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)