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 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)
return gso
def test_bounding_box_anm(self):
box = get_default_box(use_anm=True, anm_rec=5, anm_lig=3)
assert box.dimension == 7 + 5 + 3
def test_bounding_box(self):
box = get_default_box(use_anm=False, anm_rec=0, anm_lig=0)
assert box.dimension == 7
