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_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 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)