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_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)
# 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)
# ACE2 Receptor
ace2_receptor = Protein(sources=[pdb_folder + '6m1d.pdb'])
bio_explorer.add_protein('ACE2 receptor',
ace2_receptor,
rotation=Quaternion(0.5, 0.5, 1.0, 0.0))
# Restore image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=20)
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 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)
# Resources
protein_representation = BioExplorer.REPRESENTATION_ATOMS_AND_STICKS
protein_radius_multiplier = 1.0
glycan_representation = BioExplorer.REPRESENTATION_ATOMS_AND_STICKS
glycan_radius_multiplier = 1.0
# M Protein
source = pdb_folder + 'QHD43419a.pdb'
m_protein = Protein(sources=[source],
load_hydrogen=False,
load_non_polymer_chemicals=False)
name = bio_explorer.NAME_PROTEIN_M
bio_explorer.add_protein(name=name,
protein=m_protein,
atom_radius_multiplier=protein_radius_multiplier,
representation=protein_representation)
# Glycans
glycan_folder = pdb_folder + 'glycans/'
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'
]
# 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=bio_explorer.NAME_GLYCAN_HIGH_MANNOSE,
protein_name=name,
source=high_mannose_paths[0],
site_indices=indices,
representation=glycan_representation,
atom_radius_multiplier=glycan_radius_multiplier)
bio_explorer.add_glycans(high_mannose_glycans)
# Materials
bio_explorer.apply_default_color_scheme(
shading_mode=bio_explorer.SHADING_MODE_BASIC)
# 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_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_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_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_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 _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_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 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 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 _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_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)
