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)
