def set_gso(number_of_glowworms,
adapters,
scoring_functions,
initial_positions,
seed,
step_translation,
step_rotation,
configuration_file=None,
use_anm=False,
nmodes_step=0.1,
anm_rec=DEFAULT_NMODES_REC,
anm_lig=DEFAULT_NMODES_LIG,
local_minimization=False):
"""Creates a lightdock GSO simulation object"""
bounding_box = get_default_box(use_anm, anm_rec, anm_lig)
random_number_generator = MTGenerator(seed)
if configuration_file:
gso_parameters = GSOParameters(configuration_file)
else:
gso_parameters = GSOParameters()
builder = LightdockGSOBuilder()
if not use_anm:
anm_rec = anm_lig = 0
gso = builder.create_from_file(number_of_glowworms,
random_number_generator, gso_parameters,
adapters, scoring_functions, bounding_box,
initial_positions, step_translation,
step_rotation, nmodes_step,
local_minimization, anm_rec, anm_lig)
return gso
def __init__(self):
self.path = Path(__file__).absolute().parent
self.test_path = self.path / 'scratch_gso'
self.golden_data_path = self.path / 'golden_data'
self.gso_parameters = GSOParameters()
self.gso_parameters.initial_vision_range = 3.0
self.gso_parameters.max_vision_range = 3.0
def setUp(self):
self.gso_parameters = GSOParameters()
self.objective_function = J1()
self.landscape_position1 = [
LandscapePosition(self.objective_function, Coordinates([0.0, 0.0]))
]
self.landscape_position2 = [
LandscapePosition(self.objective_function, Coordinates([1.0, 1.0]))
]
self.landscape_position3 = [
LandscapePosition(self.objective_function, Coordinates([2.0, 2.0]))
]
self.landscape_position4 = [
LandscapePosition(self.objective_function, Coordinates([0.5, 0.5]))
]
self.landscape_position5 = [
LandscapePosition(self.objective_function, Coordinates([5.0, 5.0]))
]
self.landscape_position6 = [
LandscapePosition(self.objective_function, Coordinates([0.0, 1.0]))
]
self.landscape_position7 = [
LandscapePosition(self.objective_function, Coordinates([0.1, 0.0]))
]
self.landscape_position8 = [
LandscapePosition(self.objective_function, Coordinates([0.0, 0.1]))
]
self.landscape_position9 = [
LandscapePosition(self.objective_function, Coordinates([0.2, 0.0]))
]
def setUp(self):
self.golden_data_path = os.path.normpath(os.path.dirname(os.path.realpath(__file__))) + '/golden_data/'
self.gso_parameters = GSOParameters()
self.objective_function = J1()
self.bounding_box = BoundingBox([Boundary(1, 2), Boundary(10, 15)])
self.number_of_glowworms = 50
self.random_number_generator = MTGenerator(324324)
def __init__(self):
self.golden_data_path = Path(
__file__).absolute().parent / 'golden_data'
self.gso_parameters = GSOParameters()
self.objective_function = J1()
self.bounding_box = BoundingBox([Boundary(1, 2), Boundary(10, 15)])
self.number_of_glowworms = 50
self.random_number_generator = MTGenerator(324324)
def setUp(self):
self.gso_parameters = GSOParameters()
self.objective_function = J1()
self.landscape_position1 = LandscapePosition(self.objective_function,
Coordinates([0.0, 0.0]))
self.landscape_position2 = LandscapePosition(self.objective_function,
Coordinates([1.0, 1.0]))
self.positions = [[self.landscape_position1, self.landscape_position2]]
def test_create_from_interface(self):
objective_function = J1()
gso_parameters = GSOParameters()
number_of_glowworms = 50
initializer = Initializer(objective_function, number_of_glowworms,
gso_parameters)
swarm = initializer.generate_glowworms()
assert swarm.get_size() > 0
def test_read_gso_parameters(self):
parameteres = GSOParameters()
assert_almost_equals(0.4, parameteres.rho)
assert_almost_equals(0.6, parameteres.gamma)
assert_almost_equals(0.08, parameteres.beta)
assert_almost_equals(5.0, parameteres.initial_luciferin)
assert_almost_equals(0.2, parameteres.initial_vision_range)
assert_almost_equals(5.0, parameteres.max_vision_range)
assert 5 == parameteres.max_neighbors
def test_generate_landscape_positions_without_coordinates(self):
objective_function = J1()
gso_parameters = GSOParameters()
number_of_glowworms = 50
initializer = FromFileInitializer(
[objective_function], number_of_glowworms, gso_parameters, 2,
self.golden_data_path + 'initial_positions_empty.txt')
swarm = initializer.generate_glowworms()
assert swarm.get_size() > 0
def test_generate_landscape_positions_num_glowworms_different(self):
objective_function = J1()
gso_parameters = GSOParameters()
number_of_glowworms = 50
initializer = FromFileInitializer(
[objective_function], number_of_glowworms, gso_parameters, 2,
self.golden_data_path / 'initial_positions_redux.txt')
swarm = initializer.generate_glowworms()
assert swarm.get_size() > 0
def test_read_gso_parameters_with_file(self):
parameteres = GSOParameters(self.golden_data_path + 'glowworm.conf')
assert_almost_equals(0.1, parameteres.rho)
assert_almost_equals(0.2, parameteres.gamma)
assert_almost_equals(0.6, parameteres.beta)
assert_almost_equals(0.3, parameteres.initial_luciferin)
assert_almost_equals(0.4, parameteres.initial_vision_range)
assert_almost_equals(0.5, parameteres.max_vision_range)
assert 7 == parameteres.max_neighbors
def test_create_swarm(self):
objective_function = J1()
gso_parameters = GSOParameters()
number_of_glowworms = 50
initializer = FromFileInitializer(
[objective_function], number_of_glowworms, gso_parameters, 2,
self.golden_data_path + 'initial_positions.txt')
swarm = initializer.generate_glowworms()
assert number_of_glowworms == swarm.get_size()
assert "(0.617171, -2.85014) 5.00000000 0 0.200 0.00000000" == str(
swarm.glowworms[-1])
def test_generate_landscape_positions_num_glowworms_different(self):
gso_parameters = GSOParameters()
number_of_glowworms = 10
seed = 324324
random_number_generator = MTGenerator(seed)
initializer = LightdockFromFileInitializer(
self.adapter, self.scoring_function, number_of_glowworms,
gso_parameters, 7,
self.golden_data_path / 'initial_positions_1PPE.txt', 0.5, 0.5,
random_number_generator, 0.5, 10, 10)
swarm = initializer.generate_glowworms()
assert swarm.get_size() > 0
def setup(self):
self.path = os.path.dirname(os.path.realpath(__file__))
self.test_path = self.path + '/scratch/'
try:
shutil.rmtree(self.test_path)
except:
pass
os.mkdir(self.test_path)
self.golden_data_path = os.path.normpath(
os.path.dirname(os.path.realpath(__file__))) + '/golden_data/'
self.gso_parameters = GSOParameters()
self.gso_parameters.initial_vision_range = 3.0
self.gso_parameters.max_vision_range = 3.0
def test_create_swarm(self):
gso_parameters = GSOParameters()
number_of_glowworms = 5
seed = 324324
random_number_generator = MTGenerator(seed)
initializer = LightdockFromFileInitializer(
[self.adapter], [self.scoring_function], number_of_glowworms,
gso_parameters, 7,
self.golden_data_path / 'initial_positions_1PPE.txt', 0.5, 0.5,
random_number_generator, 0.5, 10, 10)
swarm = initializer.generate_glowworms()
assert number_of_glowworms == swarm.get_size()
def __init__(self):
self.path = Path(__file__).absolute().parent
self.test_path = self.path / 'scratch_lightdockbuilder'
self.golden_data_path = self.path / 'golden_data'
self.gso_parameters = GSOParameters()
self.bounding_box = BoundingBox([
Boundary(-MAX_TRANSLATION, MAX_TRANSLATION),
Boundary(-MAX_TRANSLATION, MAX_TRANSLATION),
Boundary(-MAX_TRANSLATION, MAX_TRANSLATION),
Boundary(-MAX_ROTATION, MAX_ROTATION),
Boundary(-MAX_ROTATION, MAX_ROTATION),
Boundary(-MAX_ROTATION, MAX_ROTATION),
Boundary(-MAX_ROTATION, MAX_ROTATION)
])
self.random_number_generator = MTGenerator(324324)
def test_create_swarm(self):
objective_function = J1()
gso_parameters = GSOParameters()
number_of_glowworms = 15
seed = 324324
random_number_generator = MTGenerator(seed)
bounding_box = BoundingBox([Boundary(1, 2), Boundary(10, 15)])
initializer = RandomInitializer([objective_function],
number_of_glowworms, gso_parameters,
bounding_box, random_number_generator)
swarm = initializer.generate_glowworms()
assert number_of_glowworms == swarm.get_size()
for glowworm in swarm.glowworms:
coordinates = glowworm.landscape_positions[0].coordinates
assert coordinates[0] < 2 and coordinates[0] >= 1
assert coordinates[1] < 15 and coordinates[1] >= 10
def setUp(self):
self.path = os.path.dirname(os.path.realpath(__file__))
self.test_path = self.path + '/scratch/'
try:
shutil.rmtree(self.test_path)
except:
pass
os.mkdir(self.test_path)
self.golden_data_path = os.path.normpath(
os.path.dirname(os.path.realpath(__file__))) + '/golden_data/'
self.gso_parameters = GSOParameters()
self.bounding_box = BoundingBox([
Boundary(-MAX_TRANSLATION, MAX_TRANSLATION),
Boundary(-MAX_TRANSLATION, MAX_TRANSLATION),
Boundary(-MAX_TRANSLATION, MAX_TRANSLATION),
Boundary(-MAX_ROTATION, MAX_ROTATION),
Boundary(-MAX_ROTATION, MAX_ROTATION),
Boundary(-MAX_ROTATION, MAX_ROTATION),
Boundary(-MAX_ROTATION, MAX_ROTATION)
])
self.random_number_generator = MTGenerator(324324)
def test_read_gso_parameters_wrong_file(self):
parameteres = GSOParameters(self.golden_data_path + 'no_file.conf')
assert False
#!/usr/bin/env python3
# coding: utf-8
from lightdock.gso.parameters import GSOParameters
from lightdock.gso.searchspace.benchmark_ofunctions import J2
from lightdock.gso.algorithm import GSOBuilder
from lightdock.gso.boundaries import Boundary, BoundingBox
from lightdock.mathutil.lrandom import MTGenerator
gso_parameters = GSOParameters()
objective_function = J2()
bounding_box = BoundingBox([Boundary(-4.0, 4.0), Boundary(-4.0, 4.0)])
number_of_glowworms = 200
random_number_generator = MTGenerator(324324324)
builder = GSOBuilder()
gso = builder.create(number_of_glowworms,
random_number_generator,
gso_parameters,
objective_function,
bounding_box)
gso.swarm.save(0, '.', file_name='gso_0.out')
for glowworm in gso.swarm.glowworms:
print(glowworm.landscape_positions[0])
print('Step 1')
gso.run(100)
print('Step 100')
adapter = DFIREAdapter(receptor, ligand)
scoring_function = DFIRE()
log.info("Loaded DFIRE scoring function")
bounding_box = BoundingBox([
Boundary(-MAX_TRANSLATION, MAX_TRANSLATION),
Boundary(-MAX_TRANSLATION, MAX_TRANSLATION),
Boundary(-MAX_TRANSLATION, MAX_TRANSLATION),
Boundary(-MAX_ROTATION, MAX_ROTATION),
Boundary(-MAX_ROTATION, MAX_ROTATION),
Boundary(-MAX_ROTATION, MAX_ROTATION),
Boundary(-MAX_ROTATION, MAX_ROTATION)
])
random_number_generator = MTGenerator(GSO_SEED)
gso_parameters = GSOParameters(configuration_file)
log.info("Parameters read")
positions = []
for i in range(num_glowworms):
coordinates = [
translations[i][0], translations[i][1], translations[i][2],
rotations[i].w, rotations[i].x, rotations[i].y, rotations[i].z
]
positions.append(
DockingLandscapePosition(scoring_function, coordinates,
adapter.receptor_model,
adapter.ligand_model))
log.info("%d positions loaded" % len(positions))
swarm = Swarm(positions, gso_parameters)
def test_read_gso_parameters_wrong_file(self):
parameters = GSOParameters(self.golden_data_path / 'no_file.conf')
assert parameters is not None
def test_read_gso_parameters_wrong_parameters(self):
parameteres = GSOParameters(self.golden_data_path +
'wrong_glowworm.conf')
assert False
def test_read_gso_parameters_wrong_parameters(self):
parameters = GSOParameters(self.golden_data_path / 'wrong_glowworm.conf')
assert parameters is not None