from __future__ import division 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 import cStringIO def exercise_lexing(): stream = shelx.command_stream(file=cStringIO.StringIO(ins_mundane_tiny)) i = iter(stream) try: cmd, line = i.next() assert cmd == ('TITL', ('in Pbca',)) cmd, line = i.next() assert cmd == ('CELL', (0.71073, 7.35, 9.541, 12.842, 90, 90, 90)) cmd, line = i.next() assert cmd == ('ZERR', (4, 0.002, 0.002, 0.003, 0, 0, 0)) cmd, line = i.next() assert cmd == ('LATT', (1,)) cmd, line = i.next() assert cmd == ('SYMM', ('0.5-X, -Y, 0.5+Z',)) cmd, line = i.next() assert cmd == ('SYMM', ('-X, 0.5+Y, 0.5-Z',)) cmd, line = i.next() assert cmd == ('SYMM', ('1/2+X, 0.5-Y, -Z',)) cmd, line = i.next() assert cmd == ('SFAC', ('C', 'H', 'O', 'N',)) cmd, line = i.next() assert cmd == ('UNIT', (32, 40, 16, 8)) cmd, line = i.next() assert cmd == ('TEMP', (-153,)) cmd, line = i.next() assert cmd == ('L.S.', (4,)) cmd, line = i.next() assert cmd == ('BOND', (tokens.element_token(element='H'),)) cmd, line = i.next() # FMAP cmd, line = i.next() # PLAN cmd, line = i.next() # WGHT cmd, line = i.next() # EXTI cmd, line = i.next() # FVAR cmd, line = i.next() assert cmd == ('REM', ()) cmd, line = i.next() assert cmd == ('+', '/path/to/filename.ins') cmd, line = i.next() assert cmd == ('REM', ('Protracted example of residues on command',)) cmd, line = i.next() assert cmd == ('HFIX', (tokens.residue_number_tok, 1), (23,)) cmd, line = i.next() assert cmd == ('HFIX', (tokens.residue_class_tok, 'N'), (43,)) cmd, line = i.next() assert cmd == ('EQIV', (1, '1-X, -Y, -Z')) cmd, line = i.next() 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 = i.next() assert cmd == ('DFIX', (tokens.residue_number_tok, 1), (1.5, tokens.atomname_token(name='C2'), tokens.atomname_token(name='C3'))) cmd, line = i.next() 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 = i.next() 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 = i.next() # C1 cmd, line = i.next() # C4 cmd, line = i.next() assert cmd == ('RESI', (1,)) cmd, line = i.next() # C2 cmd, line = i.next() # C3 cmd, line = i.next() assert cmd == ('RESI', ('N',)) cmd, line = i.next() # N cmd, line = i.next() # HKLF try: cmd, line = i.next() raise AssertionError except StopIteration: pass except StopIteration: raise AssertionError def exercise_lexing_bis(): stream = shelx.command_stream(file=cStringIO.StringIO(ins_equal_sign_in_rem)) i = iter(stream) try: cmd, line = i.next() assert cmd == ('REM', ('Solution 1 R1 0.100, Alpha = 0.0015 in P2(1)',)) cmd, line = i.next() assert cmd == ('REM', ('C13 O10',)) cmd, line = i.next() assert cmd == ('TITL', ('SUCROSE IN P2(1)',)) except StopIteration: raise AssertionError def exercise_crystal_symmetry_parsing(): stream = shelx.command_stream(file=cStringIO.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=cStringIO.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=cStringIO.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=cStringIO.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=cStringIO.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 = cStringIO.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 = cStringIO.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=cStringIO.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=cStringIO.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=cStringIO.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=cStringIO.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=cStringIO.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=cStringIO.StringIO(ins_invalid_scatt), set_grad_flags=set_grad_flags) raise Exception_expected except RuntimeError, e: assert str(e) == "ShelX: illegal argument '0.3.' at line 3" try: structure = xray.structure.from_shelx( file=cStringIO.StringIO(ins_invalid_scatt_1), set_grad_flags=set_grad_flags) raise Exception_expected except RuntimeError, e: assert str(e) == ("ShelX: wrong number of parameters " "for scatterer at line 3") try: structure = xray.structure.from_shelx( file=cStringIO.StringIO(ins_missing_sfac), set_grad_flags=set_grad_flags) raise Exception_expected except RuntimeError, e: assert e.args[0].startswith('ShelX:') structure = xray.structure.from_shelx( file=cStringIO.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=cStringIO.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=cStringIO.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=cStringIO.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, e: assert str(e) == "ShelX: Invalid DFIX instruction at line 3" try: proxies = parse_restraints(ins_invalid_dfix_2) except RuntimeError, 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, 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]) # 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=cStringIO.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=cStringIO.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 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() 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_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()