from __future__ import absolute_import, division, print_function from cctbx import crystal, sgtbx, xray from cctbx import geometry_restraints from cctbx.array_family import flex import iotbx.cif.restraints from libtbx.test_utils import show_diff from six.moves import cStringIO as StringIO def exercise_geometry_restraints_as_cif(): quartz = xray.structure( crystal_symmetry=crystal.symmetry( (5.01,5.01,5.47,90,90,120), "P6222"), scatterers=flex.xray_scatterer([ xray.scatterer("Si", (1/2.,1/2.,1/3.)), xray.scatterer("O", (0.197,-0.197,0.83333))])) bond_proxies = geometry_restraints.shared_bond_simple_proxy(( geometry_restraints.bond_simple_proxy( i_seqs=[0,1], rt_mx_ji=sgtbx.rt_mx("x-y,x,z-2/3"), distance_ideal=1.6, weight=3.2), geometry_restraints.bond_simple_proxy( i_seqs=[0,1], distance_ideal=1.7, weight=1.8), )) dihedral_proxies = geometry_restraints.shared_dihedral_proxy(( geometry_restraints.dihedral_proxy( i_seqs = [1,0,1,0], sym_ops = (sgtbx.rt_mx("1+y,1-x+y, z-1/3"), sgtbx.rt_mx(), sgtbx.rt_mx("x-y,x,z-2/3"), sgtbx.rt_mx("1-x,y-x,1/3-z")), angle_ideal=-30, weight=2), geometry_restraints.dihedral_proxy( i_seqs = [1,0,1,0], sym_ops = (sgtbx.rt_mx("1+y,1-x+y, z-1/3"), sgtbx.rt_mx(), sgtbx.rt_mx("-y,x-y,z-1/3"), sgtbx.rt_mx("x-y,x,1/3+z")), angle_ideal=90, weight=3), )) chirality_proxies = geometry_restraints.shared_chirality_proxy(( geometry_restraints.chirality_proxy( i_seqs = [1,0,1,0], sym_ops = (sgtbx.rt_mx("1+y,1-x+y, z-1/3"), sgtbx.rt_mx(), sgtbx.rt_mx("x-y,x,z-2/3"), sgtbx.rt_mx("1-x,y-x,1/3-z")), volume_ideal=1.2, both_signs=False, weight=2), geometry_restraints.chirality_proxy( i_seqs = [1,0,1,0], sym_ops = (sgtbx.rt_mx("1+y,1-x+y, z-1/3"), sgtbx.rt_mx(), sgtbx.rt_mx("x-y,x,z-2/3"), sgtbx.rt_mx("1-x,y-x,1/3-z")), volume_ideal=1.2, both_signs=True, weight=2), )) angle_proxies = geometry_restraints.shared_angle_proxy(( geometry_restraints.angle_proxy( i_seqs = [1,0,1], sym_ops = (sgtbx.rt_mx("x-y,x,z-2/3"), sgtbx.rt_mx(), sgtbx.rt_mx("-y,x-y,z-1/3")), angle_ideal=103, weight=2), geometry_restraints.angle_proxy( i_seqs = [1,0,1], sym_ops = (sgtbx.rt_mx("y+1,-x+y+1,z-1/3"), sgtbx.rt_mx(), sgtbx.rt_mx("-y,x-y,z-1/3")), angle_ideal=110, weight=5), geometry_restraints.angle_proxy( i_seqs = [0,1,0], sym_ops = (sgtbx.rt_mx("y,-x+y,z+2/3"), sgtbx.rt_mx(), sgtbx.rt_mx("-x+y,-x,z+1/3")), angle_ideal=150, weight=5), )) bond_similarity_proxies = geometry_restraints.shared_bond_similarity_proxy(( geometry_restraints.bond_similarity_proxy( i_seqs=[(0,1),(0,1),(0,1)], sym_ops=(sgtbx.rt_mx("x-y,x,z-2/3"), sgtbx.rt_mx("-y,x-y,z-1/3"), sgtbx.rt_mx("y+1,-x+y+1,z-1/3")), weights=(1,1,1)), )) cif_block = iotbx.cif.model.block() iotbx.cif.restraints.add_to_cif_block( cif_block, quartz, bond_proxies=bond_proxies, angle_proxies=angle_proxies, dihedral_proxies=dihedral_proxies, chirality_proxies=chirality_proxies, bond_similarity_proxies=bond_similarity_proxies) s = StringIO() cif_block.show(out=s) assert not show_diff(s.getvalue(), """\ loop_ _restr_distance_atom_site_label_1 _restr_distance_atom_site_label_2 _restr_distance_site_symmetry_2 _restr_distance_target _restr_distance_target_weight_param _restr_distance_diff Si O 2_554 1.6000 0.5590 -0.0160 Si O 1 1.7000 0.7454 -2.3838 loop_ _restr_angle_atom_site_label_1 _restr_angle_atom_site_label_2 _restr_angle_atom_site_label_3 _restr_angle_site_symmetry_1 _restr_angle_site_symmetry_2 _restr_angle_site_symmetry_3 _restr_angle_target _restr_angle_target_weight_param _restr_angle_diff O Si O 2_554 1 4_554 103.0000 0.7071 1.6926 O Si O 3_664 1 4_554 110.0000 0.4472 -1.3127 Si O Si 3 1 5 150.0000 0.4472 3.0700 loop_ _restr_torsion_atom_site_label_1 _restr_torsion_atom_site_label_2 _restr_torsion_atom_site_label_3 _restr_torsion_atom_site_label_4 _restr_torsion_site_symmetry_1 _restr_torsion_site_symmetry_2 _restr_torsion_site_symmetry_3 _restr_torsion_site_symmetry_4 _restr_torsion_angle_target _restr_torsion_weight_param _restr_torsion_diff O Si O Si 3_664 1 2_554 7_655 -30.0000 0.7071 6.9078 O Si O Si 3_664 1 4_554 2 90.0000 0.5774 11.7036 loop_ _restr_chirality_atom_site_label_1 _restr_chirality_atom_site_label_2 _restr_chirality_atom_site_label_3 _restr_chirality_atom_site_label_4 _restr_chirality_site_symmetry_1 _restr_chirality_site_symmetry_2 _restr_chirality_site_symmetry_3 _restr_chirality_site_symmetry_4 _restr_chirality_volume_target _restr_chirality_weight_param _restr_chirality_diff O Si O Si 3_664 1 2_554 7_655 1.2000 0.7071 2.4415 O Si O Si 3_664 1 2_554 7_655 1.2000 0.7071 -0.0415 loop_ _restr_equal_distance_class_class_id _restr_equal_distance_class_target_weight_param _restr_equal_distance_class_average _restr_equal_distance_class_esd _restr_equal_distance_class_diff_max 1 1.0000 1.6160 0.0000 0.0000 loop_ _restr_equal_distance_atom_site_label_1 _restr_equal_distance_atom_site_label_2 _restr_equal_distance_site_symmetry_2 _restr_equal_distance_class_id Si O 2_554 1 Si O 4_554 1 Si O 3_664 1 """) def exercise_adp_restraints_as_cif(): import libtbx.load_env if not libtbx.env.has_module("smtbx"): print("Skipping exercise_adp_restraints_as_cif(): smtbx not available") return from smtbx.refinement.restraints import adp_restraints as smtbx_adp_restraints import smtbx.development xs = smtbx.development.sucrose() rigid_bond_proxies = smtbx_adp_restraints.rigid_bond_restraints( xray_structure=xs).proxies[:3] rigu_proxies = smtbx_adp_restraints.rigu_restraints( xray_structure=xs).proxies[:3] adp_similarity_proxies = smtbx_adp_restraints.adp_similarity_restraints( xray_structure=xs).proxies[:3] isotropic_adp_proxies = smtbx_adp_restraints.isotropic_adp_restraints( xray_structure=xs).proxies[:3] cif_block = iotbx.cif.model.block() iotbx.cif.restraints.add_to_cif_block( cif_block, xs, rigid_bond_proxies=rigid_bond_proxies, rigu_proxies=rigu_proxies, adp_similarity_proxies=adp_similarity_proxies, isotropic_adp_proxies=isotropic_adp_proxies) s = StringIO() cif_block.show(out=s) assert not show_diff(s.getvalue(), """\ loop_ _restr_U_rigid_atom_site_label_1 _restr_U_rigid_atom_site_label_2 _restr_U_rigid_target_weight_param _restr_U_rigid_U_parallel _restr_U_rigid_diff O1 C1 0.0100 0.0176 0.0006 O1 C2 0.0100 0.0194 -0.0053 O1 C3 0.0100 0.0177 0.0013 loop_ _restr_RIGU_atom_site_label_1 _restr_RIGU_atom_site_label_2 _restr_RIGU_target_weight_param _restr_RIGU_U13_diff _restr_RIGU_U23_diff _restr_RIGU_U33_diff O1 C1 0.004000 -0.002618 -0.001550 0.000599 O1 C2 0.004000 -0.000752 0.002098 -0.005274 O1 C3 0.004000 -0.002608 -0.001448 0.001305 loop_ _restr_U_similar_atom_site_label_1 _restr_U_similar_atom_site_label_2 _restr_U_similar_weight_param O1 C1 0.0400 O1 C6 0.0400 O2 C2 0.0800 loop_ _restr_U_iso_atom_site_label _restr_U_iso_weight_param O1 0.1000 O2 0.2000 O3 0.2000 """) def run(): exercise_adp_restraints_as_cif() exercise_geometry_restraints_as_cif() print("OK") if __name__ == '__main__': run()