from __future__ import absolute_import, division, print_function from cctbx import crystal from cctbx import uctbx from cctbx import sgtbx from cctbx import adptbx from cctbx import xray from iotbx import shelx from iotbx.shelx import crystal_symmetry_from_ins from iotbx.shelx import tokens import iotbx.builders from libtbx.test_utils import approx_equal, Exception_expected from libtbx.math_utils import are_equivalent from six.moves import cStringIO as StringIO from six.moves import range from six.moves import zip def exercise_lexing(): stream = shelx.command_stream(file=StringIO(ins_mundane_tiny)) i = iter(stream) try: cmd, line = next(i) assert cmd == ('TITL', ('in Pbca',)) cmd, line = next(i) assert cmd == ('CELL', (0.71073, 7.35, 9.541, 12.842, 90, 90, 90)) cmd, line = next(i) assert cmd == ('ZERR', (4, 0.002, 0.002, 0.003, 0, 0, 0)) cmd, line = next(i) assert cmd == ('LATT', (1,)) cmd, line = next(i) assert cmd == ('SYMM', ('0.5-X, -Y, 0.5+Z',)) cmd, line = next(i) assert cmd == ('SYMM', ('-X, 0.5+Y, 0.5-Z',)) cmd, line = next(i) assert cmd == ('SYMM', ('1/2+X, 0.5-Y, -Z',)) cmd, line = next(i) assert cmd == ('SFAC', ('C', 'H', 'O', 'N',)) cmd, line = next(i) assert cmd == ('UNIT', (32, 40, 16, 8)) cmd, line = next(i) assert cmd == ('TEMP', (-153,)) cmd, line = next(i) assert cmd == ('L.S.', (4,)) cmd, line = next(i) assert cmd == ('BOND', (tokens.element_token(element='H'),)) cmd, line = next(i) # FMAP cmd, line = next(i) # PLAN cmd, line = next(i) # WGHT cmd, line = next(i) # EXTI cmd, line = next(i) # FVAR cmd, line = next(i) assert cmd == ('REM', ()) cmd, line = next(i) assert cmd == ('+', '/path/to/filename.ins') cmd, line = next(i) assert cmd == ('REM', ('Protracted example of residues on command',)) cmd, line = next(i) assert cmd == ('HFIX', (tokens.residue_number_tok, 1), (23,)) cmd, line = next(i) assert cmd == ('HFIX', (tokens.residue_class_tok, 'N'), (43,)) cmd, line = next(i) assert cmd == ('EQIV', (1, '1-X, -Y, -Z')) cmd, line = next(i) assert cmd == ('CONF', (tokens.atomname_token(name='C4'), tokens.atomname_token(name='N'), tokens.atomname_token(name='H'), tokens.atomname_token(name='O2', symmetry=1) ) ) cmd, line = next(i) assert cmd == ('DFIX', (tokens.residue_number_tok, 1), (1.5, tokens.atomname_token(name='C2'), tokens.atomname_token(name='C3'))) cmd, line = next(i) assert cmd == ('__ATOM__', ('O2', 3, 0.362893, 0.160589, -0.035913, 11, 0.03926, 0.02517, 0.02140, -0.00415, -0.00810, 0.01009)) cmd, line = next(i) assert cmd == ('__ATOM__', ('O3', 3, 0.696722, 0.119176, 0.260657, 11, 0.02838, 0.02133, 0.02918, 0.00011, -0.01030, -0.00048)) cmd, line = next(i) # C1 cmd, line = next(i) # C4 cmd, line = next(i) assert cmd == ('RESI', (1,)) cmd, line = next(i) # C2 cmd, line = next(i) # C3 cmd, line = next(i) assert cmd == ('RESI', ('N',)) cmd, line = next(i) # N cmd, line = next(i) # HKLF try: cmd, line = next(i) raise AssertionError except StopIteration: pass except StopIteration: raise AssertionError def exercise_lexing_bis(): stream = shelx.command_stream(file=StringIO(ins_equal_sign_in_rem)) i = iter(stream) try: cmd, line = next(i) assert cmd == ('REM', ('Solution 1 R1 0.100, Alpha = 0.0015 in P2(1)',)) cmd, line = next(i) assert cmd == ('REM', ('C13 O10',)) cmd, line = next(i) assert cmd == ('TITL', ('SUCROSE IN P2(1)',)) except StopIteration: raise AssertionError def exercise_crystal_symmetry_parsing(): stream = shelx.command_stream(file=StringIO(ins_mundane_tiny)) builder = iotbx.builders.crystal_symmetry_builder() stream = shelx.crystal_symmetry_parser(stream, builder) stream = shelx.wavelength_parser(stream.filtered_commands(), builder) stream.parse() assert builder.crystal_symmetry.is_similar_symmetry( crystal.symmetry( unit_cell=uctbx.unit_cell((7.350, 9.541, 12.842, 90, 90, 90)), space_group_symbol='Pbca'), relative_length_tolerance=1e-15, absolute_angle_tolerance=1e-15) cs = crystal_symmetry_from_ins.extract_from( file=StringIO(ins_mundane_tiny)) assert cs.is_similar_symmetry(builder.crystal_symmetry) assert approx_equal(builder.wavelength_in_angstrom, 0.71073, eps=5e-6) stream = shelx.command_stream(file=StringIO(ins_P1)) l = shelx.crystal_symmetry_parser( stream, builder=iotbx.builders.crystal_symmetry_builder()) l.parse() assert l.builder.crystal_symmetry.is_similar_symmetry( crystal.symmetry( unit_cell=uctbx.unit_cell((1,2,3,99,100,101)), space_group_symbol='P1'), relative_length_tolerance=1e-15, absolute_angle_tolerance=1e-15) cs = crystal_symmetry_from_ins.extract_from( file=StringIO(ins_P1)) assert cs.is_similar_symmetry(l.builder.crystal_symmetry) def exercise_instruction_parsing(): alternatives = (None,) try: _ = iotbx.builders.mixin_builder_class( "builder_to_test_instruction_parsing", iotbx.builders.reflection_data_source_builder, iotbx.builders.weighting_scheme_builder, iotbx.builders.twinning_builder) alternatives += (_(),) except AttributeError: pass for builder in alternatives: stream = shelx.command_stream(file=StringIO(ins_aspirin)) l = shelx.instruction_parser(stream, builder) l.parse() ins = l.instructions assert ins['hklf']['s'] == 1 assert ins['hklf']['matrix'].as_xyz() == 'z,x+y,x' assert ins['hklf']['n'] == 4 assert ins['omit_hkl'] == [[2, 3, 4], [-1, -3, 2]] assert ins['omit']['s'] == -2 assert ins['omit']['two_theta'] == 56 assert ins['wght'] == {'a':0.0687,'b':0.4463, 'c':0, 'd':0, 'e':0, 'f':1/3} assert ins['merg'] == 2 assert ins['twin']['matrix'].as_xyz() == '-x,y,-z' assert ins['twin']['n'] == 2 assert ins['basf'] == (0.352,) assert ins['temp'] == -60 if builder: assert builder.temperature_in_celsius == ins['temp'] ws = builder.weighting_scheme assert isinstance( ws, iotbx.builders.least_squares.mainstream_shelx_weighting) assert ws.a == ins['wght']['a'] assert ws.b == ins['wght']['b'] assert builder.reflection_file_format == "hklf4" assert builder.data_change_of_basis_op.as_hkl()== "l,h+k,h" if len(alternatives) != 2: return builder = alternatives[-1] ins = StringIO( "HKLF 4 1 " "0.0000 0.0000 0.3330 1.0000 0.0000 0.0000 0.0000 1.0000 -0.3330") stream = shelx.command_stream(file=ins) stream = shelx.instruction_parser(stream, builder) stream.parse() assert builder.data_change_of_basis_op.as_xyz() == "y+3*z,x,y" ins = StringIO("HKLF 4 1 -1 2 0 -1 0 0 0 -1 1") stream = shelx.command_stream(file=ins) stream = shelx.instruction_parser(stream, builder) stream.parse() assert builder.data_change_of_basis_op.as_abc() == '-a+2*b,-a,-b+c' def exercise_xray_structure_parsing(): exercise_special_positions() exercise_aspirin() exercise_disordered() exercise_invalid() exercise_atom_with_peaks() exercise_q_peaks() def exercise_atom_with_peaks(): builder = iotbx.builders.crystal_structure_builder(set_grad_flags=True) stream = shelx.command_stream( file=StringIO(ins_with_atom_peak_heights)) stream = shelx.crystal_symmetry_parser(stream, builder) stream = shelx.atom_parser(stream.filtered_commands(), builder=builder, strictly_shelxl=False) stream.parse() sc = builder.structure.scatterers() assert sc[0].label == 'O001' assert approx_equal(sc[0].site, (0.60914, 0.62292, 0.82801), eps=1e-5) assert sc[0].occupancy == 1 assert sc[0].flags.use_u_iso() assert approx_equal(sc[0].u_iso, 0.01991) assert sc[-1].label == 'C00N' assert approx_equal(sc[-1].site, (0.95213, 0.88631, 0.71108), eps=1e-5) assert sc[-1].occupancy == 1 assert sc[-1].flags.use_u_iso() assert approx_equal(sc[-1].u_iso, 0.02971) def exercise_q_peaks(): builder = iotbx.builders.crystal_structure_builder(set_grad_flags=True) stream = shelx.command_stream( file=StringIO(ins_with_q_peaks)) stream = shelx.crystal_symmetry_parser(stream, builder) stream = shelx.atom_parser(stream.filtered_commands(), builder=builder, strictly_shelxl=False) stream.parse() uc = builder.structure.unit_cell() sc = builder.structure.scatterers() q = builder.electron_density_peaks assert len(sc) == 3 assert sc[-1].label == 'O2' assert approx_equal(sc[-1].site, (0.645870, 0.883988, 0.489582), eps=1e-5) assert shelx_u_cif(uc, sc[-1].u_star) == ( "0.01055 0.00848 0.00946 0.00007 0.00427 -0.00235") assert len(q) == 3 assert approx_equal(q[0].site, (0.615600, 0.695100, 0.623900), eps=1e-6) assert approx_equal(q[0].height, 0.64, eps=1e-2) assert approx_equal(q[1].site, (0.526800, 0.678600, 0.431500), eps=1e-6) assert approx_equal(q[1].height, 0.63, eps=1e-2) assert approx_equal(q[2].site, (0.620800, 1.025100, 0.211700), eps=1e-6) assert approx_equal(q[2].height, 0.46, eps=1e-2) def exercise_special_positions(): structure = xray.structure.from_shelx( file=StringIO(ins_special_positions)) occupancies = [ sc.occupancy for sc in structure.scatterers() ] multiplicities = [ sc.multiplicity() for sc in structure.scatterers() ] assert multiplicities == [ 2, 2, 2, 2, 6 ] assert approx_equal(occupancies, [ 1, 0.9999, 1, 1, 1 ], eps=1e-15) def exercise_aspirin(): for set_grad_flags in (False, True): structure = xray.structure.from_shelx( file=StringIO(ins_aspirin), set_grad_flags=set_grad_flags) isinstance(structure, xray.structure) assert structure.crystal_symmetry().is_similar_symmetry( crystal.symmetry( unit_cell=uctbx.unit_cell((11.492, 6.621, 11.453, 90, 95.615, 90)), space_group_symbol='P2(1)/c'), relative_length_tolerance=1e-15, absolute_angle_tolerance=1e-15) scatterers = structure.scatterers() unit_cell = structure.unit_cell() assert len(scatterers) == 21 scatterer_labelled = dict([ (s.label, s) for s in scatterers ]) o2 = scatterer_labelled['O2'] assert o2.site == (0.879181, 0.140375, 0.051044) assert o2.occupancy == 1 assert not o2.flags.use_u_iso() and o2.flags.use_u_aniso() assert shelx_u_cif(unit_cell, o2.u_star) == ( "0.05893 0.05202 0.05656 0.01670 0.01559 0.01156") # copied from the .lst file h2 = scatterer_labelled['H2'] assert h2.flags.use_u_iso() and not h2.flags.use_u_aniso() assert approx_equal(h2.u_iso, 0.08277, eps=1e-5) c3 = scatterer_labelled['C3'] assert c3.flags.use_u_iso() and not c3.flags.use_u_aniso() h3 = scatterer_labelled['H3'] assert approx_equal(h3.u_iso, 0.06952, eps=1e-5) h9a, h9b, h9c = [ scatterer_labelled[lbl] for lbl in ('H9A', 'H9B', 'H9C') ] assert [ h.flags.use_u_iso() for h in (h9a, h9b, h9c) ] assert h9a.u_iso == h9b.u_iso == h9c.u_iso c9 = scatterer_labelled['C9'] assert approx_equal(h9a.u_iso, 1.5*c9.u_iso_or_equiv(unit_cell)) if not set_grad_flags: for scatt in scatterers: f = scatt.flags assert not f.grad_site() assert not f.grad_occupancy() assert not f.grad_u_iso() assert not f.grad_u_aniso() assert not f.grad_fp() assert not f.grad_fdp() else: for scatt in scatterers: f = scatt.flags assert f.grad_site() or scatt.label == 'C7' assert not f.grad_occupancy() assert are_equivalent(f.use_u_iso(), f.grad_u_iso() and not f.grad_u_aniso()) assert are_equivalent(f.use_u_aniso(), not f.grad_u_iso() and f.grad_u_aniso()) assert not f.grad_fp() assert not f.grad_fdp() def exercise_disordered(): for set_grad_flags in (False, True): builder = iotbx.builders.crystal_structure_builder( set_grad_flags=set_grad_flags) stream = shelx.command_stream(file=StringIO(ins_disordered)) cs_parser = shelx.crystal_symmetry_parser(stream, builder) xs_parser = shelx.atom_parser(cs_parser.filtered_commands(), builder) xs_parser.parse() structure = builder.structure assert structure.crystal_symmetry().is_similar_symmetry( crystal.symmetry( unit_cell=uctbx.unit_cell((6.033, 6.830, 7.862, 107.70, 103.17, 95.81)), space_group_symbol='P-1'), relative_length_tolerance=1e-15, absolute_angle_tolerance=1e-15) scatterers = structure.scatterers() unit_cell = structure.unit_cell() assert len(scatterers) == 15 scatterer_labelled = dict([ (s.label, s) for s in scatterers ]) br2, br3 = [ scatterer_labelled[x] for x in ('BR2', 'BR3') ] assert br2.occupancy == br3.occupancy assert approx_equal(br2.occupancy, 0.25054) if set_grad_flags: assert br2.flags.grad_occupancy() assert br3.flags.grad_occupancy() c12, h121, h122, h123 = [ scatterer_labelled[x] for x in ('C12', 'H121', 'H122', 'H123') ] assert c12.occupancy == h121.occupancy == h122.occupancy == h123.occupancy assert approx_equal(c12.occupancy, 1-br2.occupancy) if set_grad_flags: for a in (c12, h121, h122, h123): assert a.flags.grad_occupancy() assert approx_equal(builder.conformer_indices, [2, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2]) assert builder.sym_excl_indices.count(0) == structure.scatterers().size() def exercise_invalid(): for set_grad_flags in (False, True): try: structure = xray.structure.from_shelx( file=StringIO(ins_invalid_scatt), set_grad_flags=set_grad_flags) raise Exception_expected except RuntimeError as e: assert str(e) == "ShelX: illegal argument '0.3.' at line 3" try: structure = xray.structure.from_shelx( file=StringIO(ins_invalid_scatt_1), set_grad_flags=set_grad_flags) raise Exception_expected except RuntimeError as e: assert str(e) == ("ShelX: wrong number of parameters " "for scatterer at line 3") try: structure = xray.structure.from_shelx( file=StringIO(ins_missing_sfac), set_grad_flags=set_grad_flags) raise Exception_expected except RuntimeError as e: assert e.args[0].startswith('ShelX:') structure = xray.structure.from_shelx( file=StringIO(ins_disordered_with_part_sof)) occ = 0.89064 for sc in structure.scatterers(): if sc.label in ('CL2', 'C28', 'H28A', 'H28B'): assert approx_equal(sc.occupancy, occ) elif sc.label in ('CL2B', 'C28B'): assert approx_equal(sc.occupancy, 1-occ) def exercise_afix_parsing(): import smtbx.refinement.constraints.geometrical.hydrogens as _ builder = iotbx.builders.constrained_crystal_structure_builder() stream = shelx.command_stream(file=StringIO(ins_aspirin)) l_cs = shelx.crystal_symmetry_parser(stream, builder) l_afix = shelx.afix_parser(l_cs.filtered_commands(), builder) l_xs = shelx.atom_parser(l_afix.filtered_commands(), builder) l_xs.parse() expected_geometrical_constraints = [ _.staggered_terminal_tetrahedral_xh_site( constrained_site_indices=(1,), pivot=0), _.secondary_planar_xh_site( constrained_site_indices=(6,), pivot=5), _.secondary_planar_xh_site( constrained_site_indices=(10,), pivot=9), _.secondary_planar_xh_site( constrained_site_indices=(13,), pivot=12), _.secondary_planar_xh_site( constrained_site_indices=(16,), pivot=15), _.terminal_tetrahedral_xh3_sites( constrained_site_indices=(18,19,20), pivot=17, rotating=True) ] geometrical_constraints = [ c for c in builder.constraints if c.__module__ == 'smtbx.refinement.constraints.geometrical.hydrogens' ] assert len(geometrical_constraints) == len(expected_geometrical_constraints) for result, expected in zip(geometrical_constraints, expected_geometrical_constraints): assert (result == expected) def exercise_u_iso_proportional_to_u_eq_parsing(): import smtbx.refinement.constraints.adp as _ builder = iotbx.builders.constrained_crystal_structure_builder() stream = shelx.command_stream(file=StringIO(ins_aspirin)) l_cs = shelx.crystal_symmetry_parser(stream, builder) l_xs = shelx.atom_parser(l_cs.filtered_commands(), builder) l_xs.parse() expected_u_iso_constraints = [ _.u_iso_proportional_to_pivot_u_eq( u_iso_scatterer_idx=1, u_eq_scatterer_idx=0, multiplier=1.5), _.u_iso_proportional_to_pivot_u_eq( u_iso_scatterer_idx=6, u_eq_scatterer_idx=5, multiplier=1.5), _.u_iso_proportional_to_pivot_u_eq( u_iso_scatterer_idx=10, u_eq_scatterer_idx=9, multiplier=1.5), _.u_iso_proportional_to_pivot_u_eq( u_iso_scatterer_idx=13, u_eq_scatterer_idx=12, multiplier=1.5), _.u_iso_proportional_to_pivot_u_eq( u_iso_scatterer_idx=16, u_eq_scatterer_idx=15, multiplier=1.5), _.u_iso_proportional_to_pivot_u_eq( u_iso_scatterer_idx=18, u_eq_scatterer_idx=17, multiplier=1.5), _.u_iso_proportional_to_pivot_u_eq( u_iso_scatterer_idx=19, u_eq_scatterer_idx=17, multiplier=1.5), _.u_iso_proportional_to_pivot_u_eq( u_iso_scatterer_idx=20, u_eq_scatterer_idx=17, multiplier=1.5), ] u_iso_constraints = [ c for c in builder.constraints if c.__module__ == 'smtbx.refinement.constraints.adp' ] assert len(u_iso_constraints) == len(expected_u_iso_constraints) for result, expected in zip(u_iso_constraints, expected_u_iso_constraints): assert result == expected def exercise_restraint_parsing(): import smtbx.refinement.restraints def parse_restraints(ins_name): builder = iotbx.builders.restrained_crystal_structure_builder() stream = shelx.command_stream(file=StringIO(ins_name)) l_cs = shelx.crystal_symmetry_parser(stream, builder) l_afix = shelx.afix_parser(l_cs.filtered_commands(), builder) l_xs = shelx.atom_parser(l_afix.filtered_commands(), builder) l_restraints = shelx.restraint_parser(l_xs.filtered_commands(), builder) l_restraints.parse() assert isinstance(builder.restraints_manager, smtbx.refinement.restraints.manager) return builder.proxies() # exercise DFIX, DANG proxies = parse_restraints(ins_dfix_across_symm) shared_bond_proxy = proxies['bond'] assert len(shared_bond_proxy) == 3 assert approx_equal(shared_bond_proxy[0].distance_ideal, 1.75) assert approx_equal(shared_bond_proxy[1].distance_ideal, 1.75) assert approx_equal(shared_bond_proxy[2].distance_ideal, 1.75) assert shared_bond_proxy[0].i_seqs == (3,0) assert shared_bond_proxy[1].i_seqs == (3,2) assert shared_bond_proxy[2].i_seqs == (1,3) assert approx_equal(shared_bond_proxy[0].weight, 2500.0) assert approx_equal(shared_bond_proxy[1].weight, 1/(0.03*0.03)) assert approx_equal(shared_bond_proxy[2].weight, 2500.0) assert shared_bond_proxy[0].rt_mx_ji == sgtbx.rt_mx('-x+1,y,-z+1/2') assert shared_bond_proxy[1].rt_mx_ji == sgtbx.rt_mx('-x+1,y,-z+1/2') assert shared_bond_proxy[2].rt_mx_ji is None proxies = parse_restraints(ins_dfix_multiple) shared_bond_proxy = proxies['bond'] assert shared_bond_proxy.size() == 2 # invalid DFIX instructions try: proxies = parse_restraints(ins_invalid_dfix) except RuntimeError as e: assert str(e) == "ShelX: Invalid DFIX instruction at line 3" try: proxies = parse_restraints(ins_invalid_dfix_2) except RuntimeError as e: assert str(e) == "ShelX: Invalid DFIX instruction at line 3" # exercise FLAT proxies = parse_restraints(ins_flat) shared_planarity_proxy = proxies['planarity'] assert shared_planarity_proxy.size() == 2 assert approx_equal(shared_planarity_proxy[0].i_seqs, (0, 1, 2, 3, 4, 5, 6)) assert approx_equal(shared_planarity_proxy[1].i_seqs, (7, 8, 9, 10, 11, 12, 13)) assert shared_planarity_proxy[0].sym_ops is None assert shared_planarity_proxy[1].sym_ops is None assert approx_equal(shared_planarity_proxy[0].weights, (100, 100, 100, 100, 100, 100, 100)) assert approx_equal(shared_planarity_proxy[1].weights, (100, 100, 100, 100, 100, 100, 100)) # invalid FLAT try: proxies = parse_restraints(ins_invalid_flat) except RuntimeError as e: assert str(e) == "ShelX: Invalid FLAT instruction at line 3" # SADI simple proxies = parse_restraints(ins_sadi) shared_bond_similarity_proxy\ = proxies['bond_similarity'] assert shared_bond_similarity_proxy.size() == 1 assert approx_equal( shared_bond_similarity_proxy[0].i_seqs, ((0,2), (1,3))) assert shared_bond_similarity_proxy[0].sym_ops is None assert approx_equal( shared_bond_similarity_proxy[0].weights, (625.0, 625.0)) # SADI with symmetry proxies = parse_restraints(ins_sadi_with_sym) shared_bond_similarity_proxy\ = proxies['bond_similarity'] assert shared_bond_similarity_proxy.size() == 1 assert approx_equal( shared_bond_similarity_proxy[0].i_seqs, ((2,0), (1,3))) assert shared_bond_similarity_proxy[0].sym_ops\ == (sgtbx.rt_mx('1-X,+Y,0.5-Z'),sgtbx.rt_mx('1-X,+Y,0.5-Z')) assert approx_equal( shared_bond_similarity_proxy[0].weights, (2500.0, 2500.0)) # SIMU simple proxies = parse_restraints(ins_simu_simple) shared_apd_similarity_proxy \ = proxies['adp_similarity'] assert shared_apd_similarity_proxy.size() == 3 assert shared_apd_similarity_proxy[0].i_seqs == (0,1) assert shared_apd_similarity_proxy[1].i_seqs == (1,2) assert shared_apd_similarity_proxy[2].i_seqs == (2,3) assert approx_equal(shared_apd_similarity_proxy[0].weight, 156.25) assert approx_equal(shared_apd_similarity_proxy[1].weight, 625.0) assert approx_equal(shared_apd_similarity_proxy[2].weight, 156.25) # SIMU with sigma given proxies = parse_restraints(ins_simu_s) shared_apd_similarity_proxy \ = proxies['adp_similarity'] assert shared_apd_similarity_proxy.size() == 3 assert approx_equal(shared_apd_similarity_proxy[0].weight, 1/(0.06*0.06)) assert approx_equal(shared_apd_similarity_proxy[1].weight, 1/(0.03*0.03)) assert approx_equal(shared_apd_similarity_proxy[2].weight, 1/(0.06*0.06)) # SIMU with sigma and sigma terminal proxies = parse_restraints(ins_simu_s_st) shared_apd_similarity_proxy \ = proxies['adp_similarity'] assert shared_apd_similarity_proxy.size() == 3 assert approx_equal(shared_apd_similarity_proxy[0].weight, 1/(0.07*0.07)) assert approx_equal(shared_apd_similarity_proxy[1].weight, 1/(0.03*0.03)) assert approx_equal(shared_apd_similarity_proxy[2].weight, 1/(0.07*0.07)) # SIMU with sigma and sigma terminal and dmax proxies = parse_restraints(ins_simu_s_st_dmax) shared_apd_similarity_proxy \ = proxies['adp_similarity'] assert shared_apd_similarity_proxy.size() == 3 assert approx_equal(shared_apd_similarity_proxy[0].weight, 1/(0.07*0.07)) assert approx_equal(shared_apd_similarity_proxy[1].weight, 1/(0.03*0.03)) assert approx_equal(shared_apd_similarity_proxy[2].weight, 1/(0.07*0.07)) # SIMU with just atoms proxies = parse_restraints(ins_simu_atoms) shared_apd_similarity_proxy \ = proxies['adp_similarity'] assert shared_apd_similarity_proxy.size() == 2 assert shared_apd_similarity_proxy[0].i_seqs == (0,1) assert shared_apd_similarity_proxy[1].i_seqs == (1,2) assert approx_equal(shared_apd_similarity_proxy[0].weight, 156.25) assert approx_equal(shared_apd_similarity_proxy[1].weight, 625.0) # SIMU with sigma and atoms proxies = parse_restraints(ins_simu_s_atoms) shared_apd_similarity_proxy \ = proxies['adp_similarity'] assert shared_apd_similarity_proxy.size() == 2 assert shared_apd_similarity_proxy[0].i_seqs == (0,1) assert shared_apd_similarity_proxy[1].i_seqs == (1,2) assert approx_equal(shared_apd_similarity_proxy[0].weight, 1/(0.06*0.06)) assert approx_equal(shared_apd_similarity_proxy[1].weight, 1/(0.03*0.03)) # SIMU with sigma, sigma terminal and atoms proxies = parse_restraints(ins_simu_s_st_atoms) shared_apd_similarity_proxy \ = proxies['adp_similarity'] assert shared_apd_similarity_proxy.size() == 2 assert shared_apd_similarity_proxy[0].i_seqs == (0,1) assert shared_apd_similarity_proxy[1].i_seqs == (1,2) assert approx_equal(shared_apd_similarity_proxy[0].weight, 1/(0.07*0.07)) assert approx_equal(shared_apd_similarity_proxy[1].weight, 1/(0.03*0.03)) # SIMU with sigma, sigma terminal dmax and atoms proxies = parse_restraints(ins_simu_s_st_dmax_atoms) shared_apd_similarity_proxy \ = proxies['adp_similarity'] assert shared_apd_similarity_proxy.size() == 2 assert shared_apd_similarity_proxy[0].i_seqs == (0,1) assert shared_apd_similarity_proxy[1].i_seqs == (1,2) assert approx_equal(shared_apd_similarity_proxy[0].weight, 1/(0.07*0.07)) assert approx_equal(shared_apd_similarity_proxy[1].weight, 1/(0.03*0.03)) # DELU simple proxies = parse_restraints(ins_delu_simple) shared_rigid_bond_proxy \ = proxies['rigid_bond'] assert shared_rigid_bond_proxy.size() == 5 expected_i_seqs = ((0,1),(0,2),(1,2),(1,3),(2,3)) for i in range(5): assert shared_rigid_bond_proxy[i].i_seqs == expected_i_seqs[i] assert approx_equal(shared_rigid_bond_proxy[i].weight, 10000) # DELU with s1 proxies = parse_restraints(ins_delu_s1) shared_rigid_bond_proxy \ = proxies['rigid_bond'] assert shared_rigid_bond_proxy.size() == 5 for i in range(5): assert shared_rigid_bond_proxy[i].i_seqs == expected_i_seqs[i] assert approx_equal(shared_rigid_bond_proxy[i].weight, 2500) # DELU with s1 and s2 proxies = parse_restraints(ins_delu_s1_s2) shared_rigid_bond_proxy \ = proxies['rigid_bond'] assert shared_rigid_bond_proxy.size() == 5 expected_weights = (10000,2500,10000,2500,10000) for i in range(5): assert shared_rigid_bond_proxy[i].i_seqs == expected_i_seqs[i] assert approx_equal(shared_rigid_bond_proxy[i].weight, expected_weights[i]) # DELU with atoms proxies = parse_restraints(ins_delu_atoms) shared_rigid_bond_proxy \ = proxies['rigid_bond'] assert shared_rigid_bond_proxy.size() == 3 for i in range(3): assert shared_rigid_bond_proxy[i].i_seqs == expected_i_seqs[i] assert approx_equal(shared_rigid_bond_proxy[i].weight,10000) # DELU with s1 and atoms proxies = parse_restraints(ins_delu_s1_atoms) shared_rigid_bond_proxy \ = proxies['rigid_bond'] assert shared_rigid_bond_proxy.size() == 3 for i in range(3): assert shared_rigid_bond_proxy[i].i_seqs == expected_i_seqs[i] assert approx_equal(shared_rigid_bond_proxy[i].weight,2500) # DELU with s1, s2 and atoms proxies = parse_restraints(ins_delu_s1_s2_atoms) shared_rigid_bond_proxy \ = proxies['rigid_bond'] assert shared_rigid_bond_proxy.size() == 3 for i in range(3): assert shared_rigid_bond_proxy[i].i_seqs == expected_i_seqs[i] assert approx_equal(shared_rigid_bond_proxy[i].weight, expected_weights[i]) # RIGU simple proxies = parse_restraints(ins_rigu_simple) shared_rigu_proxy \ = proxies['rigu'] assert shared_rigu_proxy.size() == 5 expected_i_seqs = ((0,1),(0,2),(1,2),(1,3),(2,3)) for i in range(5): assert shared_rigu_proxy[i].i_seqs == expected_i_seqs[i] assert approx_equal(shared_rigu_proxy[i].weight, 62500) # RIGU with s1 proxies = parse_restraints(ins_rigu_s1) shared_rigu_proxy \ = proxies['rigu'] assert shared_rigu_proxy.size() == 5 for i in range(5): assert shared_rigu_proxy[i].i_seqs == expected_i_seqs[i] assert approx_equal(shared_rigu_proxy[i].weight, 2500) # RIGU with s1 and s2 proxies = parse_restraints(ins_rigu_s1_s2) shared_rigu_proxy \ = proxies['rigu'] assert shared_rigu_proxy.size() == 5 expected_weights = (10000,2500,10000,2500,10000) for i in range(5): assert shared_rigu_proxy[i].i_seqs == expected_i_seqs[i] assert approx_equal(shared_rigu_proxy[i].weight, expected_weights[i]) # RIGU with atoms proxies = parse_restraints(ins_rigu_atoms) shared_rigu_proxy \ = proxies['rigu'] assert shared_rigu_proxy.size() == 3 for i in range(3): assert shared_rigu_proxy[i].i_seqs == expected_i_seqs[i] assert approx_equal(shared_rigu_proxy[i].weight,62500) # RIGU with s1 and atoms proxies = parse_restraints(ins_rigu_s1_atoms) shared_rigu_proxy \ = proxies['rigu'] assert shared_rigu_proxy.size() == 3 for i in range(3): assert shared_rigu_proxy[i].i_seqs == expected_i_seqs[i] assert approx_equal(shared_rigu_proxy[i].weight,2500) # RIGU with s1, s2 and atoms proxies = parse_restraints(ins_rigu_s1_s2_atoms) shared_rigu_proxy \ = proxies['rigu'] assert shared_rigu_proxy.size() == 3 for i in range(3): assert shared_rigu_proxy[i].i_seqs == expected_i_seqs[i] assert approx_equal(shared_rigu_proxy[i].weight, expected_weights[i]) # ISOR simple proxies = parse_restraints(ins_isor_simple) shared_isotropic_adp_proxy \ = proxies['isotropic_adp'] assert shared_isotropic_adp_proxy.size() == 4 expected_i_seqs = (0,1,2,3) expected_weights = (25,100,100,25) for i in range(4): assert shared_isotropic_adp_proxy[i].i_seqs[0] == expected_i_seqs[i] assert approx_equal(shared_isotropic_adp_proxy[i].weight, expected_weights[i]) # ISOR with s proxies = parse_restraints(ins_isor_s) shared_isotropic_adp_proxy \ = proxies['isotropic_adp'] assert shared_isotropic_adp_proxy.size() == 4 expected_weights = (6.25,25,25,6.25) for i in range(4): assert shared_isotropic_adp_proxy[i].i_seqs[0] == expected_i_seqs[i] assert approx_equal(shared_isotropic_adp_proxy[i].weight, expected_weights[i]) # ISOR with s and st proxies = parse_restraints(ins_isor_s_st) shared_isotropic_adp_proxy \ = proxies['isotropic_adp'] assert shared_isotropic_adp_proxy.size() == 4 expected_weights = (1/(0.3*0.3), 25, 25, 1/(0.3*0.3)) for i in range(4): assert shared_isotropic_adp_proxy[i].i_seqs[0] == expected_i_seqs[i] assert approx_equal(shared_isotropic_adp_proxy[i].weight, expected_weights[i]) # ISOR with atoms proxies = parse_restraints(ins_isor_atoms) shared_isotropic_adp_proxy \ = proxies['isotropic_adp'] assert shared_isotropic_adp_proxy.size() == 3 expected_i_seqs = (0,1,2) expected_weights = (25,100,100) for i in range(3): assert shared_isotropic_adp_proxy[i].i_seqs[0] == expected_i_seqs[i] assert approx_equal(shared_isotropic_adp_proxy[i].weight, expected_weights[i]) # ISOR with s and atoms proxies = parse_restraints(ins_isor_s_atoms) shared_isotropic_adp_proxy \ = proxies['isotropic_adp'] assert shared_isotropic_adp_proxy.size() == 3 expected_i_seqs = (0,1,2) expected_weights = (6.25,25,25) for i in range(3): assert shared_isotropic_adp_proxy[i].i_seqs[0] == expected_i_seqs[i] assert approx_equal(shared_isotropic_adp_proxy[i].weight, expected_weights[i]) # ISOR with s, st and atoms proxies = parse_restraints(ins_isor_s_st_atoms) shared_isotropic_adp_proxy \ = proxies['isotropic_adp'] assert shared_isotropic_adp_proxy.size() == 3 expected_i_seqs = (0,1,2) expected_weights = (1/(0.3*0.3), 25, 25) for i in range(3): assert shared_isotropic_adp_proxy[i].i_seqs[0] == expected_i_seqs[i] assert approx_equal(shared_isotropic_adp_proxy[i].weight, expected_weights[i]) def exercise_residues(): proxies = parse_restraints(ins_residues) planarity_proxies = proxies['planarity'] assert planarity_proxies.size() == 2 p = planarity_proxies[1] assert approx_equal(p.i_seqs, [3, 1, 4, 2, 5]) assert approx_equal(p.weights, [4]*len(p.weights)) p = planarity_proxies[0] assert approx_equal(p.i_seqs, [15, 16, 17, 18, 12, 13, 14, 11, 10, 9, 8]) assert approx_equal(p.weights, [100]*len(p.weights)) assert p.sym_ops is None bond_proxies = proxies['bond'] assert len(bond_proxies) == 10 p = bond_proxies[0] assert p.distance_ideal == 2.24 assert p.i_seqs == (9, 11) assert approx_equal(p.weight, 100) p = bond_proxies[2] assert p.distance_ideal == 2.425 assert p.i_seqs == (1, 4) assert approx_equal(p.weight, 1479.2899408284025) p = bond_proxies[3] assert p.distance_ideal == 2.250 assert p.i_seqs == (3, 4) assert approx_equal(p.weight, 3460.207612456747) p = bond_proxies[6] assert p.i_seqs == (2, 5) assert approx_equal(p.distance_ideal, 2.435) assert approx_equal(p.weight, 625.0) p = bond_proxies[9] assert p.i_seqs == (2, 4) assert approx_equal(p.distance_ideal, 1.329) assert approx_equal(p.weight, 2500.0) adp_sim_proxies = proxies['adp_similarity'] assert len(adp_sim_proxies) == 19 p = adp_sim_proxies[0] assert p.i_seqs == (0, 1) assert approx_equal(p.weight, 25) rigid_bond = proxies['rigid_bond'] assert rigid_bond.size() == 43 p = rigid_bond[1] assert p.i_seqs == (0, 2) assert approx_equal(p.weight, 10000) isot = proxies['isotropic_adp'] assert isot.size() == 4 p = isot[0] assert p.i_seqs == (19,) assert approx_equal(p.weight, 25) p = isot[-1] assert p.i_seqs == (22,) assert approx_equal(p.weight, 25) def parse_restraints(ins_name): import smtbx.refinement.restraints builder = iotbx.builders.restrained_crystal_structure_builder() stream = shelx.command_stream(file=StringIO(ins_name)) l_cs = shelx.crystal_symmetry_parser(stream, builder) l_afix = shelx.afix_parser(l_cs.filtered_commands(), builder) l_xs = shelx.atom_parser(l_afix.filtered_commands(), builder) l_restraints = shelx.restraint_parser( l_xs.filtered_commands(), builder) l_restraints.parse() builder = l_restraints.builder assert isinstance(builder.restraints_manager, smtbx.refinement.restraints.manager) return builder.proxies() def shelx_u_cif(unit_cell, u_star): u_cif = adptbx.u_star_as_u_cif(unit_cell, u_star) u_cif = u_cif[0:3] + (u_cif[-1], u_cif[-2], u_cif[-3]) return (" "*3).join([ "%.5f" % x for x in u_cif ]) def exercise_constrained_occupancies(): from smtbx.refinement.constraints.occupancy import \ occupancy_pair_affine_constraint builder = iotbx.builders.constrained_crystal_structure_builder() stream = shelx.command_stream(file=StringIO(ins_thpp)) l_cs = shelx.crystal_symmetry_parser(stream, builder) l_xs = shelx.atom_parser(l_cs.filtered_commands(), builder) l_xs.parse() assert len(builder.constraints) == 2 sc = builder.structure.scatterers() dsu = [(sc[c.scatterer_indices[0]].label, c) for c in builder.constraints] dsu.sort() constraints = [c for _,c in dsu] c0, c1 = constraints assert isinstance(c0, occupancy_pair_affine_constraint) assert c0.scatterer_indices == (len(sc) - 4, len(sc) - 2) assert c0.linear_form == ((1,1), 1) assert isinstance(c1, occupancy_pair_affine_constraint) assert c1.scatterer_indices == (3, len(sc) - 1) assert c1.linear_form == ((1,1), 1) def exercise_wavelength(): from iotbx.shelx.parsers import wavelength_parser builder = iotbx.builders.crystal_structure_builder() stream = shelx.command_stream(file=StringIO(ins_aspirin)) stream = wavelength_parser(stream, builder) stream.parse() assert approx_equal(builder.wavelength_in_angstrom, 0.71073) def run(): exercise_lexing() exercise_lexing_bis() exercise_instruction_parsing() import libtbx.load_env if (not libtbx.env.has_module(name="smtbx")): print("Skipping some tests: smtbx module is not available.") else: exercise_restraint_parsing() exercise_constrained_occupancies() exercise_u_iso_proportional_to_u_eq_parsing() exercise_afix_parsing() exercise_residues() exercise_xray_structure_parsing() exercise_crystal_symmetry_parsing() exercise_wavelength() print('OK') ins_mundane_tiny = ( "TITL in Pbca\n" "CELL0.71073 7.350 9.541 12.842 90.000 90.000 90.000\n" "ZERR 4.00 0.002 0.002 0.003 0.000 0.000 0.000\n" "LATT 1\n" "\n" "SYMM 0.5-X, -Y, 0.5+Z\n" "SYMM -X, 0.5+Y, 0.5-Z\n" "SYMM 1/2+X, 0.5-y, -Z\n" "SFAC C H O N\n" "UNIT 32 40 16 8\n" "TEMP -153\n" " skipped\n" "L.S. 4\n" "BOND $H\n" "FMAP 2 ! Fo - Fc\n" "PLAN 5\n" "WGHT 0.054500 0.220600\n" "EXTI 0.034016\n" "FVAR 0.89220\n" "REM\n" "+/path/to/filename.ins\n" "REM Protracted example of residues on command\n" "HFIX_1 23\n" "HFIX_N 43\n" "EQIV $1 1-X, -Y, -Z\n" "CONF C4 N H O2_$1\n" "DFIX_1 1.5 C2 C3\n" "O2 3 0.362893 0.160589 -0.035913 11.00000 0.03926 0.02517 =\n" " 0.02140 -0.00415 -0.00810 0.01009\n" "O3 3 0.696722 0.119176 0.260657 = some garbage\n" " 11.00000 0.02838 0.02133 =\n" " 0.02918 0.00011 -0.01030 -0.00048\n" "C1 1 0.432360 0.196651 0.046472 11.00000 0.02226 0.01792 =\n" " 0.01857 0.00058 0.00123 0.00249\n" "C4 1 0.601261 0.176489 0.196615 11.00000 0.01844 0.01705 =\n" " 0.02123 -0.00033 -0.00071 -0.00284\n" "RESI 1\n" "C2 1 0.411568 0.336421 0.100062 11.00000 0.02867 0.01555 =\n" " 0.02069 0.00053 -0.00070 0.00268\n" "C3 1 0.522448 0.322965 0.200394 11.00000 0.02158 0.01556 =\n" " 0.02255 -0.00189 -0.00049 -0.00115\n" "RESI N\n" "N 4 0.544830 0.114061 0.104838 11.00000 0.02004 0.01586 =\n" " 0.01943 -0.00094 -0.00096 0.00161\n" " \n" "HKLF 4 \n" "END\n" " \n" "WGHT 0.0536 0.2259 \n" "REM Highest difference peak 0.330, deepest hole -0.210, 1-sigma level 0.046\n" "Q1 1 0.5622 0.2496 0.2006 11.00000 0.05 0.33\n" "Q2 1 0.4189 0.2682 0.0749 11.00000 0.05 0.33\n" "Q3 1 0.5706 0.1441 0.1462 11.00000 0.05 0.29\n" "Q4 1 0.4966 0.1552 0.0716 11.00000 0.05 0.29\n" "Q5 1 0.4666 0.3316 0.1506 11.00000 0.05 0.26\n") ins_special_positions = """TITL cr4 in P6(3) CELL 0.71073 5.1534 5.1534 8.6522 90.000 90.000 120.000 ZERR 2.00 0.0007 0.0007 0.0017 0.000 0.000 0.000 LATT -1 SYMM -Y, X-Y, Z SYMM -X+Y, -X, Z SYMM -X, -Y, 0.5+Z SYMM Y, -X+Y, 0.5+Z SYMM X-Y, X, 0.5+Z SFAC LI O S K UNIT 2 8 2 2 K1 4 0.000000 0.000000 -0.001950 10.33333 0.02427 0.02427 = 0.02379 0.00000 0.00000 0.01214 S1 3 0.333333 0.666667 0.204215 10.33330 0.01423 0.01423 = 0.01496 0.00000 0.00000 0.00712 LI1 1 0.333333 0.666667 0.815681 10.33333 0.02132 0.02132 = 0.02256 0.00000 0.00000 0.01066 O1 2 0.333333 0.666667 0.035931 10.33333 0.06532 0.06532 = 0.01669 0.00000 0.00000 0.03266 O2 2 0.343810 0.941658 0.258405 11.00000 0.02639 0.02079 = 0.05284 -0.01180 -0.00053 0.01194 HKLF 4 """ ins_P1 = ( "TITL P1\n" "CELL 0.71073 1 2 3 99 100 101\n" "ZERR 4.00 0.002 0.002 0.003 0.000 0.000 0.000\n" "SFAC C H O N\n") ins_aspirin = """TITL aspirin in P2(1)/c CELL 0.71073 11.492 6.621 11.453 90.0 95.615 90.0 ZERR 4 0.002 0.001 0.002 0.0 0.0 0.0 LATT 1 SYMM -X,0.500+Y,0.500-Z SFAC C H O UNIT 36 28 16 TEMP -60.000 L.S. 20 WGHT 0.068700 0.446300 MERG 2 OMIT -2 56 OMIT 2 3 4 OMIT -1 -3 2 BASF 0.352 REM this twin command is nonsense... TWIN -1 0 0 0 1 0 0 0 -1 2 FVAR 0.91641 O2 3 0.879181 0.140375 0.051044 11.00000 0.05893 0.05202 = 0.05656 0.01670 0.01559 0.01156 AFIX 87 H2 2 0.925036 0.046729 0.065472 11.00000 -1.50000 AFIX 0 O3 3 0.714314 0.411976 0.087940 11.00000 0.04930 0.05061 = 0.03685 -0.00419 0.00783 -0.00427 C2 1 0.846429 0.436128 -0.067477 11.00000 0.03922 0.03869 = 0.03570 -0.00268 0.00014 -0.00150 O1 3 0.989649 0.187859 -0.096470 11.00000 0.06532 0.05656 = 0.05359 0.00743 0.02230 0.01823 C3 1 0.883500 0.550173 -0.159841 11.00000 0.04635 AFIX 43 H3 2 0.945193 0.503717 -0.199359 11.00000 -1.50000 AFIX 0 C7 1 10.910013 0.242812 -0.037585 11.00000 0.04340 0.04037 = 0.03632 -0.00344 0.00282 -0.00157 C1 1 0.754688 0.511841 -0.009478 11.00000 0.04076 C6 1 0.701446 0.694836 -0.041608 11.00000 0.05003 0.04601 = 0.05788 -0.00711 0.00597 0.00688 AFIX 43 H6 2 0.640709 0.743710 -0.001563 11.00000 -1.50000 AFIX 0 O4 3 0.596499 0.219939 -0.034410 11.00000 0.07409 0.08015 = 0.04201 -0.00406 0.00247 -0.02748 C5 1 0.739822 0.803914 -0.134050 11.00000 0.05726 0.04061 = 0.06325 0.00538 0.00340 0.00642 AFIX 43 H5 2 0.704633 0.926467 -0.155929 11.00000 -1.50000 AFIX 0 C8 1 0.634563 0.262008 0.063872 11.00000 0.04357 0.05241 = 0.04294 -0.00177 0.00752 -0.00018 C4 1 0.829521 0.731819 -0.193418 11.00000 0.05444 0.04790 = 0.05321 0.00900 0.00503 -0.00209 AFIX 43 H4 2 0.854077 0.804532 -0.256010 11.00000 -1.50000 AFIX 0 C9 1 0.602602 0.163875 0.172952 11.00000 0.06769 0.07924 = 0.04765 0.01171 0.00887 -0.00967 AFIX 137 H9A 2 0.571182 0.263181 0.222267 11.00000 -1.50000 H9C 2 0.670926 0.103865 0.213827 11.00000 -1.50000 H9B 2 0.545047 0.061174 0.153241 11.00000 -1.50000 HKLF 4 1 0 0 1 1 1 0 1 0 0 REM aspirin in P2(1)/c REM R1 = 0.0455 for 1038 Fo > 4sig(Fo) and 0.0990 for all 1806 data REM 110 parameters refined using 0 restraints END WGHT 0.0534 0.3514 """ ins_disordered = """\ TITL 97srv101 in P-1 CELL 0.71073 6.033 6.830 7.862 107.70 103.17 95.81 ZERR 1.00 0.002 0.001 0.004 0.02 0.01 0.01 LATT 1 SFAC C H S BR UNIT 9 9 4 1 TEMP -123 SIZE 0.25 0.15 0.04 OMIT -3 58 ACTA L.S. 5 DFIX 1.5 C2 C12 C3 C13 BOND FMAP 2 PLAN 10 WGHT 0.035100 0.787700 FVAR 0.70431 0.25054 PART 2 BR2 4 0.210409 0.205854 0.090628 21.00000 0.01590 0.03384 = 0.03235 0.00702 -0.00500 -0.00273 PART 1 BR3 4 0.319774 0.727684 0.184240 21.00000 0.01979 0.03679 = 0.03533 0.01864 0.00196 0.01154 PART 0 S1 3 0.695496 0.257529 0.325940 11.00000 0.01668 0.02391 = 0.02776 0.00712 0.00046 0.00401 S2 3 0.795402 0.715230 0.403850 11.00000 0.01702 0.02605 = 0.03256 0.01155 0.00143 0.00484 C1 1 0.893971 0.494238 0.443049 11.00000 0.01446 0.02402 = 0.02423 0.01012 0.00393 0.00234 C2 1 0.470694 0.372115 0.231574 11.00000 0.01981 0.03196 = 0.01877 0.00819 0.00393 0.00676 C3 1 0.516311 0.578190 0.267351 11.00000 0.01544 0.03197 = 0.02369 0.01001 0.00228 0.00481 PART 1 C12 1 0.241589 0.221595 0.109681 -21.00000 0.03323 AFIX 7 H121 2 0.184843 0.141885 0.180774 -21.00000 -1.50000 H122 2 0.269551 0.125107 -0.000992 -21.00000 -1.50000 H123 2 0.125620 0.301975 0.072102 -21.00000 -1.50000 AFIX 0 PART 2 C13 1 0.349281 0.712664 0.197083 -21.00000 0.03570 AFIX 7 H131 2 0.336393 0.828845 0.303383 -21.00000 -1.50000 H132 2 0.194195 0.626606 0.130621 -21.00000 -1.50000 H133 2 0.407982 0.771230 0.112116 -21.00000 -1.50000 """ ins_disordered_with_part_sof = """\ TITL 02srv053 SADABS in P2(1)/n CELL 0.71073 12.823 13.422 18.550 90.000 103.91 90.000 ZERR 4.00 0.003 0.003 0.004 0.000 0.01 0.000 LATT 1 SYMM 0.5-X, 0.5+Y, 0.5-Z SFAC C H S CL REM ................ skipping stuff I don't test here .............. FVAR 0.31540 0.05337 FVAR 0.03075 0.89064 S1 3 0.366783 0.363927 0.347492 11.00000 0.02050 0.01721 = 0.02652 0.00339 0.00979 -0.00170 S2 3 0.151555 0.283625 0.288656 11.00000 0.02118 0.01442 = 0.01699 -0.00030 0.00306 0.00146 S3 3 0.294777 0.579144 0.332456 11.00000 0.03635 0.01521 = 0.02250 0.00137 0.01462 -0.00354 REM ............. skipping many atoms ......................... CL1 4 -0.126497 0.262053 0.433117 11.00000 0.02755 0.03548 = 0.05670 0.00439 0.01834 0.00260 PART 1 41 CL2 4 0.096994 0.328954 0.480493 31.00000 0.03167 0.04296 = 0.03718 0.00702 0.00390 -0.00524 C28 1 0.008586 0.236935 0.433750 31.00000 0.02306 0.02292 = 0.04054 0.00599 0.01598 0.00352 AFIX 3 H28A 2 0.029496 0.171785 0.457990 21.00000 0.03492 H28B 2 0.015946 0.232245 0.381920 21.00000 0.03736 AFIX 0 PART 2 -41 CL2B 4 0.068342 0.365253 0.494288 -31.00000 0.07647 C28B 1 0.028119 0.260724 0.451358 -31.00000 0.08827 PART 0 HKLF 4 """ ins_missing_sfac = """\ CELL 0 1 2 3 90 90 90 O 4 0.1 0.2 0.3 11 0.04 """ ins_invalid_scatt = """\ CELL 0 1 2 3 90 90 90 SFAC C O O 4 0.1 0.2 0.3. 11 0.04 """ ins_invalid_scatt_1 = """\ CELL 0 1 2 3 90 90 90 SFAC C O O 4 0.1 0.2 0.3 11 """ ins_dfix_across_symm="""\ TITL s031 in C2/c #15 CELL 0.71073 28.3148 15.8506 18.226 90 118.092 90 ZERR 4 0.0006 0.0003 0.0004 0 0.001 0 LATT 7 SYMM -X,+Y,0.5-Z SFAC C H Cl UNIT 282 382 6 FVAR 0.1818 WGHT 0.1 EQIV $1 1-X,+Y,0.5-Z DFIX 1.75 0.02 CL1_$1 C0AA DFIX 1.75 0.03 C0AA CL3_$1 DFIX 1.75 CL2 C0AA CL1 3 0.55003 0.45683 0.24917 10.25000 0.05233 CL2 3 0.54956 0.33497 0.36400 10.25000 0.05483 CL3 3 0.53790 0.33648 0.30419 10.25000 0.08474 C0AA 1 0.50786 0.40217 0.27444 10.25000 0.03965 HKLF 4 """ ins_sadi = """\ CELL 0 1 2 3 90 90 90 SFAC C SADI 0.04 C1 C3 C2 C4 C1 1 0.50000 0.24000 0.25000 11.00000 0.05233 C2 1 0.50000 0.26000 0.25000 11.00000 0.05233 C3 1 0.00000 0.25000 0.25000 11.00000 0.05233 C4 1 0.00000 0.25000 0.25000 11.00000 0.05233 """ ins_sadi_with_sym = """\ CELL 0 1 2 3 90 90 90 SYMM -X,+Y,0.5-Z EQIV $1 1-X,+Y,0.5-Z SFAC C SADI C1_$1 C3 C2 C4_$1 C1 1 0.50000 0.24000 0.25000 11.00000 0.05233 C2 1 0.50000 0.26000 0.25000 11.00000 0.05233 C3 1 0.00000 0.25000 0.25000 11.00000 0.05233 C4 1 0.00000 0.25000 0.25000 11.00000 0.05233 """ ins_flat="""\ TITL fred in P2(1)/c CELL 0.71073 15.149 11.4915 16.2458 90 99.462 90 ZERR 3 0.0054 0.0043 0.006 0 0.007 0 LATT 1 SYMM -X,0.5+Y,0.5-Z SFAC C H UNIT 134 142 FMAP 2.0 WGHT 0.1 FLAT 0.1 C31 C32 C33 C34 C35 C36 C37 FLAT C41 C42 C43 C44 C45 C46 C47 FVAR 0.16431 PART 1 C31 1 0.28967 0.31613 -0.02773 10.75000 0.05888 0.04514 0.10878 = -0.01962 -0.00471 -0.00143 C32 1 0.30768 0.41649 0.03308 10.75000 0.03521 0.04076 0.05711 = 0.01504 0.01485 0.01552 C33 1 0.28897 0.41092 0.11289 10.75000 0.06042 0.09876 0.06719 = 0.05095 0.03457 0.04942 C34 1 0.30734 0.50229 0.16767 10.75000 0.08796 0.14534 0.06011 = 0.03723 0.02945 0.07980 C35 1 0.34782 0.60688 0.14285 10.75000 0.09111 0.10467 0.04177 = -0.01494 0.00086 0.05687 C36 1 0.36857 0.61562 0.06124 10.75000 0.08041 0.06114 0.05218 = 0.00249 0.01982 0.01339 C37 1 0.34923 0.52118 0.01013 10.75000 0.04695 0.03550 0.04216 = -0.00583 0.00719 -0.00031 PART 2 C41 1 0.40898 0.68460 0.08429 10.25000 0.08117 0.05294 0.24136 = -0.04489 0.04281 -0.05242 C42 1 0.35781 0.57012 0.08520 10.25000 0.02162 0.06254 0.03143 = -0.00552 0.00755 -0.01371 C43 1 0.34017 0.49729 0.00895 10.25000 0.04695 0.03550 0.04216 = -0.00583 0.00719 -0.00031 C44 1 0.30214 0.37738 0.00610 10.25000 0.04686 0.18231 0.09967 = 0.09419 0.03785 0.07323 C45 1 0.27044 0.34405 0.07795 10.25000 0.03487 0.04084 0.25569 = -0.01301 -0.02616 0.01005 C46 1 0.28348 0.40879 0.14914 10.25000 0.02746 0.08814 0.07379 = 0.00346 -0.00267 0.02126 C47 1 0.32637 0.52368 0.16222 10.25000 0.03065 0.05189 0.02130 = -0.00058 0.00299 -0.00724 HKLF 4 """ def template_ins(instruction): return """\ CELL 0 5 10 15 90 90 90 SFAC C %s C1 1 0.28967 0.31613 -0.02773 10.75000 0.05888 0.04514 0.10878 = -0.01962 -0.00471 -0.00143 C2 1 0.30768 0.41649 0.03308 10.75000 0.03521 0.04076 0.05711 = 0.01504 0.01485 0.01552 C3 1 0.28897 0.41092 0.11289 10.75000 0.06042 0.09876 0.06719 = 0.05095 0.03457 0.04942 C4 1 0.30734 0.50229 0.16767 10.75000 0.08796 0.14534 0.06011 = 0.03723 0.02945 0.07980 """ %instruction ins_simu_simple = template_ins("SIMU") ins_simu_s = template_ins("SIMU 0.03") ins_simu_s_st = template_ins("SIMU 0.03 0.07") ins_simu_s_st_dmax = template_ins("SIMU 0.03 0.07 1.8") ins_simu_atoms = template_ins("SIMU C1 C2 C3") ins_simu_s_atoms = template_ins("SIMU 0.03 C1 C2 C3") ins_simu_s_st_atoms = template_ins( "SIMU 0.03 0.07 C1 C2 C3") ins_simu_s_st_dmax_atoms = template_ins( "SIMU 0.03 0.07 1.7 C1 C2 C3") ins_delu_simple = template_ins("DELU") ins_delu_s1 = template_ins("DELU 0.02") ins_delu_s1_s2 = template_ins("DELU 0.01 0.02") ins_delu_atoms = template_ins("DELU C1 C2 C3") ins_delu_s1_atoms = template_ins("DELU 0.02 C1 C2 C3") ins_delu_s1_s2_atoms = template_ins( "DELU 0.01 0.02 C1 C2 C3") ins_rigu_simple = template_ins("RIGU") ins_rigu_s1 = template_ins("RIGU 0.02") ins_rigu_s1_s2 = template_ins("RIGU 0.01 0.02") ins_rigu_atoms = template_ins("RIGU C1 C2 C3") ins_rigu_s1_atoms = template_ins("RIGU 0.02 C1 C2 C3") ins_rigu_s1_s2_atoms = template_ins( "RIGU 0.01 0.02 C1 C2 C3") ins_isor_simple = template_ins("ISOR") ins_isor_s = template_ins("ISOR 0.2") ins_isor_s_st = template_ins("ISOR 0.2 0.3") ins_isor_atoms = template_ins("ISOR C1 C2 C3") ins_isor_s_atoms = template_ins("ISOR 0.2 C1 C2 C3") ins_isor_s_st_atoms = template_ins( "ISOR 0.2 0.3 C1 C2 C3") ins_dfix_multiple = template_ins("DFIX 1.7 C1 C2 C3 C4") ins_invalid_dfix = template_ins("DFIX C1 C2") ins_invalid_dfix_2 = template_ins("DFIX 1.7 C1 C2 C3") ins_invalid_flat = template_ins("FLAT C1 C2 C3") ins_equal_sign_in_rem = """\ REM Solution 1 R1 0.100, Alpha = 0.0015 in P2(1) REM C13 O10 TITL SUCROSE IN P2(1) """ ins_with_atom_peak_heights = """\ TITL SUCROSE IN P2(1) CELL 0.71073 7.7830 8.7364 10.9002 90.000 102.984 90.000 ZERR 2 0.001 0.0012 0.0015 0 0.009 0 LATT -1 SYMM -X, 1/2+Y, -Z SFAC C H O UNIT 24 44 22 L.S. 10 BOND LIST 6 FMAP 2 PLAN 20 ANIS DELU O001 3 0.60914 0.62292 0.82801 11.00000 0.01991 18.33 O002 3 0.63134 0.57137 0.62239 11.00000 0.02191 8.21 O003 3 0.68506 0.87525 0.78808 11.00000 0.02117 8.01 O004 3 0.25196 0.53353 0.76983 11.00000 0.02850 7.89 O005 3 0.37848 0.73377 0.96996 11.00000 0.02967 7.87 O006 3 0.79443 0.65096 1.07392 11.00000 0.02911 7.82 O007 3 1.08974 0.87253 1.02226 11.00000 0.02929 7.77 O008 3 0.96030 0.73231 0.67382 11.00000 0.03335 7.69 O009 3 0.29687 0.22403 0.69006 11.00000 0.03867 7.41 O00A 3 0.71468 0.42497 0.41792 11.00000 0.03487 7.28 C00B 1 0.64414 0.15501 0.65110 11.00000 0.02137 6.85 C00C 1 0.51386 0.61153 0.69938 11.00000 0.01950 6.36 C00D 1 0.78440 0.77821 0.99237 11.00000 0.02002 6.06 C00E 1 0.36586 0.49695 0.68863 11.00000 0.01963 6.03 C00F 1 0.94543 0.80269 0.93471 11.00000 0.02056 5.97 C00G 1 0.63136 0.77807 0.87607 11.00000 0.02041 5.94 C00H 1 0.55937 0.29776 0.62561 11.00000 0.02281 5.87 C00I 1 0.45580 0.83872 0.89621 11.00000 0.02767 5.77 C00J 1 0.87184 0.90817 0.82300 11.00000 0.02382 5.76 C00K 1 0.43548 0.33306 0.71436 11.00000 0.02549 5.76 C00L 1 0.81534 0.39973 0.54440 11.00000 0.02952 5.73 C00M 1 0.70459 0.41948 0.64084 11.00000 0.02597 5.72 C00N 1 0.95213 0.88631 0.71108 11.00000 0.02971 5.35 HKLF 4 END """ ins_with_q_peaks = """\ TITL 01mrh009 in P2(1)/c CELL 0.71073 8.7925 8.2663 8.5561 90.000 111.141 90.000 ZERR 2.00 0.0018 0.0017 0.0017 0.000 0.030 0.000 LATT 1 SYMM -X, 0.5+Y, 0.5-Z SFAC C H N O P V UNIT 8 24 4 20 4 4 L.S. 30 ACTA BOND FMAP 2 PLAN 5 HTAB WGHT 0.032500 0.937600 FVAR 0.671230 MOLE 1 V1 6 0.657682 1.034967 0.322750 11.000000 0.005490 0.006760 = 0.007550 -0.000030 0.002830 -0.000560 P1 5 0.557872 0.733904 0.520843 11.000000 0.006330 0.006410 = 0.006990 0.000100 0.002880 -0.000130 O2 4 0.645870 0.883988 0.489582 11.000000 0.010550 0.008480 = 0.009460 0.000070 0.004270 -0.002350 Q1 1 0.615600 0.695100 0.623900 11.000000 0.050000 0.64 Q2 1 0.526800 0.678600 0.431500 11.000000 0.050000 0.63 Q3 1 0.620800 1.025100 0.211700 11.000000 0.050000 0.46 HKLF 4 END """ ins_residues = """\ TITL 3odl CELL 1.00000 59.140 59.140 186.740 90.00 90.00 120.00 ! lambda & Cell ZERR 6 0.059 0.059 0.187 0.00 0.00 0.00 !Z & cell esds LATT -1 !P, non centrosymmetric SYMM -Y, X-Y, 2/3+Z SYMM -X+Y, -X, 1/3+Z SYMM Y, X, -Z SYMM X-Y, -Y, 1/3-Z SYMM -X, -X+Y, 2/3-Z SFAC C H N O S P NA !scattering factor types and UNIT 9264.63 13529.27 2472 6437.14 76.02 12 6 !unit cell contents DELU $C_* $N_* $O_* $S_* $P_* ! Rigid bond restraints -ignored for iso SIMU 0.1 $C_* $N_* $O_* $S_* $P_* ! Similar U restraints - iso or anis. ISOR 0.1 O_1001 > LAST ! Approximate iso restraints for waters; FLAT_FAD AN1 AC2 AN3 AC4 AC5 AC6 AN6 AN7 AC8 AN9 AC1* DFIX_FAD 1.362 AN1 AC6 DFIX_FAD 1.368 AN1 AC2 DANG_FAD 2.240 0.10 AN9 AN7 DANG_FAD 2.196 0.10 AN9 AC5 DANG_8 2.425 0.026 CA N_+ DANG_9 2.250 0.017 O_- N DFIX_* 1.329 C_- N DANG_* 2.425 CA_- N DANG_* 2.250 O_- N DANG_* 2.435 C_- CA FLAT_8 0.5 O CA N_+ C CA_+ RESI 8 SER N 3 -0.575274 0.141191 0.113592 11.00000 0.33808 0.75677 = 1.11905 -0.27101 0.19945 -0.04973 CA 1 -0.551908 0.139429 0.115198 11.00000 0.48936 0.25522 = 0.84266 -0.05734 0.13568 -0.12284 C 1 -0.525230 0.163359 0.114621 11.00000 0.36302 0.24661 = 0.62351 0.04491 0.09919 -0.02604 O 4 -0.505790 0.161790 0.116768 11.00000 0.52134 0.27541 = 0.56288 0.00938 0.07008 0.11741 RESI 9 LYS N 3 -0.520798 0.186053 0.111792 11.00000 0.25817 0.26426 = 0.24642 -0.03698 0.01196 -0.03745 CA 1 -0.494101 0.207878 0.111725 11.00000 0.16273 0.21215 = 0.21593 -0.04270 0.01910 0.02736 C 1 -0.487071 0.220051 0.119169 11.00000 0.13133 0.19993 = 0.20434 -0.03059 0.03663 0.03709 O 4 -0.503787 0.219454 0.123261 11.00000 0.14634 0.36185 = 0.24067 -0.07422 0.04195 0.06255 RESI 415 FAD AC1* 1 0.301769 0.460821 0.091581 11.00000 0.17934 0.39185 = 0.16499 -0.02542 -0.00370 0.18623 AN9 3 0.329069 0.474690 0.094290 11.00000 0.16649 0.37106 = 0.19437 0.02459 0.01637 0.16403 AC8 1 0.338965 0.493725 0.099532 11.00000 0.19389 0.42740 = 0.20073 -0.01332 -0.03583 0.17001 AN7 3 0.363614 0.500512 0.100736 11.00000 0.18827 0.48315 = 0.29375 0.00036 -0.03961 0.17524 AC5 1 0.369875 0.488232 0.095578 11.00000 0.20021 0.53248 = 0.30473 0.04033 -0.01535 0.22652 AC6 1 0.394249 0.488600 0.094022 11.00000 0.20036 0.55609 = 0.36639 0.15609 0.05588 0.23824 AN6 3 0.416744 0.505330 0.096997 11.00000 0.20718 0.56035 = 0.55246 0.16445 0.00471 0.22417 AN1 3 0.392969 0.470604 0.089321 11.00000 0.25898 0.60811 = 0.36195 0.17095 0.09827 0.30193 AC2 1 0.370280 0.453766 0.086063 11.00000 0.28075 0.52743 = 0.37940 0.12160 0.10576 0.31394 AN3 3 0.347491 0.452243 0.087106 11.00000 0.24288 0.43252 = 0.31698 0.06838 0.08486 0.24807 AC4 1 0.348480 0.469070 0.091969 11.00000 0.20789 0.48822 = 0.24296 0.02751 0.01321 0.23800 RESI 1001 HOH O 4 -0.446670 0.031582 0.038635 11.00000 0.16482 0.14614 = 0.17802 -0.00150 -0.02394 0.01386 RESI 1002 HOH O 4 -0.368462 0.037104 0.034398 11.00000 0.17923 0.12876 = 0.18971 -0.03786 -0.01430 0.04562 RESI 1003 HOH O 4 -0.422007 0.007732 0.032882 11.00000 0.19693 0.17138 = 0.21503 -0.04115 0.01271 0.01223 RESI 1004 HOH O 4 -0.350514 0.045091 0.020274 11.00000 0.17129 0.15651 = 0.19856 -0.03983 0.01063 0.03671 """ # This is one of the test structures shipped with Olex 2 # This version has the correct modeling of the disorder C7a/C7b # plus a spurious split N3/C3 with occupancies adding up to 1. ins_thpp = """\ TITL CELL 0.71073 6.9196 14.5749 9.7248 90 90.637 90 ZERR 4 0.0001 0.0002 0.0001 0 0.001 0 LATT 1 SYMM 0.5-X,0.5+Y,0.5-Z SFAC C H F N UNIT 40 40 8 16 EXYZ N3 C3 L.S. 4 PLAN 20 more -3 fmap 2 REM thpp.hkl WGHT 0.1 FVAR 0.35838 0.87977 0.5 F1 3 0.16726 0.42638 -0.23772 11.00000 0.03596 0.02944 0.01904 = -0.00761 -0.00298 -0.00009 F2 3 0.13095 0.31497 -0.01246 11.00000 0.04052 0.01691 0.03281 = -0.00250 -0.00502 -0.00279 N8 4 0.36220 0.66937 0.07644 11.00000 0.02801 0.01729 0.01820 = -0.00038 0.00220 -0.00146 N3 4 0.22193 0.43032 0.12983 31.00000 0.02131 C9 1 0.30101 0.58265 0.04215 11.00000 0.01747 0.01804 0.01766 = -0.00073 0.00094 0.00221 C4 1 0.27507 0.51672 0.15265 11.00000 0.02018 0.01935 0.01696 = 0.00027 0.00016 0.00159 N5 4 0.30293 0.54252 0.28533 11.00000 0.03661 0.02191 0.01588 = 0.00077 -0.00090 -0.00391 C2 1 0.18838 0.40270 0.00228 11.00000 0.02311 0.01671 0.02386 = -0.00235 -0.00203 0.00103 C10 1 0.26210 0.54987 -0.09061 11.00000 0.01942 0.02080 0.01702 = -0.00001 0.00153 0.00268 C1 1 0.20604 0.45735 -0.10937 11.00000 0.02242 0.02167 0.01778 = -0.00389 -0.00127 0.00281 C11 1 0.26071 0.60304 -0.21444 11.00000 0.03058 0.02565 0.01889 = -0.00137 0.00044 0.00016 C13 1 0.26803 0.47611 0.39401 11.00000 0.03989 0.02833 0.01867 = 0.00388 -0.00072 -0.00350 C6 1 0.36454 0.63430 0.32066 11.00000 0.04896 0.02569 0.02000 = -0.00456 -0.00017 -0.00449 N12 4 0.25129 0.63888 -0.31966 11.00000 0.05489 0.03497 0.02311 = 0.00384 -0.00181 -0.00450 PART 1 C7a 1 0.30537 0.70214 0.21212 21.00000 0.03415 0.02081 0.02014 = -0.00399 0.00271 0.00061 PART 0 C14 1 0.39584 0.73936 -0.02671 11.00000 0.03778 0.02073 0.02508 = 0.00407 0.00124 -0.00460 PART 2 C7b 1 0.40368 0.69420 0.21920 -21.00000 0.02814 0.02120 0.02427 = -0.00252 -0.00560 0.00546 PART 0 C3 1 0.22193 0.43032 0.12983 -31.00000 0.02131 HKLF 4 END """ if __name__ == '__main__': run()