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