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_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