class HighGlucoseScenario():
def __init__(self,
hostname,
port,
projection,
output_folder,
image_k=4,
image_samples_per_pixel=64,
log_level=1,
shaders=list(['bio_explorer']),
magnetic=False):
self._log_level = log_level
self._hostname = hostname
self._url = hostname + ':' + str(port)
self._be = BioExplorer(self._url)
self._core = self._be.core_api()
self._image_size = [1920, 1080]
self._image_samples_per_pixel = image_samples_per_pixel
self._image_projection = projection
self._image_output_folder = output_folder
self._shaders = shaders
self._magnetic = magnetic
self._prepare_movie(projection, image_k)
self._log(
1,
'================================================================================'
)
self._log(1, '- Version : ' + self._be.version())
self._log(1, '- URL : ' + self._url)
self._log(1, '- Projection : ' + projection)
self._log(1, '- Frame size : ' + str(self._image_size))
self._log(1, '- Export folder : ' + self._image_output_folder)
self._log(1,
'- Samples per pixel: ' + str(self._image_samples_per_pixel))
self._log(
1,
'================================================================================'
)
def _log(self, level, message):
if level <= self._log_level:
print('[' + str(datetime.now()) + '] ' + message)
def _get_transformation(self, start_frame, end_frame, frame, data):
'''Progress'''
progress = (frame - start_frame) * 1.0 / (end_frame - start_frame)
progress = max(0.0, progress)
progress = min(1.0, progress)
'''Position'''
start_pos = data[0].to_list()
end_pos = data[2].to_list()
pos = start_pos
for i in range(3):
pos[i] += (end_pos[i] - start_pos[i]) * progress
'''Rotation'''
start_rot = data[1]
end_rot = data[3]
rot = Quaternion.slerp(start_rot, end_rot, progress)
if data[4] == ROTATION_MODE_SINUSOIDAL:
rot = Quaternion.slerp(start_rot, end_rot,
math.cos((progress - 0.5) * math.pi))
return [Vector3(pos[0], pos[1], pos[2]), rot, progress * 100.0]
def _add_viruses(self, frame):
virus_sequences = [
[[-1000, 2499], [2500, 2599], [2600, 2799], [2800, 2999],
[3000, 3099], [3100, 3750]],
# Virus used for the ACE2 close-up
[[0, 2100], [2200, 2299], [2300, 2499], [2500, 3049], [3050, 3149],
[3150, 3750]],
[[-800, 2549], [2550, 2649], [2650, 2849], [2850, 3199],
[3200, 3299], [3300, 3750]],
[[-1400, 3750], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6],
[1e6, 1e6]],
[[-400, 2599], [2600, 2699], [2700, 2899], [2900, 3119],
[3120, 3219], [3220, 3750]],
[[0, 2649], [2650, 2749], [2750, 2949], [2950, 3199], [3200, 3299],
[3300, 3750]],
# new Viruses
[[-1, -1], [-1, -1], [-1, -1], [-1, 3212], [3213, 3312],
[3313, 3750]],
[[-1, -1], [-1, -1], [-1, -1], [-1, 3201], [3202, 3301],
[3302, 3750]],
[[-1, -1], [-1, -1], [-1, -1], [-1, 3171], [3172, 3271],
[3272, 3750]],
[[-1, -1], [-1, -1], [-1, -1], [-1, 3152], [3153, 3252],
[3253, 3750]],
[[-1, -1], [-1, -1], [-1, -1], [-1, 3358], [3359, 3458],
[3459, 3750]]
]
virus_radii = [
45.0, 44.0, 45.0, 43.0, 44.0, 43.0, 45.0, 46.0, 44.0, 45.0, 44.0
]
virus_flights_in = [
[
Vector3(-250.0, 100.0, -70.0),
Quaternion(0.519, 0.671, 0.528, -0.036),
Vector3(-337.3, -92.3, -99.2),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_LINEAR
],
[
Vector3(-50.0, 300.0, 250.0),
Quaternion(0.456, 0.129, -0.185, -0.860),
Vector3(-74.9, -99.0, 228.8),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_LINEAR
],
[
Vector3(150.0, 100.0, 50.0),
Quaternion(0.087, 0.971, -0.147, -0.161),
Vector3(187.5, -110.4, 51.2),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_LINEAR
],
[
Vector3(40.0, 250.0, -50),
Quaternion(0.0, 0.0, 0.0, 1.0),
Vector3(4.5, 100.0, 7.5),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_LINEAR
],
[
Vector3(60.0, 100.0, -240.0),
Quaternion(-0.095, 0.652, -0.326, 0.677),
Vector3(73.9, -117.1, -190.4),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_LINEAR
],
[
Vector3(200.0, 100.0, 300.0),
Quaternion(-0.866, 0.201, 0.308, -0.336),
Vector3(211.5, -104.9, 339.2),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_LINEAR
],
# New viruses (no flying in, only flying out)
[
Vector3(),
Quaternion(),
Vector3(),
Quaternion(), ROTATION_MODE_LINEAR
],
[
Vector3(),
Quaternion(),
Vector3(),
Quaternion(), ROTATION_MODE_LINEAR
],
[
Vector3(),
Quaternion(),
Vector3(),
Quaternion(), ROTATION_MODE_LINEAR
],
[
Vector3(),
Quaternion(),
Vector3(),
Quaternion(), ROTATION_MODE_LINEAR
],
[
Vector3(),
Quaternion(),
Vector3(),
Quaternion(), ROTATION_MODE_LINEAR
]
]
virus_flights_out = [[
Vector3(-250.0, -150.0, -70.0),
Quaternion(),
Vector3(-270.0, 200.0, -99.2),
Quaternion(0.519, 0.671, 0.528, -0.036), ROTATION_MODE_LINEAR
],
[
Vector3(-50.0, -150.0, 250.0),
Quaternion(),
Vector3(-75.0, 240.0, 228.8),
Quaternion(0.456, 0.129, -0.185, -0.860),
ROTATION_MODE_LINEAR
],
[
Vector3(150.0, -150.0, 50.0),
Quaternion(),
Vector3(187.0, 300.0, 51.2),
Quaternion(0.087, 0.971, -0.147, -0.161),
ROTATION_MODE_LINEAR
],
[
Vector3(),
Quaternion(),
Vector3(),
Quaternion(), ROTATION_MODE_LINEAR
],
[
Vector3(60.0, -150.0, -240.0),
Quaternion(),
Vector3(74.0, 195.0, -220.0),
Quaternion(-0.095, 0.652, -0.326, 0.677),
ROTATION_MODE_LINEAR
],
[
Vector3(-200.0, -150.0, 300.0),
Quaternion(),
Vector3(-210.0, 205.0, 330.0),
Quaternion(-0.866, 0.201, 0.308, -0.336),
ROTATION_MODE_LINEAR
],
[
Vector3(531, -150.0, -34.0),
Quaternion(),
Vector3(500.0, 215.0, -50.0),
Quaternion(0.431, -0.145, -0.700, -0.550),
ROTATION_MODE_LINEAR
],
[
Vector3(225.0, -150.0, 554.0),
Quaternion(),
Vector3(200.0, 190.0, 520.0),
Quaternion(-0.466, -0.086, -0.616, -0.629),
ROTATION_MODE_LINEAR
],
[
Vector3(-171, -150.0, -5.0),
Quaternion(),
Vector3(-160.0, 300.0, 10.0),
Quaternion(0.227, 0.834, -0.187, 0.468),
ROTATION_MODE_LINEAR
],
[
Vector3(-331, -150.0, 343),
Quaternion(),
Vector3(-310.0, 230.0, 350.0),
Quaternion(0.417, 0.849, -0.075, -0.316),
ROTATION_MODE_LINEAR
],
[
Vector3(159.0, -150.0, -341.0),
Quaternion(),
Vector3(170.0, 100.0, -360.0),
Quaternion(0.483, -0.352, 0.769, -0.226),
ROTATION_MODE_LINEAR
]]
indices = range(len(virus_sequences))
if self._magnetic:
indices = [1]
for virus_index in indices:
name = 'Coronavirus ' + str(virus_index)
current_sequence = 0
sequences = virus_sequences[virus_index]
for i in range(len(sequences)):
if frame >= sequences[i][0]:
current_sequence = i
'''Initialize position and rotation to end-of-flight values'''
start_frame = sequences[current_sequence][0]
end_frame = sequences[current_sequence][1]
progress_in_sequence = (frame - start_frame) / (end_frame -
start_frame)
morphing_step = 0.0
if current_sequence == 0:
'''Flying'''
pos, rot, progress = self._get_transformation(
start_frame, end_frame, frame,
virus_flights_in[virus_index])
self._log(
3, '- Virus %d is flying in... (%.01f pct)' %
(virus_index, progress))
elif current_sequence == 1:
'''Landing'''
pos = virus_flights_in[virus_index][2]
rot = virus_flights_in[virus_index][3]
pos.y -= landing_distance * progress_in_sequence
self._log(3, '- Virus %d is landing...' % virus_index)
elif current_sequence == 2:
'''Merging into cell'''
pos = virus_flights_in[virus_index][2]
rot = virus_flights_in[virus_index][3]
morphing_step = (frame - start_frame) / (end_frame -
start_frame)
pos.y -= landing_distance
self._log(
3, '- Virus %d is merging in (%.01f pct)' %
(virus_index, morphing_step * 100.0))
elif current_sequence == 3:
'''Inside cell'''
self._log(3, '- Virus %d is inside cell' % virus_index)
'''Virus is not added to the scene'''
self._be.remove_assembly(name=name)
continue
elif current_sequence == 4:
'''Merging out of cell'''
pos = virus_flights_out[virus_index][0]
rot = virus_flights_out[virus_index][1]
morphing_step = 1.0 - (frame - start_frame) / (end_frame -
start_frame)
self._log(
3, '- Virus %d is merging out (%.01f pct)' %
(virus_index, morphing_step * 100.0))
else:
'''Flying out'''
pos, rot, progress = self._get_transformation(
start_frame, end_frame, frame,
virus_flights_out[virus_index])
self._log(
3, '- Virus %d is flying out... (%.01f pct)' %
(virus_index, progress))
self._be.add_coronavirus(name=name,
resource_folder=resource_folder,
representation=protein_representation,
position=pos,
rotation=rot,
add_glycans=add_glycans,
assembly_params=[
virus_radii[virus_index],
5 * frame + 2 * virus_index, 0.25,
frame + 2 * virus_index + 1, 0.1,
morphing_step
])
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
def _add_surfactant_d(self, name, position, rotation, random_seed):
surfactant_d = Surfactant(
name=name,
surfactant_protein=BioExplorer.SURFACTANT_PROTEIN_D,
head_source=surfactant_head_source,
branch_source=surfactant_branch_source)
self._be.add_surfactant(surfactant=surfactant_d,
representation=protein_representation,
position=position,
rotation=rotation,
random_seed=random_seed)
def _add_surfactant_a(self, name, position, rotation, random_seed):
surfactant_a = Surfactant(
name=name,
surfactant_protein=BioExplorer.SURFACTANT_PROTEIN_A,
head_source=surfactant_head_source,
branch_source=surfactant_branch_source)
self._be.add_surfactant(surfactant=surfactant_a,
representation=protein_representation,
position=position,
rotation=rotation,
random_seed=random_seed)
def _add_glucose_to_surfactant_head(self, name):
for index in [321, 323]:
glucose_name = name + '_' + BioExplorer.NAME_GLUCOSE + '_' + str(
index)
glucose = Sugars(assembly_name=name,
name=glucose_name,
source=glucose_path,
protein_name=name + '_' +
BioExplorer.NAME_SURFACTANT_HEAD,
representation=glycan_representation,
site_indices=[index])
self._be.add_sugars(glucose)
def _add_surfactants_d(self, frame):
spd_sequences = [[-1550, 3750], [0, 3750], [0, 3750]]
spd_random_seeds = [1, 2, 6]
spd_flights = [[
Vector3(-340.0, 0.0, -100.0),
Quaternion(-0.095, 0.652, -0.326, 0.677),
Vector3(74.0 + (74.0 + 340), 24.0 + (24.0 - 0.0),
-45.0 + (-45.0 + 100)),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_SINUSOIDAL
],
[
Vector3(-200, 0.0, -200.0),
Quaternion(0.087, 0.971, -0.147, -0.161),
Vector3(304.0, 75.0, -100.0),
Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_SINUSOIDAL
],
[
Vector3(-460.0, 50.0, 0.0),
Quaternion(0.519, 0.671, 0.528, -0.036),
Vector3(160.0, -50.0, -50.0),
Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_SINUSOIDAL
]]
for surfactant_index in range(len(spd_sequences)):
name = 'Surfactant-D ' + str(surfactant_index)
sequence = spd_sequences[surfactant_index]
pos, rot, progress = self._get_transformation(
start_frame=sequence[0],
end_frame=sequence[1],
frame=frame,
data=spd_flights[surfactant_index])
self._log(3, '- ' + name + ' (%.01f pct)' % progress)
self._add_surfactant_d(
name=name,
position=pos,
rotation=rot,
random_seed=spd_random_seeds[surfactant_index])
self._add_glucose_to_surfactant_head(name=name)
def _add_surfactants_a(self, frame):
spa_sequences = [[0, 3750]]
spa_random_seeds = [2]
spa_frames = [
[
Vector3(-400.0, -100.0, 100.0),
Quaternion(-0.095, 0.652, -0.326, 0.677),
Vector3(250.0, -50.0, 100.0),
Quaternion(1.0, 0.0, 0.0, 0.0), ROTATION_MODE_SINUSOIDAL
],
]
for surfactant_index in range(len(spa_frames)):
name = 'Surfactant-A ' + str(surfactant_index)
sequence = spa_sequences[surfactant_index]
pos, rot, progress = self._get_transformation(
start_frame=sequence[0],
end_frame=sequence[1],
frame=frame,
data=spa_frames[surfactant_index])
self._log(3, '- ' + name + ' (%.01f pct)' % progress)
self._add_surfactant_a(
name=name,
position=pos,
rotation=rot,
random_seed=spa_random_seeds[surfactant_index])
self._add_glucose_to_surfactant_head(name=name)
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)
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_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 _set_materials(self):
'''Default materials'''
self._be.apply_default_color_scheme(
shading_mode=BioExplorer.SHADING_MODE_DIFFUSE,
specular_exponent=50.0)
def _create_snapshot(self, shader, frame, movie_maker):
samples_per_pixel = self._image_samples_per_pixel
'''Renderer'''
if shader == 'albedo':
self._core.set_renderer(current='albedo')
elif shader == 'ambient_occlusion':
self._core.set_renderer(current='ambient_occlusion',
samples_per_pixel=1,
subsampling=1,
max_accum_frames=1)
params = self._core.AmbientOcclusionRendererParams()
params.samplesPerFrame = 32
params.rayLength = 5.0
self._core.set_renderer_params(params)
samples_per_pixel = 4
elif shader == 'depth':
status = self._core.set_renderer(current='depth',
samples_per_pixel=1,
subsampling=1,
max_accum_frames=1)
params = status = self._core.DepthRendererParams()
params.infinity = 2000.0
status = self._core.set_renderer_params(params)
samples_per_pixel = 2
elif shader == 'raycast_Ns':
status = self._core.set_renderer(current='raycast_Ns',
samples_per_pixel=1,
subsampling=1,
max_accum_frames=1)
samples_per_pixel = 2
else:
status = self._core.set_renderer(
background_color=[96 / 255, 125 / 255, 139 / 255],
current='bio_explorer',
head_light=False,
samples_per_pixel=1,
subsampling=1,
max_accum_frames=1)
params = self._core.BioExplorerRendererParams()
params.exposure = 1.0
params.gi_samples = 1
params.gi_weight = 0.3
params.gi_distance = 5000
params.shadows = 0.8
params.soft_shadows = 0.05
params.fog_start = 1000
params.fog_thickness = 300
params.max_bounces = 1
params.use_hardware_randomizer = True
status = self._core.set_renderer_params(params)
samples_per_pixel = self._image_samples_per_pixel
'''Lights'''
status = self._core.clear_lights()
status = self._core.add_light_directional(
angularDiameter=0.5,
color=[1, 1, 1],
direction=[-0.7, -0.4, -1],
intensity=1.0,
is_visible=False)
movie_maker.create_snapshot(size=self._image_size,
path=self._image_output_folder + '/' +
shader,
base_name='%05d' % frame,
samples_per_pixel=samples_per_pixel)
'''Camera'''
status = self._core.set_camera(current='bio_explorer_perspective')
def _build_frame(self, frame):
self._log(2, '- Resetting scene...')
self._be.reset()
self._log(2, '- Building surfactants...')
self._add_surfactants_d(frame)
self._add_surfactants_a(frame)
self._log(2, '- Building glucose...')
self._add_glucose(frame)
self._log(2, '- Building lactoferrins...')
self._add_lactoferrins(frame)
self._log(2, '- Building defensins...')
self._add_defensins(frame)
self._log(2, '- Building viruses...')
self._add_viruses(frame)
self._log(2, '- Building cell...')
self._add_cell(frame)
if self._magnetic:
self._log(2, '- Building fields...')
self._be.go_magnetic(colormap_filename=colormap_folder +
'high_glucose_v2.1dt',
voxel_size=0.5,
density=0.1,
colormap_range=[0.0, 1.0])
else:
self._log(2, '- Setting materials...')
self._set_materials()
self._log(2, '- Showing models...')
status = self._be.set_models_visibility(True)
status = self._core.set_renderer()
def _make_export_folder(self, folder):
import os
path = self._image_output_folder + '/' + folder
command_line = 'mkdir -p ' + path
os.system(command_line)
command_line = 'ls ' + path
if os.system(command_line) != 0:
self._log(3, 'ERROR: Failed to create folder ' + path)
def _make_export_folders(self):
for folder in self._shaders:
self._make_export_folder(folder)
def _prepare_movie(self, projection, image_k):
if projection == 'perspective':
aperture_ratio = 1.0
self._image_size = [image_k * 960, image_k * 540]
self._core.set_camera(current='bio_explorer_perspective')
elif projection == 'fisheye':
self._image_size = [int(image_k * 1024), int(image_k * 1024)]
self._core.set_camera(current='fisheye')
elif projection == 'panoramic':
self._image_size = [int(image_k * 1024), int(image_k * 1024)]
self._core.set_camera(current='panoramic')
elif projection == 'opendeck':
self._image_size = [7 * 2160, 3840]
self._core.set_camera(current='cylindric')
self._image_output_folder = self._image_output_folder + '/' + \
projection + '/' + str(self._image_size[0]) + 'x' + str(self._image_size[1])
self._make_export_folders()
def _set_clipping_planes(self):
'''Clipping planes'''
clip_planes = list()
if self._magnetic:
pos = Vector3(-74.9, -99.0, 228.8)
size = Vector3(70.0, 100.0, 70.0)
clip_planes.append([1.0, 0.0, 0.0, -pos.x + size.x])
clip_planes.append([-1.0, 0.0, 0.0, pos.x + size.x])
clip_planes.append([0.0, 1.0, 0.0, -pos.y + size.y])
clip_planes.append([0.0, -1.0, 0.0, pos.y + size.y])
clip_planes.append([0.0, 0.0, 1.0, -pos.z + size.z])
clip_planes.append([0.0, 0.0, -1.0, pos.z + size.z])
else:
clip_planes.append([1.0, 0.0, 0.0, scene_size * 1.5 + 5])
clip_planes.append([-1.0, 0.0, 0.0, scene_size * 1.5 + 5])
clip_planes.append([0.0, 0.0, 1.0, scene_size + 5])
clip_planes.append([0.0, 0.0, -1.0, scene_size + 5])
cps = self._core.get_clip_planes()
ids = list()
if cps:
for cp in cps:
ids.append(cp['id'])
self._core.remove_clip_planes(ids)
for plane in clip_planes:
self._core.add_clip_plane(plane)
def render_movie(self,
start_frame=0,
end_frame=0,
frame_step=1,
frame_list=list()):
'''Accelerate loading by not showing models as they are loaded'''
status = self._be.set_general_settings(
model_visibility_on_creation=False)
aperture_ratio = 0.0
cameras_key_frames = [
{ # 1. Cell view (frame 0)
'apertureRadius': aperture_ratio * 0.0,
'direction': [0.0, 0.0, -1.0],
'focusDistance': 1.0,
'origin': [150.0, -170.0, 400.0],
'up': [0.0, 1.0, 0.0]
},
{ # 2. Virus view (frame 500)
'apertureRadius': aperture_ratio * 0.0,
'direction': [0.0, 0.0, -1.0],
'focusDistance': 449.50,
'origin': [-67.501, -17.451, 254.786],
'up': [0.0, 1.0, 0.0]
},
{ # 3. Surfactant Head (frame 1000)
'apertureRadius': aperture_ratio * 0.02,
'direction': [0.276, -0.049, -0.959],
'focusDistance': 25.54,
'origin': [38.749, 35.228, 5.536],
'up': [0.0, 1.0, 0.0]
},
{ # 4. Virus overview (frame 1500)
'apertureRadius': aperture_ratio * 0.0,
'direction': [0.009, 0.055, -0.998],
'focusDistance': 109.59,
'origin': [-0.832, 72.134, 387.389],
'up': [0.017, 0.998, 0.055]
},
{ # 5. ACE2 receptor (frame 2000)
'apertureRadius': aperture_ratio * 0.02,
'direction': [-0.436, 0.035, -0.898],
'focusDistance': 62.17,
'origin': [-33.619, -164.994, 276.296],
'up': [0.011, 0.999, 0.033]
},
{ # 6. Membrane overview (frame 2500)
'apertureRadius': aperture_ratio * 0.0,
'direction': [0.009, 0.055, -0.998],
'focusDistance': 1.0,
'origin': [0.293, 19.604, 1000],
'up': [0.017, 0.998, 0.055]
},
{ # 7. (frame 3000)
'apertureRadius': aperture_ratio * 0.0,
'focusDistance': 1.0,
'direction': [0.009, 0.055, -0.998],
'origin': [0.293, 19.604, 1000],
'up': [0.017, 0.998, 0.055]
},
{ # 8. (frame 3500)
'apertureRadius': aperture_ratio * 0.0,
'focusDistance': 60,
'direction': [0.009, 0.055, -0.998],
'origin': [0.293, 19.604, 1000],
'up': [0.017, 0.998, 0.055]
}
]
'''Double the frames to make it smoother'''
key_frames = list()
for cameras_key_frame in cameras_key_frames:
key_frames.append(cameras_key_frame)
key_frames.append(cameras_key_frame)
mm = MovieMaker(self._be)
mm.build_camera_path(key_frames, 250, 150)
self._log(1, '- Total number of frames: %d' % mm.get_nb_frames())
self._core.set_application_parameters(viewport=self._image_size)
self._core.set_application_parameters(image_stream_fps=0)
frames_to_render = list()
if len(frame_list) != 0:
frames_to_render = frame_list
else:
if end_frame == 0:
end_frame = mm.get_nb_frames()
for i in range(start_frame, end_frame + 1, frame_step):
frames_to_render.append(i)
cumulated_rendering_time = 0
nb_frames = len(frames_to_render)
frame_count = 1
'''Clipping planes'''
self._set_clipping_planes()
'''Frames'''
for frame in frames_to_render:
try:
start = time.time()
self._log(
1, '- Rendering frame %i (%i/%i)' %
(frame, frame_count, nb_frames))
self._log(1, '------------------------------')
'''Stop rendering during the loading of the scene'''
status = self._core.set_renderer(samples_per_pixel=1,
subsampling=1,
max_accum_frames=1)
'''Frame setup'''
self._build_frame(frame)
mm.set_current_frame(frame=frame,
camera_params=self._core.
BioExplorerPerspectiveCameraParams())
self._log(1, '- Frame buffers')
for shader in self._shaders:
'''Rendering settings'''
self._log(2, '- ' + shader)
self._create_snapshot(shader, frame, mm)
end = time.time()
rendering_time = end - start
cumulated_rendering_time += rendering_time
average_rendering_time = cumulated_rendering_time / frame_count
remaining_rendering_time = (
nb_frames - frame_count) * average_rendering_time
self._log(1, '------------------------------')
self._log(
1, 'Frame %i successfully rendered in %i seconds' %
(frame, rendering_time))
hours = math.floor(remaining_rendering_time / 3600)
minutes = math.floor(
(remaining_rendering_time - hours * 3600) / 60)
seconds = math.floor(remaining_rendering_time - hours * 3600 -
minutes * 60)
expected_end_time = datetime.now() + timedelta(
seconds=remaining_rendering_time)
self._log(
1,
'Estimated remaining time: %i hours, %i minutes, %i seconds'
% (hours, minutes, seconds))
self._log(1,
'Expected end time : %s' % expected_end_time)
self._log(
1,
'--------------------------------------------------------------------------------'
)
frame_count += 1
except Exception as e:
self._log(1, 'ERROR: Failed to render frame %i' % frame)
self._log(1, str(e))
time.sleep(10)
self._be = BioExplorer(self._url)
self._core = self._be.core_api()
mm = MovieMaker(self._be)
self._core.set_application_parameters(image_stream_fps=20)
self._log(1, 'Movie rendered, live long and prosper \V/')
def test_virus():
resource_folder = 'tests/test_files/'
pdb_folder = resource_folder + 'pdb/'
rna_folder = resource_folder + 'rna/'
glycan_folder = pdb_folder + 'glycans/'
bio_explorer = BioExplorer('localhost:5000')
bio_explorer.reset()
# Settings
virus_radius = 45.0
add_glycans = True
protein_radius_multiplier = 1.0
protein_representation = BioExplorer.REPRESENTATION_ATOMS
protein_load_hydrogen = False
# Virus configuration
nb_protein_s = 62
nb_protein_s_indices = [1, 27, 43]
nb_protein_e = 42
nb_protein_m = 50
show_rna = True
# Virus parameters
show_functional_regions = False
show_glycosylation_sites = False
# Suspend image streaming
bio_explorer.core_api().set_application_parameters(image_stream_fps=0)
# Protein S
open_conformation_indices = nb_protein_s_indices
closed_conformation_indices = list()
for i in range(nb_protein_s):
if i not in open_conformation_indices:
closed_conformation_indices.append(i)
params = [11.5, 0, 0.0, 0, 0.0, 0.0]
virus_protein_s = Protein(
sources=[pdb_folder + '6vyb.pdb', pdb_folder + 'sars-cov-2-v1.pdb'],
load_hydrogen=protein_load_hydrogen, occurences=nb_protein_s,
assembly_params=params, rotation=Quaternion(0.087, 0.0, 0.996, 0.0),
instance_indices=[open_conformation_indices, closed_conformation_indices])
# Protein M (QHD43419)
params = [2.5, 0, 0.0, 0, 0.0, 0.0]
virus_protein_m = Protein(
sources=[pdb_folder + 'QHD43419a.pdb'],
load_hydrogen=protein_load_hydrogen, occurences=nb_protein_m,
assembly_params=params, rotation=Quaternion(0.99, 0.0, 0.0, 0.135))
# Protein E (QHD43418 P0DTC4)
params = [2.5, 0, 0.0, 0, 0.0, 0.0]
virus_protein_e = Protein(
sources=[pdb_folder + 'QHD43418a.pdb'], load_hydrogen=protein_load_hydrogen,
occurences=nb_protein_e, assembly_params=params,
rotation=Quaternion(0.705, 0.705, -0.04, -0.04))
# Virus membrane
virus_membrane = ParametricMembrane(
sources=[pdb_folder + 'membrane/popc.pdb'],
occurences=15000)
# RNA Sequence
clip_planes = list()
rna_sequence = None
if show_rna:
clip_planes.append([0.0, 0.0, -1.0, 15.0])
rna_sequence = RNASequence(
source=rna_folder + 'sars-cov-2.rna', assembly_params=[11.0, 0.5],
t_range=Vector2(0, 30.5 * math.pi), shape=bio_explorer.RNA_SHAPE_TREFOIL_KNOT,
shape_params=Vector3(1.51, 1.12, 1.93))
# Coronavirus
name = 'Coronavirus'
coronavirus = Virus(
name=name, protein_s=virus_protein_s, protein_e=virus_protein_e, protein_m=virus_protein_m,
membrane=virus_membrane, rna_sequence=rna_sequence,
assembly_params=[virus_radius, 1, 0.025, 2, 0.4, 0.0])
bio_explorer.add_virus(
virus=coronavirus, position=Vector3(-70.0, -100.0, 230.0),
representation=protein_representation, atom_radius_multiplier=protein_radius_multiplier,
clipping_planes=clip_planes)
# Glycans
if add_glycans:
complex_paths = [glycan_folder + 'complex/5.pdb', glycan_folder + 'complex/15.pdb',
glycan_folder + 'complex/25.pdb', glycan_folder + 'complex/35.pdb']
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']
o_glycan_paths = [glycan_folder + 'o-glycan/12.pdb']
# High-mannose
indices_closed = [61, 122, 234, 603, 709, 717, 801, 1074]
indices_open = [61, 122, 234, 709, 717, 801, 1074]
bio_explorer.add_multiple_glycans(
assembly_name=name, glycan_type=bio_explorer.NAME_GLYCAN_HIGH_MANNOSE,
protein_name=bio_explorer.NAME_PROTEIN_S_CLOSED, paths=high_mannose_paths,
indices=indices_closed, representation=protein_representation,
atom_radius_multiplier=protein_radius_multiplier)
bio_explorer.add_multiple_glycans(
assembly_name=name, glycan_type=bio_explorer.NAME_GLYCAN_HIGH_MANNOSE,
protein_name=bio_explorer.NAME_PROTEIN_S_OPEN, paths=high_mannose_paths,
indices=indices_open, representation=protein_representation,
atom_radius_multiplier=protein_radius_multiplier)
# Complex
indices1 = [17, 74, 149, 165, 282, 331, 343, 616, 657, 1098, 1134, 1158, 1173, 1194]
indices2 = [17, 74, 149, 165, 282, 331, 343, 1098, 657, 1134, 1158, 1173, 1194]
bio_explorer.add_multiple_glycans(
assembly_name=name, glycan_type=bio_explorer.NAME_GLYCAN_COMPLEX,
protein_name=bio_explorer.NAME_PROTEIN_S_CLOSED, paths=complex_paths, indices=indices1,
representation=protein_representation, atom_radius_multiplier=protein_radius_multiplier)
bio_explorer.add_multiple_glycans(
assembly_name=name, glycan_type=bio_explorer.NAME_GLYCAN_COMPLEX,
protein_name=bio_explorer.NAME_PROTEIN_S_OPEN, paths=complex_paths, indices=indices2,
representation=protein_representation, atom_radius_multiplier=protein_radius_multiplier)
# O-Glycans
for index in [323, 325]:
o_glycan_name = name + '_' + bio_explorer.NAME_GLYCAN_O_GLYCAN + '_' + str(index)
o_glycan = Sugars(
assembly_name=name, name=o_glycan_name, source=o_glycan_paths[0],
protein_name=name + '_' + bio_explorer.NAME_PROTEIN_S_CLOSED,
representation=protein_representation, site_indices=[index],
atom_radius_multiplier=protein_radius_multiplier)
bio_explorer.add_sugars(o_glycan)
# High-mannose glycans on Protein M
indices = [5]
protein_name = name + '_' + bio_explorer.NAME_PROTEIN_M
high_mannose_glycans = Sugars(
rotation=Quaternion(0.707, 0.0, 0.0, 0.707),
assembly_name=name, name=protein_name + '_' + bio_explorer.NAME_GLYCAN_HIGH_MANNOSE,
protein_name=protein_name, source=high_mannose_paths[0],
site_indices=indices,
representation=protein_representation
)
bio_explorer.add_glycans(high_mannose_glycans)
# Complex glycans on Protein E
indices = [48, 66]
protein_name = name + '_' + bio_explorer.NAME_PROTEIN_E
complex_glycans = Sugars(
rotation=Quaternion(0.707, 0.0, 0.0, 0.707),
assembly_name=name, name=protein_name + '_' + bio_explorer.NAME_GLYCAN_COMPLEX,
protein_name=protein_name, source=complex_paths[0],
site_indices=indices,
representation=protein_representation
)
bio_explorer.add_glycans(complex_glycans)
# Apply default materials
bio_explorer.apply_default_color_scheme(shading_mode=bio_explorer.SHADING_MODE_BASIC)
# Functional regions on open spike
if show_functional_regions:
indices = [1, 16, 306, 330, 438, 507, 522, 816, 835, 908, 986, 1076, 1274, 2000]
region_colors = [
[1.0, 1.0, 1.0], [0.0, 0.0, 1.0], [1.0, 1.0, 1.0], [0.0, 1.0, 0.0], [0.4, 0.1, 0.1],
[0.0, 1.0, 0.0], [1.0, 1.0, 1.0], [1.0, 0.0, 0.0], [1.0, 1.0, 1.0], [1.0, 1.0, 0.0],
[1.0, 1.0, 1.0], [1.0, 0.0, 1.0], [1.0, 1.0, 1.0], [1.0, 1.0, 1.0]]
palette = list()
for index in range(len(indices) - 1):
for i in range(0, indices[index + 1] - indices[index]):
color = list()
for j in range(3):
color.append(region_colors[index][j] * 1)
palette.append(color)
bio_explorer.set_protein_color_scheme(
assembly_name=name, name=name + '_' + bio_explorer.NAME_PROTEIN_S_OPEN,
color_scheme=bio_explorer.COLOR_SCHEME_REGION, palette=palette)
# Display glycosylation sites
if show_glycosylation_sites:
palette = sns.color_palette('Set2', 2)
bio_explorer.set_protein_color_scheme(
assembly_name=name, name=name + '_' + bio_explorer.NAME_PROTEIN_S_OPEN,
color_scheme=bio_explorer.COLOR_SCHEME_GLYCOSYLATION_SITE, palette=palette)
bio_explorer.set_protein_color_scheme(
assembly_name=name, name=name + '_' + bio_explorer.NAME_PROTEIN_S_CLOSED,
color_scheme=bio_explorer.COLOR_SCHEME_GLYCOSYLATION_SITE, palette=palette)
# 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)
class LowGlucoseScenario():
def __init__(self, hostname, port, projection, output_folder, image_k=4,
image_samples_per_pixel=64, log_level=1, shaders=list(['bio_explorer'])):
self._log_level = log_level
self._hostname = hostname
self._url = hostname + ':' + str(port)
self._be = BioExplorer(self._url)
self._core = self._be.core_api()
self._image_size = [1920, 1080]
self._image_samples_per_pixel = image_samples_per_pixel
self._image_projection = projection
self._image_output_folder = output_folder
self._shaders = shaders
self._prepare_movie(projection, image_k)
self._log(1, '================================================================================')
self._log(1, '- Version : ' + self._be.version())
self._log(1, '- URL : ' + self._url)
self._log(1, '- Projection : ' + projection)
self._log(1, '- Frame size : ' + str(self._image_size))
self._log(1, '- Export folder : ' + self._image_output_folder)
self._log(1, '- Samples per pixel: ' + str(self._image_samples_per_pixel))
self._log(1, '================================================================================')
def _log(self, level, message):
if level <= self._log_level:
print('[' + str(datetime.now()) + '] ' + message)
def _get_transformation(self, start_frame, end_frame, frame, data):
'''Progress'''
progress = (frame - start_frame) * 1.0 / (end_frame - start_frame)
progress = max(0.0, progress)
progress = min(1.0, progress)
'''Position'''
start_pos = data[0].to_list()
end_pos = data[2].to_list()
pos = start_pos
for i in range(3):
pos[i] += (end_pos[i] - start_pos[i]) * progress
'''Rotation'''
start_rot = data[1]
end_rot = data[3]
rot = Quaternion.slerp(start_rot, end_rot, progress)
if data[4] == ROTATION_MODE_SINUSOIDAL:
rot = Quaternion.slerp(start_rot, end_rot, math.cos((progress - 0.5) * math.pi))
return [Vector3(pos[0], pos[1], pos[2]), rot, progress * 100.0]
def _add_viruses(self, frame):
virus_radii = [45.0, 44.0, 45.0, 43.0, 44.0]
virus_sequences = [
[[0, 2599], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6]],
[[0, 2599], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6]],
[[0, 2599], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6]],
[[0, 2999], [3000, 3099], [3100, 3299], [3300, 3750], [1e6, 1e6], [1e6, 1e6]],
[[0, 599], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1e6, 1e6], [1600, 3750]],
]
virus_flights_in = [
[Vector3(-35.0, 300.0, -70.0), Quaternion(0.519, 0.671, 0.528, -0.036),
Vector3(-5.0, 45.0, -33.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
[Vector3(153.0, 300.0, -200.0), Quaternion(0.456, 0.129, -0.185, -0.860),
Vector3(73.0, 93.0, -130.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
# Virus used for SP-D zoom
[Vector3(-100.0, 300.0, 20.0), Quaternion(0.087, 0.971, -0.147, -0.161),
Vector3(-79.0, 108.0, 80.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
# Virus getting inside cell
[Vector3(224.9, 300.0, -220.0), Quaternion(-0.095, 0.652, -0.326, 0.677),
Vector3(211.5, -104.9, -339.2), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
# Virus used for detailed view of the Spike
[Vector3(200.0, 20.0, -150.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(200.0, 20.0, -150.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR]
]
virus_flights_out = [
# Unused
[Vector3(-5.0, 45.0, -33.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(-105.0, 45.0, -33.0), Quaternion(0.0, 1.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
# Unused
[Vector3(73.0, 93.0, -130.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(-33.0, 93.0, -130.0), Quaternion(0.0, 0.0, 1.0, 0.0),
ROTATION_MODE_LINEAR],
# Virus used for SP-D zoom
[Vector3(-84.0, 110.0, 75.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(-100.0, -100.0, 51.2), Quaternion(0.087, 0.971, -0.147, -0.161),
ROTATION_MODE_LINEAR],
# Unused
[Vector3(0.0, 0.0, 0.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(0.0, 0.0, 0.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
# Virus used for detailed view of the Spike
[Vector3(200.0, 20.0, -150.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(300.0, -100.0, -100.0), Quaternion(0.456, 0.129, -0.185, -0.860),
ROTATION_MODE_LINEAR]
]
for virus_index in range(len(virus_sequences)):
name = 'Coronavirus ' + str(virus_index)
current_sequence = 0
sequences = virus_sequences[virus_index]
for i in range(len(sequences)):
if frame >= sequences[i][0]:
current_sequence = i
'''Initialize position and rotation to end-of-flight values'''
start_frame = sequences[current_sequence][0]
end_frame = sequences[current_sequence][1]
progress_in_sequence = (frame - start_frame) / (end_frame - start_frame)
morphing_step = 0.0
if current_sequence == 0:
'''Flying'''
pos, rot, progress = self._get_transformation(start_frame, end_frame,
frame, virus_flights_in[virus_index])
self._log(3, '- Virus %d is flying in... (%.01f pct)' % (virus_index, progress))
elif current_sequence == 1:
'''Landing'''
pos = virus_flights_in[virus_index][2]
rot = virus_flights_in[virus_index][3]
pos.y -= landing_distance * progress_in_sequence
self._log(3, '- Virus %d is landing...' % virus_index)
elif current_sequence == 2:
'''Merging into cell'''
pos = virus_flights_in[virus_index][2]
rot = virus_flights_in[virus_index][3]
morphing_step = (frame - start_frame) / (end_frame - start_frame)
pos.y -= landing_distance
self._log(3, '- Virus %d is merging in (%.01f pct)' %
(virus_index, morphing_step * 100.0))
elif current_sequence == 3:
'''Inside cell'''
self._log(3, '- Virus %d is inside cell' % virus_index)
'''Virus is not added to the scene'''
self._be.remove_assembly(name=name)
continue
elif current_sequence == 4:
'''Merging out of cell'''
pos = virus_flights_out[virus_index][0]
rot = virus_flights_out[virus_index][1]
morphing_step = 1.0 - (frame - start_frame) / (end_frame - start_frame)
self._log(3, '- Virus %d is merging out (%.01f pct)' %
(virus_index, morphing_step * 100.0))
else:
'''Flying out'''
pos, rot, progress = self._get_transformation(start_frame, end_frame,
frame, virus_flights_out[virus_index])
self._log(3, '- Virus %d is flying out... (%.01f pct)' % (virus_index, progress))
if False:
self._be.add_sphere(name=name, position=pos, radius=virus_radii[virus_index])
else:
self._be.add_coronavirus(
name=name, resource_folder=resource_folder,
representation=protein_representation, position=pos, rotation=rot,
add_glycans=add_glycans,
assembly_params=[virus_radii[virus_index], 5 * frame + 2 * virus_index,
0.25, frame + 2 * virus_index + 1, 0.1, morphing_step]
)
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 = [37]
receptors_sequences = [[3000, 3099]]
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
def _add_surfactant_d(self, name, position, rotation, random_seed):
surfactant_d = Surfactant(
name=name, surfactant_protein=BioExplorer.SURFACTANT_PROTEIN_D,
head_source=surfactant_head_source,
branch_source=surfactant_branch_source)
self._be.add_surfactant(
surfactant=surfactant_d, representation=protein_representation,
position=position, rotation=rotation, random_seed=random_seed)
def _add_surfactant_a(self, name, position, rotation, random_seed):
surfactant_a = Surfactant(
name=name, surfactant_protein=BioExplorer.SURFACTANT_PROTEIN_A,
head_source=surfactant_head_source,
branch_source=surfactant_branch_source)
self._be.add_surfactant(
surfactant=surfactant_a, representation=protein_representation,
position=position, rotation=rotation, random_seed=random_seed)
def _add_surfactants_d(self, frame):
spd_sequences = [[0, 3750], [0, 2600], [0, 2600], [0, 3750]]
spd_random_seeds = [1, 1, 1, 2]
spd_flights = [
[Vector3(300, 124.0, 0.0), Quaternion(-0.095, 0.652, -0.326, 0.677),
Vector3(74.0, 24.0, -45.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_SINUSOIDAL],
# SP-D is used for the head focus on 3rd virus spike
[Vector3(-50, 250.0, 20.0), Quaternion(0.087, 0.971, -0.147, -0.161),
Vector3(-11.0, 108.0, 20.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
# SP-D attaching to lymphocyte
[Vector3(-200.0, 100.0, 100.0), Quaternion(0.519, 0.671, 0.528, -0.036),
Vector3(-135.0, 135.0, 140.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_LINEAR],
[Vector3(100.0, 0.0, -80.0), Quaternion(-0.095, 0.652, -0.326, 0.677),
Vector3(-260.0, 50.0, 150.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_SINUSOIDAL]
]
for surfactant_index in range(len(spd_sequences)):
name = 'Surfactant-D ' + str(surfactant_index)
sequence = spd_sequences[surfactant_index]
pos, rot, progress = self._get_transformation(
start_frame=sequence[0], end_frame=sequence[1],
frame=frame, data=spd_flights[surfactant_index])
self._log(3, '- ' + name + ' (%.01f pct)' % progress)
self._add_surfactant_d(
name=name, position=pos, rotation=rot,
random_seed=spd_random_seeds[surfactant_index])
def _add_surfactants_a(self, frame):
spa_sequences = [[0, 3750]]
spa_random_seeds = [2]
spa_frames = [
[Vector3(300.0, -50.0, -50.0), Quaternion(-0.095, 0.652, -0.326, 0.677),
Vector3(100.0, 50.0, 150.0), Quaternion(1.0, 0.0, 0.0, 0.0),
ROTATION_MODE_SINUSOIDAL],
]
for surfactant_index in range(len(spa_frames)):
name = 'Surfactant-A ' + str(surfactant_index)
sequence = spa_sequences[surfactant_index]
pos, rot, progress = self._get_transformation(
start_frame=sequence[0], end_frame=sequence[1],
frame=frame, data=spa_frames[surfactant_index])
self._log(3, '- ' + name + ' (%.01f pct)' % progress)
self._add_surfactant_a(
name=name, position=pos, rotation=rot,
random_seed=spa_random_seeds[surfactant_index])
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)
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_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_lymphocyte(self, frame):
if frame < 1400:
'''Lymphocyte is not in the field of view'''
return
'''Protein animation params'''
params = [0, 0, 0.0, frame + 2, 0.2]
clip_planes = [
[1.0, 0.0, 0.0, scene_size * 1.5 + 5],
[-1.0, 0.0, 0.0, scene_size * 1.5 + 5],
[0.0, 0.0, 1.0, scene_size + 5],
[0.0, 0.0, -1.0, scene_size + 5]
]
name = 'Emile'
lymphocyte_sequence = [0, 3750]
lymphocyte_frames = [Vector3(-2500.0, 100.0, 30.0), Quaternion(1.0, 0.0, 0.0, 0.0),
Vector3(-830.0, 100.0, 30.0), Quaternion(0.707, 0.707, 0.0, 0.0),
ROTATION_MODE_LINEAR]
protein_sources = [
membrane_folder + 'segA.pdb',
membrane_folder + 'segB.pdb',
membrane_folder + 'segC.pdb',
membrane_folder + 'segD.pdb'
]
mesh_based_membrane = MeshBasedMembrane(
mesh_source=lymphocyte_path, protein_sources=protein_sources,
density=lymphocyte_density, surface_variable_offset=lymphocyte_surface_variable_offset,
assembly_params=params
)
pos, rot, progress = self._get_transformation(
start_frame=lymphocyte_sequence[0], end_frame=lymphocyte_sequence[1],
frame=frame, data=lymphocyte_frames)
self._log(3, '- ' + name + ' (%.01f pct)' % progress)
scale = Vector3(1.0, 1.0, 1.0)
status = self._be.add_mesh_based_membrane(
name, mesh_based_membrane, position=pos,
rotation=rot, scale=scale,
clipping_planes=clip_planes
)
for i in range(len(protein_sources)):
status = self._be.set_protein_color_scheme(
assembly_name=name, name=BioExplorer.NAME_MEMBRANE + '_' + str(i),
color_scheme=BioExplorer.COLOR_SCHEME_CHAINS,
palette_name='OrRd', palette_size=5)
def _set_materials(self):
'''Default materials'''
self._be.apply_default_color_scheme(
shading_mode=BioExplorer.SHADING_MODE_DIFFUSE, specular_exponent=50.0)
def _create_snapshot(self, shader, frame, movie_maker):
samples_per_pixel = self._image_samples_per_pixel
'''Renderer'''
if shader == 'albedo':
self._core.set_renderer(current='albedo')
elif shader == 'ambient_occlusion':
self._core.set_renderer(
current='ambient_occlusion', samples_per_pixel=1, subsampling=1, max_accum_frames=1)
params = self._core.AmbientOcclusionRendererParams()
params.samplesPerFrame = 32
params.rayLength = 5.0
self._core.set_renderer_params(params)
samples_per_pixel = 4
elif shader == 'depth':
status = self._core.set_renderer(
current='depth', samples_per_pixel=1, subsampling=1, max_accum_frames=1)
params = status = self._core.DepthRendererParams()
params.infinity = 2000.0
status = self._core.set_renderer_params(params)
samples_per_pixel = 2
elif shader == 'raycast_Ns':
status = self._core.set_renderer(
current='raycast_Ns', samples_per_pixel=1, subsampling=1, max_accum_frames=1)
samples_per_pixel = 2
else:
status = self._core.set_renderer(
background_color=[96 / 255, 125 / 255, 139 / 255],
current='bio_explorer', head_light=False,
samples_per_pixel=1, subsampling=1, max_accum_frames=1)
params = self._core.BioExplorerRendererParams()
params.exposure = 1.0
params.gi_samples = 1
params.gi_weight = 0.3
params.gi_distance = 5000
params.shadows = 0.8
params.soft_shadows = 0.05
params.fog_start = 1000
params.fog_thickness = 300
params.max_bounces = 1
params.use_hardware_randomizer = True
status = self._core.set_renderer_params(params)
samples_per_pixel = self._image_samples_per_pixel
'''Lights'''
status = self._core.clear_lights()
status = self._core.add_light_directional(
angularDiameter=0.5, color=[1, 1, 1], direction=[-0.7, -0.4, -1],
intensity=1.0, is_visible=False
)
movie_maker.create_snapshot(
size=self._image_size, path=self._image_output_folder + '/' + shader,
base_name='%05d' % frame, samples_per_pixel=samples_per_pixel)
'''Camera'''
status = self._core.set_camera(current='bio_explorer_perspective')
def _build_frame(self, frame):
self._log(2, '- Resetting scene...')
self._be.reset()
self._log(2, '- Building surfactants...')
self._add_surfactants_d(frame)
self._add_surfactants_a(frame)
self._log(2, '- Building glucose...')
self._add_glucose(frame)
self._log(2, '- Building lactoferrins...')
self._add_lactoferrins(frame)
self._log(2, '- Building defensins...')
self._add_defensins(frame)
self._log(2, '- Building viruses...')
self._add_viruses(frame)
self._log(2, '- Building cell...')
self._add_cell(frame)
self._log(2, '- Building lymphocyte...')
self._add_lymphocyte(frame)
self._log(2, '- Setting materials...')
self._set_materials()
self._log(2, '- Showing models...')
status = self._be.set_models_visibility(True)
status = self._core.set_renderer()
def _make_export_folder(self, folder):
import os
path = self._image_output_folder + '/' + folder
command_line = 'mkdir -p ' + path
os.system(command_line)
command_line = 'ls ' + path
if os.system(command_line) != 0:
self._log(3, 'ERROR: Failed to create folder ' + path)
def _make_export_folders(self):
for folder in self._shaders:
self._make_export_folder(folder)
def _prepare_movie(self, projection, image_k):
if projection == 'perspective':
aperture_ratio = 1.0
self._image_size = [image_k*960, image_k*540]
self._core.set_camera(current='bio_explorer_perspective')
elif projection == 'fisheye':
self._image_size = [int(image_k*1024), int(image_k*1024)]
self._core.set_camera(current='fisheye')
elif projection == 'panoramic':
self._image_size = [int(image_k*1024), int(image_k*1024)]
self._core.set_camera(current='panoramic')
elif projection == 'opendeck':
self._image_size = [7*2160, 3840]
self._core.set_camera(current='cylindric')
self._image_output_folder = self._image_output_folder + '/' + \
projection + '/' + str(self._image_size[0]) + 'x' + str(self._image_size[1])
self._make_export_folders()
def _set_clipping_planes(self):
'''Clipping planes'''
clip_planes = [
[1.0, 0.0, 0.0, scene_size * 1.5 + 5],
[-1.0, 0.0, 0.0, scene_size * 1.5 + 5],
[0.0, 0.0, 1.0, scene_size + 5],
[0.0, 0.0, -1.0, scene_size + 5]
]
cps = self._core.get_clip_planes()
ids = list()
if cps:
for cp in cps:
ids.append(cp['id'])
self._core.remove_clip_planes(ids)
for plane in clip_planes:
self._core.add_clip_plane(plane)
def render_movie(self, start_frame=0, end_frame=0, frame_step=1, frame_list=list()):
'''Accelerate loading by not showing models as they are loaded'''
status = self._be.set_general_settings(model_visibility_on_creation=False)
aperture_ratio = 0.0
cameras_key_frames = [
{ # Virus overview (on 5th virus)
'apertureRadius': aperture_ratio * 0.02,
'direction': [0.0, 0.0, -1.0],
'focusDistance': 139.56,
'origin': [199.840, 20.634, 34.664],
'up': [0.0, 1.0, 0.0]
},
{ # Protein S (on 5th virus)
'apertureRadius': aperture_ratio * 0.02,
'direction': [0.0, 0.0, -1.0],
'focusDistance': 23.60,
'origin': [195.937, 74.319, -111.767],
'up': [0.0, 1.0, 0.0]
},
{ # Protein M and E
'apertureRadius': aperture_ratio * 0.02,
'direction': [-0.047, -0.298, -0.953],
'focusDistance': 54.56,
'origin': [208.156, 55.792, -59.805],
'up': [0.003, 0.954, -0.298]
},
{ # Overview SPA
'apertureRadius': aperture_ratio * 0.001,
'direction': [-0.471, -0.006, -0.882],
'focusDistance': 444.63,
'origin': [238.163, 46.437, 372.585],
'up': [0.0, 1.0, 0.0]
},
{ # Overview SPD
'apertureRadius': aperture_ratio * 0.001,
'focusDistance': 444.63,
'direction': [-0.471, -0.005, -0.881],
'origin': [238.163, 46.436, 372.584],
'up': [0.0, 1.0, 0.0]
},
{ # Zoom SPD (on 3rd virus)
'apertureRadius': aperture_ratio * 0.02,
'focusDistance': 31.86,
'direction': [-0.821, 0.202, -0.533],
'origin': [-9.827, 110.720, 60.944],
'up': [0.178, 0.979, 0.098]
},
{ # Overview scene
'apertureRadius': aperture_ratio * 0.0,
'focusDistance': 1.0,
'direction': [-1.0, 0.0, 0.0],
'origin': [1008.957, 29.057, 113.283],
'up': [0.0, 1.0, 0.0]
},
{ # Cell view
'apertureRadius': aperture_ratio * 0.0,
'direction': [0.0, 0.0, -1.0],
'focusDistance': 1.0,
'origin': [150.0, -170.0, 400.0],
'up': [0.0, 1.0, 0.0]
}
]
'''Double the frames to make it smoother'''
key_frames = list()
for cameras_key_frame in cameras_key_frames:
key_frames.append(cameras_key_frame)
key_frames.append(cameras_key_frame)
mm = MovieMaker(self._be)
mm.build_camera_path(key_frames, 250, 150)
self._log(1, '- Total number of frames: %d' % mm.get_nb_frames())
self._core.set_application_parameters(viewport=self._image_size)
self._core.set_application_parameters(image_stream_fps=0)
frames_to_render = list()
if len(frame_list) != 0:
frames_to_render = frame_list
else:
if end_frame == 0:
end_frame = mm.get_nb_frames()
for i in range(start_frame, end_frame + 1, frame_step):
frames_to_render.append(i)
cumulated_rendering_time = 0
nb_frames = len(frames_to_render)
frame_count = 1
'''Clipping planes'''
self._set_clipping_planes()
'''Frames'''
for frame in frames_to_render:
try:
start = time.time()
self._log(1, '- Rendering frame %i (%i/%i)' % (frame, frame_count, nb_frames))
self._log(1, '------------------------------')
'''Stop rendering during the loading of the scene'''
status = self._core.set_renderer(
samples_per_pixel=1, subsampling=1, max_accum_frames=1)
'''Frame setup'''
self._build_frame(frame)
mm.set_current_frame(
frame=frame, camera_params=self._core.BioExplorerPerspectiveCameraParams())
self._log(1, '- Frame buffers')
for shader in self._shaders:
'''Rendering settings'''
self._log(2, '- ' + shader)
self._create_snapshot(shader, frame, mm)
end = time.time()
rendering_time = end - start
cumulated_rendering_time += rendering_time
average_rendering_time = cumulated_rendering_time / frame_count
remaining_rendering_time = (nb_frames - frame_count) * average_rendering_time
self._log(1, '------------------------------')
self._log(1, 'Frame %i successfully rendered in %i seconds' %
(frame, rendering_time))
hours = math.floor(remaining_rendering_time / 3600)
minutes = math.floor((remaining_rendering_time - hours * 3600) / 60)
seconds = math.floor(remaining_rendering_time - hours * 3600 - minutes * 60)
expected_end_time = datetime.now() + timedelta(seconds=remaining_rendering_time)
self._log(1, 'Estimated remaining time: %i hours, %i minutes, %i seconds' %
(hours, minutes, seconds))
self._log(1, 'Expected end time : %s' % expected_end_time)
self._log(
1, '--------------------------------------------------------------------------------')
frame_count += 1
except Exception as e:
self._log(1, 'ERROR: Failed to render frame %i' % frame)
self._log(1, str(e))
time.sleep(10)
self._be = BioExplorer(self._url)
self._core = self._be.core_api()
mm = MovieMaker(self._be)
self._core.set_application_parameters(image_stream_fps=20)
self._log(1, 'Movie rendered, live long and prosper \V/')