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_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_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_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)