + '6m18.pdb'],
occurences=nb_receptors,
position=Vector3(0.0, 6.0, 0.0))
membrane = ParametricMembrane(sources=[
membrane_folder + 'segA.pdb', membrane_folder + 'segB.pdb',
membrane_folder + 'segC.pdb', membrane_folder + 'segD.pdb'
],
occurences=cell_nb_lipids)
cell = Cell(name=name,
size=size,
extra_parameters=[height],
shape=BioExplorer.ASSEMBLY_SHAPE_SINUSOIDAL,
membrane=membrane,
receptor=ace2_receptor,
random_position_seed=frame + 1,
random_position_strength=0.025,
random_rotation_seed=frame + 2,
random_rotation_strength=0.2)
self._be.add_cell(cell=cell,
position=position,
representation=protein_representation,
random_seed=random_seed)
'''Modify receptor position when attached virus enters the cell'''
receptors_instances = [90, 23, 24, 98, 37, 44]
receptors_sequences = [[2500, 2599], [2200, 2299], [2550, 2649],
[2600, 2699], [2650, 2749], [-1, -1]]
for i in range(len(receptors_instances)):
instance_index = receptors_instances[i]
sequence = receptors_sequences[i]
start_frame = sequence[0]
end_frame = sequence[1]
if frame >= start_frame:
if frame > end_frame:
'''Send receptor to outter space'''
status = self._be.set_protein_instance_transformation(
assembly_name=name,
name=name + '_' + BioExplorer.NAME_RECEPTOR,
instance_index=instance_index,
position=Vector3(0.0, 1e6, 0.0))
else:
'''Current receptor transformation'''
transformation = self._be.get_protein_instance_transformation(
assembly_name=name,
name=name + '_' + BioExplorer.NAME_RECEPTOR,
instance_index=instance_index)
p = transformation['position'].split(',')
q = transformation['rotation'].split(',')
pos = Vector3(float(p[0]), float(p[1]), float(p[2]))
q2 = Quaternion(float(q[0]), float(q[1]), float(q[2]),
float(q[3]))
'''Bend receptor'''
progress = (frame - start_frame) * 1.0 / (end_frame -
start_frame)
q1 = Quaternion(axis=[0, 1, 0], angle=math.pi * progress)
rot = q2 * q1
pos.x += landing_distance * progress * 0.3
pos.y -= landing_distance * progress * 0.3
status = self._be.set_protein_instance_transformation(
assembly_name=name,
name=name + '_' + BioExplorer.NAME_RECEPTOR,
instance_index=instance_index,
position=pos,
rotation=rot)
'''Glycans'''
if nb_receptors != 0 and add_glycans:
self._be.add_multiple_glycans(
representation=glycan_representation,
assembly_name=name,
glycan_type=BioExplorer.NAME_GLYCAN_COMPLEX,
protein_name=BioExplorer.NAME_RECEPTOR,
paths=complex_paths,
indices=[53, 90, 103, 322, 432, 690],
assembly_params=[0, 0, 0.0, frame + 3, 0.2])
self._be.add_multiple_glycans(
representation=glycan_representation,
assembly_name=name,
glycan_type=BioExplorer.NAME_GLYCAN_HYBRID,
protein_name=BioExplorer.NAME_RECEPTOR,
paths=hybrid_paths,
indices=[546],
assembly_params=[0, 0, 0.0, frame + 4, 0.2])
indices = [[155, Quaternion(0.707, 0.0, 0.707, 0.0)],
[730, Quaternion(0.707, 0.0, 0.707, 0.0)]]
count = 0
for index in indices:
o_glycan_name = name + '_' + BioExplorer.NAME_GLYCAN_O_GLYCAN + '_' + str(
index[0])
o_glycan = Sugars(
assembly_name=name,
name=o_glycan_name,
source=o_glycan_paths[0],
protein_name=name + '_' + BioExplorer.NAME_RECEPTOR,
representation=glycan_representation,
chain_ids=[2, 4],
site_indices=[index[0]],
rotation=index[1],
assembly_params=[0, 0, 0.0, frame + count + 5, 0.2])
self._be.add_sugars(o_glycan)
count += 1
def test_vector3_4():
try:
Vector3(1, 2, 3, 4)
assert False
except RuntimeError:
assert True
def add_virus(bioexplorer, name, position, open_conformation_indices=list()):
closed_conformation_indices = list()
for i in range(NB_PROTEIN_S):
if i not in open_conformation_indices:
closed_conformation_indices.append(i)
params = [11.5, 0, 0.0, 0, 0.0, 0.0]
virus_protein_s = Protein(
sources=[
PDB_FOLDER + '6vyb.pdb', # Open conformation
PDB_FOLDER + 'sars-cov-2-v1.pdb' # Closed conformation
],
load_hydrogen=PROTEIN_LOAD_HYDROGEN,
occurences=NB_PROTEIN_S,
assembly_params=params,
rotation=Quaternion(0.0, 1.0, 0.0, 0.0),
instance_indices=[
open_conformation_indices, closed_conformation_indices
])
params = [2.5, 0, 0.0, 0, 0.0, 0.0]
virus_protein_m = Protein(sources=[PDB_FOLDER + 'QHD43419a.pdb'],
load_hydrogen=PROTEIN_LOAD_HYDROGEN,
occurences=NB_PROTEIN_M,
assembly_params=params,
rotation=Quaternion(0.99, 0.0, 0.0, 0.135))
params = [2.5, 0, 0.0, 0, 0.0, 0.0]
virus_protein_e = Protein(sources=[PDB_FOLDER + 'QHD43418a.pdb'],
load_hydrogen=PROTEIN_LOAD_HYDROGEN,
occurences=NB_PROTEIN_E,
assembly_params=params,
rotation=Quaternion(0.705, 0.705, -0.04, -0.04))
virus_membrane = Membrane(sources=[PDB_FOLDER + 'membrane/popc.pdb'],
occurences=15000)
rna_sequence = None
if ADD_RNA:
rna_sequence = RNASequence(source=RNA_FOLDER + 'sars-cov-2.rna',
assembly_params=[11.0, 0.5],
t_range=Vector2(0, 30.5 * math.pi),
shape=bioexplorer.RNA_SHAPE_TREFOIL_KNOT,
shape_params=Vector3(1.51, 1.12, 1.93))
coronavirus = Virus(name=name,
protein_s=virus_protein_s,
protein_e=virus_protein_e,
protein_m=virus_protein_m,
membrane=virus_membrane,
rna_sequence=rna_sequence,
assembly_params=[45.0, 1, 0.025, 2, 0.4, 0.0])
clip_planes = list()
if ADD_RNA:
clip_planes.append([0, 0, -1, 15])
bioexplorer.add_virus(virus=coronavirus,
position=position,
representation=PROTEIN_REPRESENTATION,
atom_radius_multiplier=PROTEIN_RADIUS_MULTIPLIER,
clipping_planes=clip_planes)
if ADD_GLYCANS:
# High-mannose
indices_closed = [61, 122, 234, 603, 709, 717, 801, 1074]
indices_open = [61, 122, 234, 709, 717, 801, 1074]
bioexplorer.add_multiple_glycans(
assembly_name=name,
glycan_type=bioexplorer.NAME_GLYCAN_HIGH_MANNOSE,
protein_name=bioexplorer.NAME_PROTEIN_S_CLOSED,
paths=HIGH_MANNOSE_PATHS,
indices=indices_closed,
representation=PROTEIN_REPRESENTATION)
if open_conformation_indices:
bioexplorer.add_multiple_glycans(
assembly_name=name,
glycan_type=bioexplorer.NAME_GLYCAN_HIGH_MANNOSE,
protein_name=bioexplorer.NAME_PROTEIN_S_OPEN,
paths=HIGH_MANNOSE_PATHS,
indices=indices_open,
representation=PROTEIN_REPRESENTATION)
# Complex
indices_closed = [
17, 74, 149, 165, 282, 331, 343, 616, 657, 1098, 1134, 1158, 1173,
1194
]
indices_open = [
17, 74, 149, 165, 282, 331, 343, 657, 1098, 1134, 1158, 1173, 1194
]
bioexplorer.add_multiple_glycans(
assembly_name=name,
glycan_type=bioexplorer.NAME_GLYCAN_COMPLEX,
protein_name=bioexplorer.NAME_PROTEIN_S_CLOSED,
paths=COMPLEX_PATHS,
indices=indices_closed,
representation=PROTEIN_REPRESENTATION)
if open_conformation_indices:
bioexplorer.add_multiple_glycans(
assembly_name=name,
glycan_type=bioexplorer.NAME_GLYCAN_COMPLEX,
protein_name=bioexplorer.NAME_PROTEIN_S_OPEN,
paths=COMPLEX_PATHS,
indices=indices_open,
representation=PROTEIN_REPRESENTATION)
# O-Glycans
for index in [323, 325]:
o_glycan_name = name + '_' + bioexplorer.NAME_GLYCAN_O_GLYCAN + '_' + str(
index)
o_glycan = Sugars(assembly_name=name,
name=o_glycan_name,
source=O_GLYCAN_PATHS[0],
protein_name=name + '_' +
bioexplorer.NAME_PROTEIN_S_CLOSED,
representation=PROTEIN_REPRESENTATION,
site_indices=[index])
bioexplorer.add_sugars(o_glycan)
# High-mannose glycans on Protein M
indices = [5]
high_mannose_glycans = Sugars(
rotation=Quaternion(0.707, 0.0, 0.0, 0.707),
assembly_name=name,
name=bioexplorer.NAME_GLYCAN_HIGH_MANNOSE,
protein_name=name + '_' + bioexplorer.NAME_PROTEIN_M,
source=HIGH_MANNOSE_PATHS[0],
site_indices=indices,
representation=PROTEIN_REPRESENTATION)
bioexplorer.add_glycans(high_mannose_glycans)
# Complex glycans on Protein E
indices = [48, 66]
complex_glycans = Sugars(rotation=Quaternion(0.707, 0.0, 0.0, 0.707),
assembly_name=name,
name=bioexplorer.NAME_GLYCAN_COMPLEX,
protein_name=name + '_' +
bioexplorer.NAME_PROTEIN_E,
source=COMPLEX_PATHS[0],
site_indices=indices,
representation=PROTEIN_REPRESENTATION)
bioexplorer.add_glycans(complex_glycans)
for i in range(NB_DEFENSINS):
defensin = AssemblyProtein(
assembly_name=name,
name=name + '_' + bioexplorer.NAME_DEFENSIN + '_' + str(i),
source=DEFENSINS_PATH,
assembly_params=[2.0, 0, 0.0, 0, 0.0, 0.0],
shape=bioexplorer.ASSEMBLY_SHAPE_SPHERICAL,
atom_radius_multiplier=PROTEIN_RADIUS_MULTIPLIER,
representation=PROTEIN_REPRESENTATION,
random_seed=100 + i + 1)
bioexplorer.add_assembly_protein(defensin)
def test_layout():
resource_folder = 'tests/test_files/'
pdb_folder = resource_folder + 'pdb/'
bio_explorer = BioExplorer('localhost:5000')
bio_explorer.reset()
print('BioExplorer version ' + bio_explorer.version())
# Suspend image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=0)
line_surfactant = 5
line_virus = 25
line_defense = 45
# Camera
brayns = bio_explorer.core_api()
brayns.set_camera(
current='orthographic',
orientation=[0.0, 0.0, 0.0, 1.0],
position=[23.927943790322814, 24.84577580212592, 260.43975983632527],
target=[23.927943790322814, 24.84577580212592, 39.93749999999999])
params = brayns.OrthographicCameraParams()
params.height = 55
brayns.set_camera_params(params)
# Grid
bio_explorer.add_grid(min_value=0,
max_value=100,
interval=1,
radius=0.005,
colored=False,
position=Vector3(-10.0, -10.0, -10.0))
# Layout
virus_protein_s = Protein(sources=[
pdb_folder + '6vyb.pdb', # Open conformation
pdb_folder + 'sars-cov-2-v1.pdb' # Closed conformation
])
bio_explorer.add_protein(name='Protein S (open)',
protein=virus_protein_s,
conformation_index=0,
position=Vector3(5.0, line_virus, 0.0),
rotation=Quaternion(0.0, 0.0, 1.0, 0.0))
bio_explorer.add_protein(name='Protein S (closed)',
protein=virus_protein_s,
conformation_index=1,
position=Vector3(20.0, line_virus, 0.0),
rotation=Quaternion(0.0, 0.0, 1.0, 0.0))
# Protein M (QHD43419)
virus_protein_m = Protein(sources=[pdb_folder + 'QHD43419a.pdb'])
bio_explorer.add_protein(name='Protein M',
protein=virus_protein_m,
position=Vector3(35.0, line_virus, 0.0))
# Protein E (QHD43418 P0DTC4)
virus_protein_e = Protein(sources=[pdb_folder + 'QHD43418a.pdb'])
bio_explorer.add_protein(name='Protein E',
protein=virus_protein_e,
position=Vector3(45.0, line_virus, 0.0))
# Lactoferrin
lactoferrin = Protein(sources=[pdb_folder + 'immune/1b0l.pdb'])
bio_explorer.add_protein(name='Lactoferrin',
protein=lactoferrin,
position=Vector3(5.0, line_defense, 0.0))
# Defensin
defensin = Protein(sources=[pdb_folder + 'immune/1ijv.pdb'])
bio_explorer.add_protein(name='Defensin',
protein=defensin,
position=Vector3(20.0, line_defense, 0.0))
# Glucose
glucose = Protein(sources=[pdb_folder + 'glucose.pdb'],
load_non_polymer_chemicals=True)
bio_explorer.add_protein(name='Glucose',
protein=glucose,
position=Vector3(30.0, line_defense, 0.0),
rotation=Quaternion(0.0, 0.0, 0.707, 0.707))
# ACE2 Receptor
ace2_receptor = Protein(sources=[pdb_folder + '6m18.pdb'])
bio_explorer.add_protein(name='ACE2 receptor',
protein=ace2_receptor,
position=Vector3(45.0, line_defense - 2.5, 0.0),
rotation=Quaternion(0.5, 0.5, 1.0, 0.0))
# Surfactant
head_source = pdb_folder + 'surfactant/1pw9.pdb'
branch_source = pdb_folder + 'surfactant/1k6f.pdb'
surfactant_d = Surfactant(
name='Surfactant',
surfactant_protein=bio_explorer.SURFACTANT_BRANCH,
head_source=head_source,
branch_source=branch_source)
bio_explorer.add_surfactant(surfactant=surfactant_d,
position=Vector3(5.0, line_surfactant, 0.0))
# Restore image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=20)
def test_low_glucose():
try:
# Connect to BioExplorer server
bio_explorer = BioExplorer('localhost:5000')
core = bio_explorer.core_api()
print('BioExplorer version ' + bio_explorer.version())
bio_explorer.reset()
# Suspend image streaming
core.set_application_parameters(image_stream_fps=0)
# Build full model
add_virus(bio_explorer,
name='Coronavirus 1',
position=Vector3(-5.0, 19.0, -36.0))
add_virus(bio_explorer,
name='Coronavirus 2',
position=Vector3(73.0, 93.0, -115.0))
add_virus(bio_explorer,
name='Coronavirus 3',
position=Vector3(-84.0, 110.0, 75.0))
add_virus(bio_explorer,
name='Coronavirus 4',
position=Vector3(-70.0, -100.0, 230.0),
open_conformation_indices=[1])
add_virus(bio_explorer,
name='Coronavirus 5',
position=Vector3(200.0, 20.0, -150.0))
add_cell(bio_explorer,
name='Cell 1',
size=CELL_SIZE,
height=CELL_HEIGHT,
position=Vector3(4.5, -186.0, 7.0))
add_surfactant_d(bio_explorer,
name='Surfactant-D 1',
position=Vector3(74.0, 24.0, -45.0),
random_seed=1)
add_surfactant_d(bio_explorer,
name='Surfactant-D 2',
position=Vector3(-30.0, 91.0, 20.0),
random_seed=2)
add_surfactant_d(bio_explorer,
name='Surfactant-D 3',
position=Vector3(-165.0, 140.0, 105.0),
random_seed=1)
add_surfactant_d(bio_explorer,
name='Surfactant-D 4',
position=Vector3(-260.0, 50.0, 0.0),
random_seed=6)
add_surfactant_a(bio_explorer,
name='Surfactant-A 1',
position=Vector3(200.0, 50.0, 150.0),
random_seed=2)
add_glucose(bio_explorer, CELL_SIZE, 120000)
add_lactoferrins(bio_explorer, CELL_SIZE, 150)
add_defensins(bio_explorer, CELL_SIZE, 300)
# BBP only
#
# core.add_model(name='Emile', path=LYMPHOCYTE_PATH)
# models = core.scene.models
# lymphocyte_model_id = models[len(models) - 1]['id']
# transformation = {'rotation': [0.707, 0.707, 0.0, 0.0],
# 'rotation_center': [0.0, 0.0, 0.0],
# 'scale': [2.0, 2.0, 2.0],
# 'translation': [-935.0, 0.0, 0.0]}
# core.update_model(
# id=lymphocyte_model_id, transformation=transformation)
# Apply default materials
bio_explorer.apply_default_color_scheme(
bio_explorer.SHADING_MODE_BASIC)
# Set rendering settings
core.set_renderer(background_color=[96 / 255, 125 / 255, 139 / 255],
current='bio_explorer',
samples_per_pixel=1,
subsampling=4,
max_accum_frames=64)
params = core.BioExplorerRendererParams()
params.shadows = 0.75
params.soft_shadows = 1.0
core.set_renderer_params(params)
# Restore image streaming
core.set_application_parameters(image_stream_fps=20)
except Exception as ex:
print(ex)
raise
def _add_viruses(self, frame):
virus_sequences = [
[[-1000, 2499], [2500, 2599], [2600, 2799], [2800, 2999],
[3000, 3099], [3100, 3750]],
# Virus used for the ACE2 close-up
[[0, 2100], [2200, 2299], [2300, 2499], [2500, 3049], [3050, 3149],
[3150, 3750]],
[[-800, 2549], [2550, 2649], [2650, 2849], [2850, 3199],
[3200, 3299], [3300, 3750]],
[[-1400, 3750], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6],
[1e6, 1e6]],
[[-400, 2599], [2600, 2699], [2700, 2899], [2900, 3119],
[3120, 3219], [3220, 3750]],
[[0, 2649], [2650, 2749], [2750, 2949], [2950, 3199], [3200, 3299],
[3300, 3750]],
# new Viruses
[[-1, -1], [-1, -1], [-1, -1], [-1, 3212], [3213, 3312],
[3313, 3750]],
[[-1, -1], [-1, -1], [-1, -1], [-1, 3201], [3202, 3301],
[3302, 3750]],
[[-1, -1], [-1, -1], [-1, -1], [-1, 3171], [3172, 3271],
[3272, 3750]],
[[-1, -1], [-1, -1], [-1, -1], [-1, 3152], [3153, 3252],
[3253, 3750]],
[[-1, -1], [-1, -1], [-1, -1], [-1, 3358], [3359, 3458],
[3459, 3750]]
]
virus_radii = [
45.0, 44.0, 45.0, 43.0, 44.0, 43.0, 45.0, 46.0, 44.0, 45.0, 44.0
]
virus_flights_in = [
[
Vector3(-250.0, 100.0, -70.0),
Quaternion(0.519, 0.671, 0.528, -0.036),
Vector3(-337.3, -92.3, -99.2),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_LINEAR
],
[
Vector3(-50.0, 300.0, 250.0),
Quaternion(0.456, 0.129, -0.185, -0.860),
Vector3(-74.9, -99.0, 228.8),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_LINEAR
],
[
Vector3(150.0, 100.0, 50.0),
Quaternion(0.087, 0.971, -0.147, -0.161),
Vector3(187.5, -110.4, 51.2),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_LINEAR
],
[
Vector3(40.0, 250.0, -50),
Quaternion(0.0, 0.0, 0.0, 1.0),
Vector3(4.5, 100.0, 7.5),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_LINEAR
],
[
Vector3(60.0, 100.0, -240.0),
Quaternion(-0.095, 0.652, -0.326, 0.677),
Vector3(73.9, -117.1, -190.4),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_LINEAR
],
[
Vector3(200.0, 100.0, 300.0),
Quaternion(-0.866, 0.201, 0.308, -0.336),
Vector3(211.5, -104.9, 339.2),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_LINEAR
],
# New viruses (no flying in, only flying out)
[
Vector3(),
Quaternion(),
Vector3(),
Quaternion(), ROTATION_MODE_LINEAR
],
[
Vector3(),
Quaternion(),
Vector3(),
Quaternion(), ROTATION_MODE_LINEAR
],
[
Vector3(),
Quaternion(),
Vector3(),
Quaternion(), ROTATION_MODE_LINEAR
],
[
Vector3(),
Quaternion(),
Vector3(),
Quaternion(), ROTATION_MODE_LINEAR
],
[
Vector3(),
Quaternion(),
Vector3(),
Quaternion(), ROTATION_MODE_LINEAR
]
]
virus_flights_out = [[
Vector3(-250.0, -150.0, -70.0),
Quaternion(),
Vector3(-270.0, 200.0, -99.2),
Quaternion(0.519, 0.671, 0.528, -0.036), ROTATION_MODE_LINEAR
],
[
Vector3(-50.0, -150.0, 250.0),
Quaternion(),
Vector3(-75.0, 240.0, 228.8),
Quaternion(0.456, 0.129, -0.185, -0.860),
ROTATION_MODE_LINEAR
],
[
Vector3(150.0, -150.0, 50.0),
Quaternion(),
Vector3(187.0, 300.0, 51.2),
Quaternion(0.087, 0.971, -0.147, -0.161),
ROTATION_MODE_LINEAR
],
[
Vector3(),
Quaternion(),
Vector3(),
Quaternion(), ROTATION_MODE_LINEAR
],
[
Vector3(60.0, -150.0, -240.0),
Quaternion(),
Vector3(74.0, 195.0, -220.0),
Quaternion(-0.095, 0.652, -0.326, 0.677),
ROTATION_MODE_LINEAR
],
[
Vector3(-200.0, -150.0, 300.0),
Quaternion(),
Vector3(-210.0, 205.0, 330.0),
Quaternion(-0.866, 0.201, 0.308, -0.336),
ROTATION_MODE_LINEAR
],
[
Vector3(531, -150.0, -34.0),
Quaternion(),
Vector3(500.0, 215.0, -50.0),
Quaternion(0.431, -0.145, -0.700, -0.550),
ROTATION_MODE_LINEAR
],
[
Vector3(225.0, -150.0, 554.0),
Quaternion(),
Vector3(200.0, 190.0, 520.0),
Quaternion(-0.466, -0.086, -0.616, -0.629),
ROTATION_MODE_LINEAR
],
[
Vector3(-171, -150.0, -5.0),
Quaternion(),
Vector3(-160.0, 300.0, 10.0),
Quaternion(0.227, 0.834, -0.187, 0.468),
ROTATION_MODE_LINEAR
],
[
Vector3(-331, -150.0, 343),
Quaternion(),
Vector3(-310.0, 230.0, 350.0),
Quaternion(0.417, 0.849, -0.075, -0.316),
ROTATION_MODE_LINEAR
],
[
Vector3(159.0, -150.0, -341.0),
Quaternion(),
Vector3(170.0, 100.0, -360.0),
Quaternion(0.483, -0.352, 0.769, -0.226),
ROTATION_MODE_LINEAR
]]
indices = range(len(virus_sequences))
if self._magnetic:
indices = [1]
for virus_index in indices:
name = 'Coronavirus ' + str(virus_index)
current_sequence = 0
sequences = virus_sequences[virus_index]
for i in range(len(sequences)):
if frame >= sequences[i][0]:
current_sequence = i
'''Initialize position and rotation to end-of-flight values'''
start_frame = sequences[current_sequence][0]
end_frame = sequences[current_sequence][1]
progress_in_sequence = (frame - start_frame) / (end_frame -
start_frame)
morphing_step = 0.0
if current_sequence == 0:
'''Flying'''
pos, rot, progress = self._get_transformation(
start_frame, end_frame, frame,
virus_flights_in[virus_index])
self._log(
3, '- Virus %d is flying in... (%.01f pct)' %
(virus_index, progress))
elif current_sequence == 1:
'''Landing'''
pos = virus_flights_in[virus_index][2]
rot = virus_flights_in[virus_index][3]
pos.y -= landing_distance * progress_in_sequence
self._log(3, '- Virus %d is landing...' % virus_index)
elif current_sequence == 2:
'''Merging into cell'''
pos = virus_flights_in[virus_index][2]
rot = virus_flights_in[virus_index][3]
morphing_step = (frame - start_frame) / (end_frame -
start_frame)
pos.y -= landing_distance
self._log(
3, '- Virus %d is merging in (%.01f pct)' %
(virus_index, morphing_step * 100.0))
elif current_sequence == 3:
'''Inside cell'''
self._log(3, '- Virus %d is inside cell' % virus_index)
'''Virus is not added to the scene'''
self._be.remove_assembly(name=name)
continue
elif current_sequence == 4:
'''Merging out of cell'''
pos = virus_flights_out[virus_index][0]
rot = virus_flights_out[virus_index][1]
morphing_step = 1.0 - (frame - start_frame) / (end_frame -
start_frame)
self._log(
3, '- Virus %d is merging out (%.01f pct)' %
(virus_index, morphing_step * 100.0))
else:
'''Flying out'''
pos, rot, progress = self._get_transformation(
start_frame, end_frame, frame,
virus_flights_out[virus_index])
self._log(
3, '- Virus %d is flying out... (%.01f pct)' %
(virus_index, progress))
self._be.add_coronavirus(name=name,
resource_folder=resource_folder,
representation=protein_representation,
position=pos,
rotation=rot,
add_glycans=add_glycans,
assembly_params=[
virus_radii[virus_index],
5 * frame + 2 * virus_index, 0.25,
frame + 2 * virus_index + 1, 0.1,
morphing_step
])
def test_virus():
resource_folder = 'tests/test_files/'
pdb_folder = resource_folder + 'pdb/'
rna_folder = resource_folder + 'rna/'
glycan_folder = pdb_folder + 'glycans/'
bio_explorer = BioExplorer('localhost:5000')
bio_explorer.reset()
# Settings
virus_radius = 45.0
add_glycans = True
protein_radius_multiplier = 1.0
protein_representation = BioExplorer.REPRESENTATION_ATOMS
protein_load_hydrogen = False
# Virus configuration
nb_protein_s = 62
nb_protein_s_indices = [1, 27, 43]
nb_protein_e = 42
nb_protein_m = 50
show_rna = True
# Virus parameters
show_functional_regions = False
show_glycosylation_sites = False
# Suspend image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=0)
# Protein S
open_conformation_indices = nb_protein_s_indices
closed_conformation_indices = list()
for i in range(nb_protein_s):
if i not in open_conformation_indices:
closed_conformation_indices.append(i)
params = [11.5, 0, 0.0, 0, 0.0, 0.0]
virus_protein_s = Protein(
sources=[pdb_folder + '6vyb.pdb', pdb_folder + 'sars-cov-2-v1.pdb'],
load_hydrogen=protein_load_hydrogen, occurences=nb_protein_s,
assembly_params=params, rotation=Quaternion(0.087, 0.0, 0.996, 0.0),
instance_indices=[open_conformation_indices, closed_conformation_indices])
# Protein M (QHD43419)
params = [2.5, 0, 0.0, 0, 0.0, 0.0]
virus_protein_m = Protein(
sources=[pdb_folder + 'QHD43419a.pdb'],
load_hydrogen=protein_load_hydrogen, occurences=nb_protein_m,
assembly_params=params, rotation=Quaternion(0.99, 0.0, 0.0, 0.135))
# Protein E (QHD43418 P0DTC4)
params = [2.5, 0, 0.0, 0, 0.0, 0.0]
virus_protein_e = Protein(
sources=[pdb_folder + 'QHD43418a.pdb'], load_hydrogen=protein_load_hydrogen,
occurences=nb_protein_e, assembly_params=params,
rotation=Quaternion(0.705, 0.705, -0.04, -0.04))
# Virus membrane
virus_membrane = ParametricMembrane(
sources=[pdb_folder + 'membrane/popc.pdb'],
occurences=15000)
# RNA Sequence
clip_planes = list()
rna_sequence = None
if show_rna:
clip_planes.append([0.0, 0.0, -1.0, 15.0])
rna_sequence = RNASequence(
source=rna_folder + 'sars-cov-2.rna', assembly_params=[11.0, 0.5],
t_range=Vector2(0, 30.5 * math.pi), shape=bio_explorer.RNA_SHAPE_TREFOIL_KNOT,
shape_params=Vector3(1.51, 1.12, 1.93))
# Coronavirus
name = 'Coronavirus'
coronavirus = Virus(
name=name, protein_s=virus_protein_s, protein_e=virus_protein_e, protein_m=virus_protein_m,
membrane=virus_membrane, rna_sequence=rna_sequence,
assembly_params=[virus_radius, 1, 0.025, 2, 0.4, 0.0])
bio_explorer.add_virus(
virus=coronavirus, position=Vector3(-70.0, -100.0, 230.0),
representation=protein_representation, atom_radius_multiplier=protein_radius_multiplier,
clipping_planes=clip_planes)
# Glycans
if add_glycans:
complex_paths = [glycan_folder + 'complex/5.pdb', glycan_folder + 'complex/15.pdb',
glycan_folder + 'complex/25.pdb', glycan_folder + 'complex/35.pdb']
high_mannose_paths = [
glycan_folder + 'high-mannose/1.pdb', glycan_folder + 'high-mannose/2.pdb',
glycan_folder + 'high-mannose/3.pdb', glycan_folder + 'high-mannose/4.pdb']
o_glycan_paths = [glycan_folder + 'o-glycan/12.pdb']
# High-mannose
indices_closed = [61, 122, 234, 603, 709, 717, 801, 1074]
indices_open = [61, 122, 234, 709, 717, 801, 1074]
bio_explorer.add_multiple_glycans(
assembly_name=name, glycan_type=bio_explorer.NAME_GLYCAN_HIGH_MANNOSE,
protein_name=bio_explorer.NAME_PROTEIN_S_CLOSED, paths=high_mannose_paths,
indices=indices_closed, representation=protein_representation,
atom_radius_multiplier=protein_radius_multiplier)
bio_explorer.add_multiple_glycans(
assembly_name=name, glycan_type=bio_explorer.NAME_GLYCAN_HIGH_MANNOSE,
protein_name=bio_explorer.NAME_PROTEIN_S_OPEN, paths=high_mannose_paths,
indices=indices_open, representation=protein_representation,
atom_radius_multiplier=protein_radius_multiplier)
# Complex
indices1 = [17, 74, 149, 165, 282, 331, 343, 616, 657, 1098, 1134, 1158, 1173, 1194]
indices2 = [17, 74, 149, 165, 282, 331, 343, 1098, 657, 1134, 1158, 1173, 1194]
bio_explorer.add_multiple_glycans(
assembly_name=name, glycan_type=bio_explorer.NAME_GLYCAN_COMPLEX,
protein_name=bio_explorer.NAME_PROTEIN_S_CLOSED, paths=complex_paths, indices=indices1,
representation=protein_representation, atom_radius_multiplier=protein_radius_multiplier)
bio_explorer.add_multiple_glycans(
assembly_name=name, glycan_type=bio_explorer.NAME_GLYCAN_COMPLEX,
protein_name=bio_explorer.NAME_PROTEIN_S_OPEN, paths=complex_paths, indices=indices2,
representation=protein_representation, atom_radius_multiplier=protein_radius_multiplier)
# O-Glycans
for index in [323, 325]:
o_glycan_name = name + '_' + bio_explorer.NAME_GLYCAN_O_GLYCAN + '_' + str(index)
o_glycan = Sugars(
assembly_name=name, name=o_glycan_name, source=o_glycan_paths[0],
protein_name=name + '_' + bio_explorer.NAME_PROTEIN_S_CLOSED,
representation=protein_representation, site_indices=[index],
atom_radius_multiplier=protein_radius_multiplier)
bio_explorer.add_sugars(o_glycan)
# High-mannose glycans on Protein M
indices = [5]
protein_name = name + '_' + bio_explorer.NAME_PROTEIN_M
high_mannose_glycans = Sugars(
rotation=Quaternion(0.707, 0.0, 0.0, 0.707),
assembly_name=name, name=protein_name + '_' + bio_explorer.NAME_GLYCAN_HIGH_MANNOSE,
protein_name=protein_name, source=high_mannose_paths[0],
site_indices=indices,
representation=protein_representation
)
bio_explorer.add_glycans(high_mannose_glycans)
# Complex glycans on Protein E
indices = [48, 66]
protein_name = name + '_' + bio_explorer.NAME_PROTEIN_E
complex_glycans = Sugars(
rotation=Quaternion(0.707, 0.0, 0.0, 0.707),
assembly_name=name, name=protein_name + '_' + bio_explorer.NAME_GLYCAN_COMPLEX,
protein_name=protein_name, source=complex_paths[0],
site_indices=indices,
representation=protein_representation
)
bio_explorer.add_glycans(complex_glycans)
# Apply default materials
bio_explorer.apply_default_color_scheme(shading_mode=bio_explorer.SHADING_MODE_BASIC)
# Functional regions on open spike
if show_functional_regions:
indices = [1, 16, 306, 330, 438, 507, 522, 816, 835, 908, 986, 1076, 1274, 2000]
region_colors = [
[1.0, 1.0, 1.0], [0.0, 0.0, 1.0], [1.0, 1.0, 1.0], [0.0, 1.0, 0.0], [0.4, 0.1, 0.1],
[0.0, 1.0, 0.0], [1.0, 1.0, 1.0], [1.0, 0.0, 0.0], [1.0, 1.0, 1.0], [1.0, 1.0, 0.0],
[1.0, 1.0, 1.0], [1.0, 0.0, 1.0], [1.0, 1.0, 1.0], [1.0, 1.0, 1.0]]
palette = list()
for index in range(len(indices) - 1):
for i in range(0, indices[index + 1] - indices[index]):
color = list()
for j in range(3):
color.append(region_colors[index][j] * 1)
palette.append(color)
bio_explorer.set_protein_color_scheme(
assembly_name=name, name=name + '_' + bio_explorer.NAME_PROTEIN_S_OPEN,
color_scheme=bio_explorer.COLOR_SCHEME_REGION, palette=palette)
# Display glycosylation sites
if show_glycosylation_sites:
palette = sns.color_palette('Set2', 2)
bio_explorer.set_protein_color_scheme(
assembly_name=name, name=name + '_' + bio_explorer.NAME_PROTEIN_S_OPEN,
color_scheme=bio_explorer.COLOR_SCHEME_GLYCOSYLATION_SITE, palette=palette)
bio_explorer.set_protein_color_scheme(
assembly_name=name, name=name + '_' + bio_explorer.NAME_PROTEIN_S_CLOSED,
color_scheme=bio_explorer.COLOR_SCHEME_GLYCOSYLATION_SITE, palette=palette)
# Set rendering settings
bio_explorer.core_api().set_renderer(
background_color=[96 / 255, 125 / 255, 139 / 255], current='bio_explorer',
samples_per_pixel=1, subsampling=4, max_accum_frames=64)
params = bio_explorer.core_api().BioExplorerRendererParams()
params.shadows = 0.75
params.soft_shadows = 1.0
bio_explorer.core_api().set_renderer_params(params)
# Restore image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=20)
def test_vector3_1():
try:
Vector3(1)
assert False
except RuntimeError:
assert True