class TestBoundingBox:
def setUp(self):
self.dimension1 = Boundary(0, 1)
self.dimension2 = Boundary(0, 5)
self.boundaries = [self.dimension1, self.dimension2]
self.box = BoundingBox(self.boundaries)
def tearDown(self):
pass
def test_check_dimension_bounding_box(self):
assert 2 == self.box.dimension
def test_get_boundaries(self):
expected1 = self.dimension1.clone()
expected2 = self.dimension2.clone()
assert expected1 == self.box.get_boundary_of_dimension(0)
assert expected2 == self.box.get_boundary_of_dimension(1)
assert expected1 != self.box.get_boundary_of_dimension(1)
def test_boundary_representation(self):
assert "[0, 1]" == str(self.dimension1)
def test_bounding_box_representation(self):
assert "[0, 1] [0, 5]" == str(self.box)
def setUp(self):
self.dimension1 = Boundary(0, 1)
self.dimension2 = Boundary(0, 5)
self.boundaries = [self.dimension1, self.dimension2]
self.box = BoundingBox(self.boundaries)
class TestBoundingBox:
def __init__(self):
self.dimension1 = Boundary(0, 1)
self.dimension2 = Boundary(0, 5)
self.boundaries = [self.dimension1, self.dimension2]
self.box = BoundingBox(self.boundaries)
def test_check_dimension_bounding_box(self):
assert self.box.dimension == 2
def test_get_boundaries(self):
expected1 = self.dimension1.clone()
expected2 = self.dimension2.clone()
assert expected1 == self.box.get_boundary_of_dimension(0)
assert expected2 == self.box.get_boundary_of_dimension(1)
assert expected1 != self.box.get_boundary_of_dimension(1)
def test_boundary_representation(self):
assert str(self.dimension1) == "[0, 1]"
def test_bounding_box_representation(self):
assert str(self.box) == "[0, 1] [0, 5]"
def test_GSO_with_report_in_file_and_saving_intermediary_files(self):
objective_function = J5()
self.gso_parameters.initial_vision_range = 3.0
self.gso_parameters.max_vision_range = 3.0
bounding_box = BoundingBox(
[Boundary(-2.0 * pi, 2.0 * pi),
Boundary(-2.0 * pi, 2.0 * pi)])
number_of_glowworms = 5
random_number_generator = MTGenerator(324324)
builder = GSOBuilder()
gso = builder.create_from_file(
number_of_glowworms, random_number_generator, self.gso_parameters,
objective_function, bounding_box,
self.golden_data_path + 'initial_positions_redux.txt')
gso.run(5,
saving_path=self.test_path,
save_intermediary=True,
save_all_intermediary=True)
for i in range(5):
assert os.path.exists(self.test_path + 'gso_%d.out' % (i + 1))
gso.report(self.test_path + 'report.out')
lines = open(self.test_path + 'report.out').readlines()
assert 14 == len(lines)
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 __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_GSO_with_J1(self):
objective_function = J1()
bounding_box = BoundingBox([Boundary(-3.0, 3.0), Boundary(-3.0, 3.0)])
number_of_glowworms = 50
random_number_generator = MTGenerator(324324)
builder = GSOBuilder()
gso = builder.create(number_of_glowworms, random_number_generator,
self.gso_parameters, objective_function,
bounding_box)
gso.run(200)
# Function peak coordinates
peak_coordinates = [[1.28, 0.0], [0.0, 1.58], [-0.46, -0.63]]
# Check with auxiliar function the position of the glowworms
assert self.found_peaks(peak_coordinates, 2, gso.swarm.glowworms)
def get_default_box(use_anm, anm_rec, anm_lig):
"""Get the default bounding box"""
boundaries = [
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)
]
if use_anm:
boundaries.extend(
[Boundary(MIN_EXTENT, MAX_EXTENT) for _ in range(anm_rec)])
boundaries.extend(
[Boundary(MIN_EXTENT, MAX_EXTENT) for _ in range(anm_lig)])
return BoundingBox(boundaries)
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 test_GSO_with_J2(self):
objective_function = J2()
self.gso_parameters.initial_vision_range = 2.0
self.gso_parameters.max_vision_range = 2.0
bounding_box = BoundingBox([Boundary(-1.0, 1.0), Boundary(-1.0, 1.0)])
number_of_glowworms = 70
random_number_generator = MTGenerator(324324)
builder = GSOBuilder()
gso = builder.create(number_of_glowworms, random_number_generator,
self.gso_parameters, objective_function,
bounding_box)
gso.run(200)
# Function peak coordinates
peak_coordinates = [[-0.5, -0.5], [-0.5, 0.5], [0.5, -0.5], [0.5, 0.5]]
# Check with auxiliar function the position of the glowworms
assert self.found_peaks(peak_coordinates, 2, gso.swarm.glowworms, 3)
def test_GSO_with_report(self):
objective_function = J5()
self.gso_parameters.initial_vision_range = 3.0
self.gso_parameters.max_vision_range = 3.0
bounding_box = BoundingBox(
[Boundary(-2.0 * pi, 2.0 * pi),
Boundary(-2.0 * pi, 2.0 * pi)])
number_of_glowworms = 5
random_number_generator = MTGenerator(324324)
builder = GSOBuilder()
gso = builder.create(number_of_glowworms, random_number_generator,
self.gso_parameters, objective_function,
bounding_box)
gso.run(5)
report = gso.report()
assert 14 == len(report.split(os.linesep))
assert str(gso) == report
def test_GSO_with_J4(self):
objective_function = J4()
self.gso_parameters.initial_vision_range = 0.75
self.gso_parameters.max_vision_range = 0.75
bounding_box = BoundingBox([Boundary(-2.0, 2.0), Boundary(-2.0, 2.0)])
number_of_glowworms = 100
random_number_generator = MTGenerator(324324)
builder = GSOBuilder()
gso = builder.create(number_of_glowworms, random_number_generator,
self.gso_parameters, objective_function,
bounding_box)
gso.run(50)
# Save last step
gso.swarm.save(50, self.test_path, 'gso_j4_50.out')
assert filecmp.cmp(self.test_path + 'gso_j4_50.out',
self.golden_data_path + 'gso_j4_50.out')
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)
# Start from results positions
log.info("Reading calculated data from %s" % starting_file)
translations, rotations, luciferin, neighbors, vision_range, scoring = parse_output_file(
starting_file)
num_glowworms = len(translations)
log.info("%d glowworms loaded" % num_glowworms)
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(
#!/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')
