from __future__ import absolute_import, division, print_function from libtbx.test_utils import approx_equal from smtbx.refinement.restraints import adp_restraints from smtbx import development from cctbx.array_family import flex from cctbx import crystal from six.moves import range def get_pair_sym_table(xray_structure): asu_mappings = xray_structure.asu_mappings(buffer_thickness=3.5) pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings) scattering_types = xray_structure.scatterers().extract_scattering_types() pair_asu_table.add_covalent_pairs( scattering_types, exclude_scattering_types=flex.std_string(("H","D"))) return pair_asu_table.extract_pair_sym_table() def test_adp_similarity(): xray_structure = development.sucrose() pair_sym_table = get_pair_sym_table(xray_structure) for table in (None,pair_sym_table): if table is None: xs = xray_structure else: xs = None restraints = \ adp_restraints.adp_similarity_restraints( xray_structure=xs, pair_sym_table=table) assert restraints.proxies.size() == 24 i_seqs = (9,14,28,32,36,38) restraints = \ adp_restraints.adp_similarity_restraints( xray_structure=xs, pair_sym_table=table, i_seqs=i_seqs) expected_i_seqs = ((9,32),(14,36),(32,36),(36,38)) expected_weights = (625,156.25,625,625) proxies = restraints.proxies assert proxies.size() == len(expected_i_seqs) for i in range(proxies.size()): assert approx_equal(proxies[i].i_seqs, expected_i_seqs[i]) assert approx_equal(proxies[i].weight, expected_weights[i]) # add more restraints to same shared proxy i_seqs = (3,23,40,42) restraints = \ adp_restraints.adp_similarity_restraints( xray_structure=xs, pair_sym_table=table, proxies=proxies, i_seqs=i_seqs) expected_i_seqs = ( (9,32),(14,36),(32,36),(36,38),(3,23),(40,42)) expected_weights = (625,156.25,625,625,156.25,625) proxies = restraints.proxies assert proxies.size() == len(expected_i_seqs) for i in range(proxies.size()): assert approx_equal(proxies[i].i_seqs, expected_i_seqs[i]) assert approx_equal(proxies[i].weight, expected_weights[i]) def test_rigid_bond(): xray_structure = development.sucrose() pair_sym_table = get_pair_sym_table(xray_structure) for table in (None,pair_sym_table): if table is None: xs = xray_structure else: xs = None restraints = \ adp_restraints.rigid_bond_restraints( xray_structure=xs, pair_sym_table=table) assert restraints.proxies.size() == 60 i_seqs = (9,14,28,32,36,38) restraints = \ adp_restraints.rigid_bond_restraints( xray_structure=xs, pair_sym_table=table, i_seqs=i_seqs) expected_i_seqs = ( (9,32),(9,36),(14,36),(14,32),(14,38),(32,36),(32,38),(36,38)) expected_weights = [10000]*len(expected_i_seqs) proxies = restraints.proxies assert proxies.size() == len(expected_i_seqs) for i in range(proxies.size()): assert approx_equal(proxies[i].i_seqs, expected_i_seqs[i]) assert approx_equal(proxies[i].weight, expected_weights[i]) # add more restraints to same shared proxy i_seqs = (10,40,42) restraints = \ adp_restraints.rigid_bond_restraints( xray_structure=xs, pair_sym_table=table, proxies=proxies, i_seqs=i_seqs) expected_i_seqs = ( (9,32),(9,36),(14,36),(14,32),(14,38),(32,36), (32,38),(36,38),(10,42),(10,40),(40,42)) expected_weights = [10000]*len(expected_i_seqs) proxies = restraints.proxies assert proxies.size() == len(expected_i_seqs) for i in range(proxies.size()): assert approx_equal(proxies[i].i_seqs, expected_i_seqs[i]) assert approx_equal(proxies[i].weight, expected_weights[i]) def test_isotropic_adp(): xray_structure = development.sucrose() xray_structure.scatterers()[10].set_use_u_iso_only() pair_sym_table = get_pair_sym_table(xray_structure) for table in (None,pair_sym_table): restraints = \ adp_restraints.isotropic_adp_restraints( xray_structure=xray_structure, pair_sym_table=table) assert restraints.proxies.size() == 22 i_seqs = (9,14,28,32,36,38) expected_weights = (100,25,100,100,100,100) restraints = \ adp_restraints.isotropic_adp_restraints( xray_structure=xray_structure, pair_sym_table=table, i_seqs=i_seqs) proxies = restraints.proxies assert proxies.size() == len(i_seqs) for i in range(proxies.size()): assert approx_equal(proxies[i].i_seqs[0], i_seqs[i]) assert approx_equal(proxies[i].weight, expected_weights[i]) # add more restraints to same shared proxy i_seqs = (3,5,42) restraints = \ adp_restraints.isotropic_adp_restraints( xray_structure=xray_structure, pair_sym_table=table, proxies=proxies, i_seqs=i_seqs) expected_i_seqs = (9,14,28,32,36,38,3,5,42) expected_weights = (100,25,100,100,100,100,25,25,100) proxies = restraints.proxies assert proxies.size() == len(expected_i_seqs) for i in range(proxies.size()): assert approx_equal(proxies[i].i_seqs[0], expected_i_seqs[i]) assert approx_equal(proxies[i].weight, expected_weights[i]) def test_rigu(): xray_structure = development.sucrose() pair_sym_table = get_pair_sym_table(xray_structure) for table in (None,pair_sym_table): if table is None: xs = xray_structure else: xs = None restraints = \ adp_restraints.rigu_restraints( xray_structure=xs, pair_sym_table=table) assert restraints.proxies.size() == 60 i_seqs = (9,14,28,32,36,38) restraints = \ adp_restraints.rigu_restraints( xray_structure=xs, pair_sym_table=table, i_seqs=i_seqs) expected_i_seqs = ( (9,32),(9,36),(14,36),(14,32),(14,38),(32,36),(32,38),(36,38)) expected_weights = [62500]*len(expected_i_seqs) proxies = restraints.proxies assert proxies.size() == len(expected_i_seqs) for i in range(proxies.size()): assert approx_equal(proxies[i].i_seqs, expected_i_seqs[i]) assert approx_equal(proxies[i].weight, expected_weights[i]) # add more restraints to same shared proxy i_seqs = (10,40,42) restraints = \ adp_restraints.rigu_restraints( xray_structure=xs, pair_sym_table=table, proxies=proxies, i_seqs=i_seqs) expected_i_seqs = ( (9,32),(9,36),(14,36),(14,32),(14,38),(32,36), (32,38),(36,38),(10,42),(10,40),(40,42)) expected_weights = [62500]*len(expected_i_seqs) proxies = restraints.proxies assert proxies.size() == len(expected_i_seqs) for i in range(proxies.size()): assert approx_equal(proxies[i].i_seqs, expected_i_seqs[i]) assert approx_equal(proxies[i].weight, expected_weights[i])