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_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)
