def quartz(): return xray.structure( crystal_symmetry=crystal.symmetry( (5.01,5.01,5.47,90,90,120), "P6222"), scatterers=flex.xray_scatterer([ xray.scatterer("Si", (1/2.,1/2.,1/3.)), xray.scatterer("O", (0.197,-0.197,0.83333))]))
def __init__(self, with_special_position_pivot): self.with_special_position_pivot = with_special_position_pivot self.uc = uctbx.unit_cell((1, 2, 3)) self.sg = sgtbx.space_group("P 6") self.c0 = xray.scatterer("C0", site=(1e-5, 0., 0.1)) self.site_symm = sgtbx.site_symmetry(self.uc, self.sg, self.c0.site) self.c0.flags.set_grad_site(True) self.c1 = xray.scatterer("C1", site=(0.09, 0.11, 0.)) self.c1.flags.set_grad_site(True) self.h = xray.scatterer("H") self.reparam = constraints.ext.reparametrisation(self.uc) if with_special_position_pivot: x0 = self.reparam.add(constraints.special_position_site_parameter, self.site_symm, self.c0) else: x0 = self.reparam.add(constraints.independent_site_parameter, self.c0) x1 = self.reparam.add(constraints.independent_site_parameter, self.c1) l = self.reparam.add(constraints.independent_scalar_parameter, self.bond_length, variable=False) x_h = self.reparam.add(constraints.terminal_linear_ch_site, pivot=x0, pivot_neighbour=x1, length=l, hydrogen=self.h) self.reparam.finalise() self.x0, self.x1, self.x_h, self.l = [ x.index for x in (x0, x1, x_h, l) ] if self.with_special_position_pivot: self.y0 = x0.independent_params.index
def test_spacegroup_tidy_pickling(): quartz_structure = xray.structure( crystal_symmetry=crystal.symmetry( unit_cell=(5.01,5.01,5.47,90,90,120), space_group_symbol="P6222"), scatterers=flex.xray_scatterer( [ xray.scatterer(label="Si", site=(1/2.,1/2.,1/3.), u=0.2), xray.scatterer(label="O", site=(0.197,-0.197,0.83333), u=0) ]) ) asu_mappings = quartz_structure.asu_mappings(buffer_thickness=2) pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings) pair_asu_table.add_all_pairs(distance_cutoff=1.7) pair_sym_table = pair_asu_table.extract_pair_sym_table() new_asu_mappings = quartz_structure.asu_mappings(buffer_thickness=5) new_pair_asu_table = crystal.pair_asu_table(asu_mappings=new_asu_mappings) new_pair_asu_table.add_pair_sym_table(sym_table=pair_sym_table) spg = new_pair_asu_table.asu_mappings().space_group() pspg = pickle.loads(pickle.dumps(spg)) mstr = "" pmstr = "" for rt in spg.all_ops(): mstr += rt.r().as_xyz() + "\n" for rt in pspg.all_ops(): pmstr += rt.r().as_xyz() + "\n" assert mstr == pmstr
def exercise_is_simple_interaction(): for space_group_symbol in ["P1", "P41"]: for shifts in flex.nested_loop((-2,-2,-2),(2,2,2),False): shifts = matrix.col(shifts) structure = xray.structure( crystal_symmetry=crystal.symmetry( unit_cell=(10,10,20,90,90,90), space_group_symbol=space_group_symbol), scatterers=flex.xray_scatterer([ xray.scatterer(label="O", site=shifts+matrix.col((0,0,0))), xray.scatterer(label="N", site=shifts+matrix.col((0.5,0.5,0))), xray.scatterer(label="C", site=shifts+matrix.col((0.25,0.25,0)))])) asu_mappings = structure.asu_mappings(buffer_thickness=7) pair_generator = crystal.neighbors_simple_pair_generator( asu_mappings=asu_mappings, distance_cutoff=7) simple_interactions = {} for i_pair,pair in enumerate(pair_generator): if (asu_mappings.is_simple_interaction(pair)): assert asu_mappings_is_simple_interaction_emulation( asu_mappings, pair) key = (pair.i_seq,pair.j_seq) assert simple_interactions.get(key, None) is None simple_interactions[key] = 1 else: assert not asu_mappings_is_simple_interaction_emulation( asu_mappings, pair) assert len(simple_interactions) == 2 assert simple_interactions[(0,2)] == 1 assert simple_interactions[(1,2)] == 1
def __init__(self, n_runs, **kwds): libtbx.adopt_optional_init_args(self, kwds) self.n_runs = n_runs self.crystal_symmetry = crystal.symmetry( unit_cell=uctbx.unit_cell((5.1534, 5.1534, 8.6522, 90, 90, 120)), space_group_symbol='Hall: P 6c') self.structure = xray.structure( self.crystal_symmetry.special_position_settings(), flex.xray_scatterer(( xray.scatterer('K1', site=(0, 0, -0.00195), u=self.u_cif_as_u_star((0.02427, 0.02427, 0.02379, 0.01214, 0.00000, 0.00000))), xray.scatterer('S1', site=(1/3, 2/3, 0.204215), u=self.u_cif_as_u_star((0.01423, 0.01423, 0.01496, 0.00712, 0.00000, 0.00000 ))), xray.scatterer('Li1', site=(1/3, 2/3, 0.815681), u=self.u_cif_as_u_star((0.02132, 0.02132, 0.02256, 0.01066, 0.00000, 0.00000 ))), xray.scatterer('O1', site=(1/3, 2/3, 0.035931), u=self.u_cif_as_u_star((0.06532, 0.06532, 0.01669, 0.03266, 0.00000, 0.00000 ))), xray.scatterer('O2', site=(0.343810, 0.941658, 0.258405), u=self.u_cif_as_u_star((0.02639, 0.02079, 0.05284, 0.01194, -0.00053,-0.01180 ))) ))) mi = self.crystal_symmetry.build_miller_set(anomalous_flag=False, d_min=0.5) fo_sq = mi.structure_factors_from_scatterers( self.structure, algorithm="direct").f_calc().norm() self.fo_sq = fo_sq.customized_copy(sigmas=flex.double(fo_sq.size(), 1))
def demo(): """ Result of ICSD query: N * -Cr2O3-[R3-CH] Baster, M.;Bouree, F.;Kowalska, A.;Latacz, Z(2000) C 4.961950 4.961950 13.597400 90.000000 90.000000 120.000000 S GRUP R -3 C A Cr1 0.000000 0.000000 0.347570 0.000000 A O1 0.305830 0.000000 0.250000 """ crystal_symmetry = crystal.symmetry( unit_cell="4.961950 4.961950 13.597400 90.000000 90.000000 120.000000", space_group_symbol="R -3 C") scatterers = flex.xray_scatterer() scatterers.append(xray.scatterer( label="Cr1", site=(0.000000,0.000000,0.347570))) scatterers.append(xray.scatterer( label="O1", site=(0.305830,0.000000,0.250000))) icsd_structure = xray.structure( crystal_symmetry=crystal_symmetry, scatterers=scatterers) icsd_structure.show_summary().show_scatterers() print icsd_structure.show_distances(distance_cutoff=2.5) print primitive_structure = icsd_structure.primitive_setting() primitive_structure.show_summary().show_scatterers() print p1_structure = primitive_structure.expand_to_p1() p1_structure.show_summary().show_scatterers() print print "OK"
def exercise_unmerged () : quartz_structure = xray.structure( special_position_settings=crystal.special_position_settings( crystal_symmetry=crystal.symmetry( unit_cell=(5.01,5.01,5.47,90,90,120), space_group_symbol="P6222")), scatterers=flex.xray_scatterer([ xray.scatterer( label="Si", site=(1/2.,1/2.,1/3.), u=0.2), xray.scatterer( label="O", site=(0.197,-0.197,0.83333), u=0.1)])) quartz_structure.set_inelastic_form_factors( photon=1.54, table="sasaki") fc = abs(quartz_structure.structure_factors(d_min=1.0).f_calc()) symm = fc.crystal_symmetry() icalc = fc.expand_to_p1().f_as_f_sq().set_observation_type_xray_intensity() # generate 'unmerged' data i_obs = icalc.customized_copy(crystal_symmetry=symm) # now make up sigmas and some (hopefully realistic) error flex.set_random_seed(12345) n_refl = i_obs.size() sigmas = flex.random_double(n_refl) * flex.mean(fc.data()) sigmas = icalc.customized_copy(data=sigmas).apply_debye_waller_factors( u_iso=0.15) err = (flex.double(n_refl, 0.5) - flex.random_double(n_refl)) * 2 i_obs = i_obs.customized_copy( sigmas=sigmas.data(), data=i_obs.data() + err) # check for unmerged acentrics assert i_obs.is_unmerged_intensity_array() i_obs_centric = i_obs.select(i_obs.centric_flags().data()) i_obs_acentric = i_obs.select(~(i_obs.centric_flags().data())) i_mrg_acentric = i_obs_acentric.merge_equivalents().array() i_mixed = i_mrg_acentric.concatenate(i_obs_centric) assert not i_mixed.is_unmerged_intensity_array() # XXX These results of these functions are heavily dependent on the # behavior of the random number generator, which is not consistent across # platforms - therefore we can only check for very approximate values. # Exact numerical results are tested with real data (stored elsewhere). # CC1/2, etc. assert approx_equal(i_obs.cc_one_half(), 0.9998, eps=0.001) assert i_obs.resolution_filter(d_max=1.2).cc_one_half() > 0 assert i_obs.cc_anom() > 0.1 r_ano = i_obs.r_anom() assert approx_equal(r_ano, 0.080756, eps=0.0001) # merging stats i_mrg = i_obs.merge_equivalents() assert i_mrg.r_merge() < 0.1 assert i_mrg.r_meas() < 0.1 assert i_mrg.r_pim() < 0.05
def demo(): """ Result of ICSD query: N * -Cr2O3-[R3-CH] Baster, M.;Bouree, F.;Kowalska, A.;Latacz, Z(2000) C 4.961950 4.961950 13.597400 90.000000 90.000000 120.000000 S GRUP R -3 C A Cr1 0.000000 0.000000 0.347570 0.000000 A O1 0.305830 0.000000 0.250000 """ crystal_symmetry = crystal.symmetry( unit_cell="4.961950 4.961950 13.597400 90.000000 90.000000 120.000000", space_group_symbol="R -3 C") scatterers = flex.xray_scatterer() scatterers.append(xray.scatterer( label="Cr1", site=(0.000000,0.000000,0.347570))) scatterers.append(xray.scatterer( label="O1", site=(0.305830,0.000000,0.250000))) icsd_structure = xray.structure( crystal_symmetry=crystal_symmetry, scatterers=scatterers) icsd_structure.show_summary().show_scatterers() print icsd_pairs = icsd_structure.show_distances( distance_cutoff=2.5, keep_pair_asu_table=True) print primitive_structure = icsd_structure.primitive_setting() primitive_structure.show_summary().show_scatterers() print p1_structure = primitive_structure.expand_to_p1() p1_structure.show_summary().show_scatterers() print p1_pairs = p1_structure.show_distances( distance_cutoff=2.5, keep_pair_asu_table=True) print for label,structure,pairs in [("ICSD", icsd_structure,icsd_pairs), ("P1", p1_structure,p1_pairs)]: print "Coordination sequences for", label, "structure" term_table = crystal.coordination_sequences.simple( pair_asu_table=pairs.pair_asu_table, max_shell=10) crystal.coordination_sequences.show_terms( structure=structure, term_table=term_table) print icsd_f_calc = icsd_structure.structure_factors( d_min=1, algorithm="direct").f_calc() icsd_f_calc_in_p1 = icsd_f_calc.primitive_setting().expand_to_p1() p1_f_calc = icsd_f_calc_in_p1.structure_factors_from_scatterers( xray_structure=p1_structure, algorithm="direct").f_calc() for h,i,p in zip(icsd_f_calc_in_p1.indices(), icsd_f_calc_in_p1.data(), p1_f_calc.data()): print h, abs(i), abs(p)*3 print "OK"
def exercise_covariance(): xs = xray.structure( crystal_symmetry=crystal.symmetry( (5.01,5.01,5.47,90,90,120), "P6222"), scatterers=flex.xray_scatterer([ xray.scatterer("Si", (1/2.,1/2.,1/3.)), xray.scatterer("O", (0.197,-0.197,0.83333))])) uc = xs.unit_cell() flags = xs.scatterer_flags() for f in flags: f.set_grad_site(True) xs.set_scatterer_flags(flags) cov = flex.double((1e-8,1e-9,2e-9,3e-9,4e-9,5e-9, 2e-8,1e-9,2e-9,3e-9,4e-9, 3e-8,1e-9,2e-9,3e-9, 2e-8,1e-9,2e-9, 3e-8,1e-9, 4e-8)) param_map = xs.parameter_map() assert approx_equal(cov, covariance.extract_covariance_matrix_for_sites(flex.size_t([0,1]), cov, param_map)) cov_cart = covariance.orthogonalize_covariance_matrix(cov, uc, param_map) O = matrix.sqr(uc.orthogonalization_matrix()) for i in range(param_map.n_scatterers): cov_i = covariance.extract_covariance_matrix_for_sites(flex.size_t([i]), cov, param_map) cov_i_cart = covariance.extract_covariance_matrix_for_sites(flex.size_t([i]), cov_cart, param_map) assert approx_equal( O * matrix.sym(sym_mat3=cov_i) * O.transpose(), matrix.sym(sym_mat3=cov_i_cart).as_mat3()) for f in flags: f.set_grads(False) flags[0].set_grad_u_aniso(True) flags[0].set_use_u_aniso(True) flags[1].set_grad_u_iso(True) flags[1].set_use_u_iso(True) xs.set_scatterer_flags(flags) param_map = xs.parameter_map() cov = flex.double(7*7, 0) cov.reshape(flex.grid(7,7)) cov.matrix_diagonal_set_in_place(flex.double([i for i in range(7)])) cov = cov.matrix_symmetric_as_packed_u() assert approx_equal([i for i in range(6)], covariance.extract_covariance_matrix_for_u_aniso( 0, cov, param_map).matrix_packed_u_diagonal()) assert covariance.variance_for_u_iso(1, cov, param_map) == 6 try: covariance.variance_for_u_iso(0, cov, param_map) except RuntimeError: pass else: raise Exception_expected try: covariance.extract_covariance_matrix_for_u_aniso(1, cov, param_map) except RuntimeError: pass else: raise Exception_expected approx_equal(covariance.extract_covariance_matrix_for_sites( flex.size_t([1]), cov, param_map), (0,0,0,0,0,0))
def add_new_solvent(self): if(self.params.b_iso is None): sol_sel = self.model.solvent_selection() xrs_mac_h = self.model.xray_structure.select(~sol_sel) hd_mac = self.model.xray_structure.hd_selection().select(~sol_sel) xrs_mac = xrs_mac_h.select(~hd_mac) b = xrs_mac.extract_u_iso_or_u_equiv() * math.pi**2*8 b_solv = flex.mean_default(b, None) if(b_solv is not None and b_solv < self.params.b_iso_min or b_solv > self.params.b_iso_max): b_solv = (self.params.b_iso_min + self.params.b_iso_max) / 2. else: b_solv = self.params.b_iso if(self.params.new_solvent == "isotropic"): new_scatterers = flex.xray_scatterer( self.sites.size(), xray.scatterer(occupancy = self.params.occupancy, b = b_solv, scattering_type = self.params.scattering_type)) elif(self.params.new_solvent == "anisotropic"): u_star = adptbx.u_iso_as_u_star(self.model.xray_structure.unit_cell(), adptbx.b_as_u(b_solv)) new_scatterers = flex.xray_scatterer( self.sites.size(), xray.scatterer( occupancy = self.params.occupancy, u = u_star, scattering_type = self.params.scattering_type)) else: raise RuntimeError new_scatterers.set_sites(self.sites) solvent_xray_structure = xray.structure( special_position_settings = self.model.xray_structure, scatterers = new_scatterers) xrs_sol = self.model.xray_structure.select(self.model.solvent_selection()) xrs_mac = self.model.xray_structure.select(~self.model.solvent_selection()) xrs_sol = xrs_sol.concatenate(other = solvent_xray_structure) sol_sel = flex.bool(xrs_mac.scatterers().size(), False) sol_sel.extend( flex.bool(xrs_sol.scatterers().size(), True) ) self.model.add_solvent( solvent_xray_structure = solvent_xray_structure, residue_name = self.params.output_residue_name, atom_name = self.params.output_atom_name, chain_id = self.params.output_chain_id, refine_occupancies = self.params.refine_occupancies, refine_adp = self.params.new_solvent) self.fmodel.update_xray_structure( xray_structure = self.model.xray_structure, update_f_calc = True)
def __init__(self,unitcell,spacegroup,scatterers): self.sg=sgtbx.space_group_info(spacegroup) self.uc=uctbx.unit_cell(unitcell) self.scatt=scatterers self.cctbx_scatterers=flex.xray_scatterer() for s in self.scatt: self.cctbx_scatterers.append(xray.scatterer(label=s.label,site=s.site,occupancy=s.occupancy,u=s.u_iso)) try: #old cctbx version xray.add_scatterers_ext(unit_cell=self.uc, space_group=self.sg.group(), scatterers=self.cctbx_scatterers, site_symmetry_table=sgtbx.site_symmetry_table(), site_symmetry_table_for_new=sgtbx.site_symmetry_table(), min_distance_sym_equiv=0.5, u_star_tolerance=0, assert_min_distance_sym_equiv=True) except: # cctbx version >= 2011_04_06_0217 #print "Whoops, cctbx version 2011" xray.add_scatterers_ext(unit_cell=self.uc, space_group=self.sg.group(), scatterers=self.cctbx_scatterers, site_symmetry_table=sgtbx.site_symmetry_table(), site_symmetry_table_for_new=sgtbx.site_symmetry_table(), min_distance_sym_equiv=0.5, u_star_tolerance=0, assert_min_distance_sym_equiv=True, non_unit_occupancy_implies_min_distance_sym_equiv_zero=False) cs=crystal.symmetry(self.uc,spacegroup) sp=crystal.special_position_settings(cs) self.structure=xray.structure(sp,self.cctbx_scatterers) self.structure_as_P1=self.structure.expand_to_p1()
def iass_as_xray_structure(self, iass): ias_xray_structure = xray.structure( crystal_symmetry = self.xray_structure.crystal_symmetry()) for ias in iass: assert ias.status is not None if(ias.status): if(self.params.use_map): site_cart = ias.peak_position_cart b_iso = ias.b_iso q = ias.q else: site_cart = ias.site_cart_predicted b_iso = (ias.atom_1.b_iso + ias.atom_2.b_iso)*0.5 q = self.params.initial_ias_occupancy if(b_iso is None): b_iso = (ias.atom_1.b_iso + ias.atom_2.b_iso)*0.5 if(q is None): q = self.params.initial_ias_occupancy if(site_cart is None): site_cart = ias.site_cart_predicted assert [b_iso, q].count(None) == 0 if(site_cart is not None): ias_scatterer = xray.scatterer( label = ias.name, scattering_type = ias.name, site = self.xray_structure.unit_cell().fractionalize(site_cart), u = adptbx.b_as_u(b_iso), occupancy = q) ias_xray_structure.add_scatterer(ias_scatterer) ias_xray_structure.scattering_type_registry( custom_dict = ias_scattering_dict) return ias_xray_structure
def exercise_trigonometric_ff(): from math import cos, sin, pi sgi = sgtbx.space_group_info("P1") cs = sgi.any_compatible_crystal_symmetry(volume=1000) miller_set = miller.build_set(cs, anomalous_flag=False, d_min=1) miller_set = miller_set.select(flex.random_double(miller_set.size()) < 0.2) for i in xrange(5): sites = flex.random_double(9) x1, x2, x3 = (matrix.col(sites[:3]), matrix.col(sites[3:6]), matrix.col(sites[6:])) xs = xray.structure(crystal.special_position_settings(cs)) for x in (x1, x2, x3): sc = xray.scatterer(site=x, scattering_type="const") sc.flags.set_grad_site(True) xs.add_scatterer(sc) f_sq = structure_factors.f_calc_modulus_squared(xs) for h in miller_set.indices(): h = matrix.col(h) phi1, phi2, phi3 = 2 * pi * h.dot(x1), 2 * pi * h.dot(x2), 2 * pi * h.dot(x3) fc_mod_sq = 3 + 2 * (cos(phi1 - phi2) + cos(phi2 - phi3) + cos(phi3 - phi1)) g = [] g.extend(-2 * (sin(phi1 - phi2) - sin(phi3 - phi1)) * 2 * pi * h) g.extend(-2 * (sin(phi2 - phi3) - sin(phi1 - phi2)) * 2 * pi * h) g.extend(-2 * (sin(phi3 - phi1) - sin(phi2 - phi3)) * 2 * pi * h) grad_fc_mod_sq = g f_sq.linearise(h) assert approx_equal(f_sq.observable, fc_mod_sq) assert approx_equal(f_sq.grad_observable, grad_fc_mod_sq)
def iass_as_xray_structure(self, iass): ias_xray_structure = xray.structure( crystal_symmetry=self.xray_structure.crystal_symmetry()) for ias in iass: assert ias.status is not None if (ias.status): if (self.params.use_map): site_cart = ias.peak_position_cart b_iso = ias.b_iso q = ias.q else: site_cart = ias.site_cart_predicted b_iso = (ias.atom_1.b_iso + ias.atom_2.b_iso) * 0.5 q = self.params.initial_ias_occupancy if (b_iso is None): b_iso = (ias.atom_1.b_iso + ias.atom_2.b_iso) * 0.5 if (q is None): q = self.params.initial_ias_occupancy if (site_cart is None): site_cart = ias.site_cart_predicted assert [b_iso, q].count(None) == 0 if (site_cart is not None): ias_scatterer = xray.scatterer( label=ias.name, scattering_type=ias.name, site=self.xray_structure.unit_cell().fractionalize( site_cart), u=adptbx.b_as_u(b_iso), occupancy=q) ias_xray_structure.add_scatterer(ias_scatterer) ias_xray_structure.scattering_type_registry( custom_dict=ias_scattering_dict) return ias_xray_structure
def add_new_solvent(self): b_solv = self.params.b_iso new_scatterers = flex.xray_scatterer( self.sites.size(), xray.scatterer(occupancy = self.params.occupancy, b = b_solv, scattering_type = self.params.scattering_type, label = 'HOH')) new_scatterers.set_sites(self.sites) solvent_xray_structure = xray.structure( special_position_settings = self.model.xray_structure, scatterers = new_scatterers) xrs_sol = self.model.xray_structure.select(self.model.solvent_selection()) xrs_mac = self.model.xray_structure.select(~self.model.solvent_selection()) xrs_sol = xrs_sol.concatenate(other = solvent_xray_structure) sol_sel = flex.bool(xrs_mac.scatterers().size(), False) sol_sel.extend( flex.bool(xrs_sol.scatterers().size(), True) ) self.model.add_solvent( solvent_xray_structure = solvent_xray_structure, residue_name = self.params.output_residue_name, atom_name = self.params.output_atom_name, chain_id = self.params.output_chain_id, refine_occupancies = self.params.refine_occupancies, refine_adp = self.params.new_solvent) self.fmodel.update_xray_structure( xray_structure = self.model.xray_structure, update_f_calc = False)
def scatterer_from_list(l): if (len(l) == 7): return xray.scatterer( site=l[:3], u=l[3], occupancy=l[4], scattering_type="const", fp=l[5], fdp=l[6]) return xray.scatterer( site=l[:3], u=l[3:9], occupancy=l[9], scattering_type="const", fp=l[10], fdp=l[11])
def extract_structure(self, phase_nr=1): """This method tries to extract the crystal structure from the parsed pcrfile. :returns: the extracted structure :rtype: cctbx.xray.structure """ from cctbx import xray from cctbx import crystal from cctbx.array_family import flex p = self.cfg['phases'][str(phase_nr)] atoms = p['atoms'] unit_cell = [ p['a'], p['b'], p['c'], p['alpha'], p['beta'], p['gamma'] ] special_position_settings=crystal.special_position_settings( crystal_symmetry=crystal.symmetry( unit_cell=unit_cell, space_group_symbol=p['SYMB'])) scatterers = [] for k, a in atoms.iteritems(): scatterers.append(xray.scatterer(label=a['LABEL'], scattering_type=a['NTYP'], site=(a['X'], a['Y'], a['Z']), b=a['B'])) scatterers_flex=flex.xray_scatterer(scatterers) structure = xray.structure(special_position_settings=special_position_settings, scatterers=scatterers_flex) return structure.as_py_code()
def exercise_symmetry_equivalent(): xs = xray.structure( crystal_symmetry=crystal.symmetry( unit_cell=(1, 2, 3), space_group_symbol='hall: P 2x'), scatterers=flex.xray_scatterer(( xray.scatterer("C", site=(0.1, 0.2, 0.3)), ))) xs.scatterers()[0].flags.set_grad_site(True) connectivity_table = smtbx.utils.connectivity_table(xs) reparametrisation = constraints.reparametrisation( xs, [], connectivity_table) site_0 = reparametrisation.add(constraints.independent_site_parameter, scatterer=xs.scatterers()[0]) g = sgtbx.rt_mx('x,-y,-z') symm_eq = reparametrisation.add( constraints.symmetry_equivalent_site_parameter, site=site_0, motion=g) reparametrisation.finalise() assert approx_equal(symm_eq.original.scatterers[0].site, (0.1, 0.2, 0.3), eps=1e-15) assert str(symm_eq.motion) == 'x,-y,-z' assert symm_eq.is_variable reparametrisation.linearise() assert approx_equal(symm_eq.value, g*site_0.value, eps=1e-15) reparametrisation.store() assert approx_equal(symm_eq.value, (0.1, -0.2, -0.3), eps=1e-15) assert approx_equal(site_0.value, (0.1, 0.2, 0.3), eps=1e-15)
def read_scatterer(flds, default_b_iso=3.0): scatterer = xray.scatterer(scattering_type="const") # Label [ScatFact] x y z [Occ [Biso]] try: scatterer.label = flds[0] try: float(flds[1]) except Exception: offs = 2 scatterer.scattering_type = eltbx.xray_scattering.get_standard_label(label=flds[1], exact=True) else: offs = 1 scatterer.scattering_type = eltbx.xray_scattering.get_standard_label(label=flds[0], exact=False) site = flds[offs : offs + 3] for i in xrange(3): site[i] = float(site[i]) scatterer.site = site scatterer.occupancy = 1.0 scatterer.set_use_u_iso_only() scatterer.u_iso = adptbx.b_as_u(default_b_iso) if len(flds) >= offs + 4: scatterer.occupancy = float(flds[offs + 3]) if len(flds) == offs + 5: scatterer.u_iso = adptbx.b_as_u(float(flds[offs + 4])) else: assert len(flds) < offs + 5 except Exception: raise cgi_utils.FormatError, flds return scatterer
def __init__(self, space_group=SpaceGroup('P 1'), lattice=Lattice(1.0, 1.0, 1.0, 90.0, 90.0, 90.0), sites=[]): """ Crystal object. Functions as a wrapper to a cctbx xray.structure object, but adds additional variables and functionality. Core object of this package. Input: SpaceGroup space_group space group for the current crystal List of Site objects sites List of Site objects. Warning: 'crystal_structure' must be given, or 'space_group', 'lattice', and 'sites' must be given, or creation of the crystal will fail. """ try: crystal_symmetry = crystal.symmetry( unit_cell=str(lattice), space_group_symbol=space_group.cctbx_name) except Exception as e: raise SymmetryError( "SpaceGroup {s} is incompatible with Lattice -> {l} cctbx error {e}" .format(l=str(lattice), s=SpaceGroup.cctbx_name, e=e)) scatterers = flex.xray_scatterer() for i, site in enumerate(sites): # the element name can be pulled from scatterer via the s.element_symbol() method (if it's an element!!!) # example: 'atom-b-12',or 'vacancy-c-3' # we need to set the scattering_type so we can freely use the label to store metadata #scattering_type = something #scatterers.append(xray.scatterer(label=atom.name, site=tuple(atom.abc), occupancy=atom.occupancy), scattering_type=atom.name) #Method #2 # explicitly add metadata to _meta st_temp, dash, num = site.label.partition("-") if dash == "-": k = site.label else: k = "-".join([site.label, str(i)]) # problems here not sure what's up k = str(k) # print "label = ", k, ' type of label = ', type(k) # print "site = ", tuple(site.abc) # print "occupancy = ", site.occupancy scatterers.append( xray.scatterer(label=k, site=tuple(site.abc), occupancy=site.occupancy)) # Test for coherency of Lattice and SpaceGroup self.crystal_structure = xray.structure( crystal_symmetry=crystal_symmetry, scatterers=scatterers)
def get_xrs(): crystal_symmetry = crystal.symmetry( unit_cell=(10,10,10,90,90,90), space_group_symbol="P 1") return xray.structure( crystal_symmetry=crystal_symmetry, scatterers=flex.xray_scatterer([ xray.scatterer(label="C", site=(0,0,0))]))
def scatterer_from_list(l): return xray.scatterer( site=l[:3], u=l[3], occupancy=l[4], scattering_type="const", fp=l[5], fdp=l[6])
def exercise_2(): symmetry = crystal.symmetry( unit_cell=(5.67, 10.37, 10.37, 90, 135.49, 90), space_group_symbol="C2") structure = xray.structure(crystal_symmetry=symmetry) atmrad = flex.double() xyzf = flex.vec3_double() for k in xrange(100): scatterer = xray.scatterer( site = ((1.+k*abs(math.sin(k)))/1000.0, (1.+k*abs(math.cos(k)))/1000.0, (1.+ k)/1000.0), scattering_type = "C") structure.add_scatterer(scatterer) atmrad.append(van_der_waals_radii.vdw.table[scatterer.element_symbol()]) xyzf.append(scatterer.site) miller_set = miller.build_set( crystal_symmetry=structure, d_min=1.0, anomalous_flag=False) step = 0.5 crystal_gridding = maptbx.crystal_gridding( unit_cell=structure.unit_cell(), step=step) nxyz = crystal_gridding.n_real() shrink_truncation_radius = 1.0 solvent_radius = 1.0 m1 = around_atoms( structure.unit_cell(), structure.space_group().order_z(), structure.sites_frac(), atmrad, nxyz, solvent_radius, shrink_truncation_radius) assert m1.solvent_radius == 1 assert m1.shrink_truncation_radius == 1 assert flex.max(m1.data) == 1 assert flex.min(m1.data) == 0 assert m1.data.size() == m1.data.count(1) + m1.data.count(0) m2 = mmtbx.masks.bulk_solvent( xray_structure=structure, gridding_n_real=nxyz, ignore_zero_occupancy_atoms = False, solvent_radius=solvent_radius, shrink_truncation_radius=shrink_truncation_radius) assert m2.data.all_eq(m1.data) m3 = mmtbx.masks.bulk_solvent( xray_structure=structure, grid_step=step, ignore_zero_occupancy_atoms = False, solvent_radius=solvent_radius, shrink_truncation_radius=shrink_truncation_radius) assert m3.data.all_eq(m1.data) f_mask2 = m2.structure_factors(miller_set=miller_set) f_mask3 = m3.structure_factors(miller_set=miller_set) assert approx_equal(f_mask2.data(), f_mask3.data()) assert approx_equal(flex.sum(flex.abs(f_mask3.data())), 1095.17999134)
def run(): quartz_structure = xray.structure( special_position_settings=crystal.special_position_settings( crystal_symmetry=crystal.symmetry( unit_cell=(5.01,5.01,5.47,90,90,120), space_group_symbol="P6222")), scatterers=flex.xray_scatterer([ xray.scatterer( label="Si", site=(1/2.,1/2.,1/3.), u=0.2), xray.scatterer( label="O", site=(0.197,-0.197,0.83333), u=0)])) quartz_structure.show_summary().show_scatterers() from libtbx import easy_pickle easy_pickle.dump("beach", quartz_structure) from libtbx import easy_pickle quartz_structure = easy_pickle.load("beach") for scatterer in quartz_structure.scatterers(): print("%s:" % scatterer.label, "%8.4f %8.4f %8.4f" % scatterer.site) site_symmetry = quartz_structure.site_symmetry(scatterer.site) print(" point group type:", site_symmetry.point_group_type()) print(" special position operator:", site_symmetry.special_op_simplified()) for table in ["xray", "electron"]: print("Scattering type table:", table) reg = quartz_structure.scattering_type_registry(table=table) reg.show_summary() f_calc = quartz_structure.structure_factors(d_min=2).f_calc() f_calc.show_summary().show_array() f_calc.d_spacings().show_array() low_resolution_only = f_calc.select(f_calc.d_spacings().data() > 2.5) low_resolution_only.show_array() print()
def run(): quartz_structure = xray.structure( special_position_settings=crystal.special_position_settings( crystal_symmetry=crystal.symmetry( unit_cell=(5.01,5.01,5.47,90,90,120), space_group_symbol="P6222")), scatterers=flex.xray_scatterer([ xray.scatterer( label="Si", site=(1/2.,1/2.,1/3.), u=0.2), xray.scatterer( label="O", site=(0.197,-0.197,0.83333), u=0)])) quartz_structure.show_summary().show_scatterers() from libtbx import easy_pickle easy_pickle.dump("beach", quartz_structure) from libtbx import easy_pickle quartz_structure = easy_pickle.load("beach") for scatterer in quartz_structure.scatterers(): print "%s:" % scatterer.label, "%8.4f %8.4f %8.4f" % scatterer.site site_symmetry = quartz_structure.site_symmetry(scatterer.site) print " point group type:", site_symmetry.point_group_type() print " special position operator:", site_symmetry.special_op_simplified() for table in ["xray", "electron"]: print "Scattering type table:", table reg = quartz_structure.scattering_type_registry(table=table) reg.show_summary() f_calc = quartz_structure.structure_factors(d_min=2).f_calc() f_calc.show_summary().show_array() f_calc.d_spacings().show_array() low_resolution_only = f_calc.select(f_calc.d_spacings().data() > 2.5) low_resolution_only.show_array() print
def get_transformed_model2(self, output_pdb=None, scattering_type="SE", f=sys.stdout, return_superposed_model2=True, template_pdb_inp=None): # tt 2013-01-25; 2016-10-31 from cctbx import xray xray_scatterer = xray.scatterer(scattering_type=scattering_type) model2 = self.ref_model2.as_xray_structure(xray_scatterer) from cctbx.array_family import flex new_coords = flex.vec3_double() for i_model2 in range(self.ref_model2.size()): c2 = matrix.col(self.eucl_symop * self.ref_model2[i_model2].site) c2 += self.adjusted_shift c2 = inside_zero_one(c2) new_coords.append(c2) model2.set_sites_frac(new_coords) if output_pdb is not None: assert template_pdb_inp is not None # Set up new xrs with these sites and with scattering types, occ, b, # labels from original 2nd model xrs = xray.structure(model2.xray_structure()) assert len(model2.scatterers()) == len(template_pdb_inp.atoms()) b_iso_values = flex.double() for scatterer, atom in zip(model2.scatterers(), template_pdb_inp.atoms()): b_iso_values.append(atom.b) new_scatterer = xray.scatterer(scattering_type=atom.element, label=atom.name, occupancy=atom.occ, site=scatterer.site) xrs.add_scatterer(new_scatterer) xrs.set_b_iso(values=b_iso_values) pdb_string = xrs.as_pdb_file() ff = open(output_pdb, 'w') print(pdb_string, file=ff) ff.close() print("\nWrote model 2 mapped to model 1 to file %s " % (output_pdb), file=f) if return_superposed_model2: return model2.as_emma_model()
def exercise_real_space_refinement(verbose): if (verbose): out = sys.stdout else: out = StringIO() out_of_bounds_clamp = maptbx.out_of_bounds_clamp(0) out_of_bounds_raise = maptbx.out_of_bounds_raise() crystal_symmetry = crystal.symmetry(unit_cell=(10, 10, 10, 90, 90, 90), space_group_symbol="P 1") xray_structure = xray.structure(crystal_symmetry=crystal_symmetry, scatterers=flex.xray_scatterer([ xray.scatterer(label="C", site=(0, 0, 0)) ])) miller_set = miller.build_set(crystal_symmetry=crystal_symmetry, anomalous_flag=False, d_min=1) f_calc = miller_set.structure_factors_from_scatterers( xray_structure=xray_structure).f_calc() fft_map = f_calc.fft_map() fft_map.apply_sigma_scaling() real_map = fft_map.real_map_unpadded() #### unit_cell test delta_h = .005 basic_map = maptbx.basic_map( maptbx.basic_map_unit_cell_flag(), real_map, real_map.focus(), crystal_symmetry.unit_cell().orthogonalization_matrix(), out_of_bounds_clamp.as_handle(), crystal_symmetry.unit_cell()) testing_function_for_rsfit(basic_map, delta_h, xray_structure, out) ### non_symmetric test # minfrac = crystal_symmetry.unit_cell().fractionalize((-5, -5, -5)) maxfrac = crystal_symmetry.unit_cell().fractionalize((5, 5, 5)) gridding_first = [ifloor(n * b) for n, b in zip(fft_map.n_real(), minfrac)] gridding_last = [iceil(n * b) for n, b in zip(fft_map.n_real(), maxfrac)] data = maptbx.copy(real_map, gridding_first, gridding_last) # basic_map = maptbx.basic_map( maptbx.basic_map_non_symmetric_flag(), data, fft_map.n_real(), crystal_symmetry.unit_cell().orthogonalization_matrix(), out_of_bounds_clamp.as_handle(), crystal_symmetry.unit_cell()) testing_function_for_rsfit(basic_map, delta_h, xray_structure, out) ### asu test # minfrac = crystal_symmetry.unit_cell().fractionalize((0, 0, 0)) maxfrac = crystal_symmetry.unit_cell().fractionalize((10, 10, 10)) gridding_first = [ifloor(n * b) for n, b in zip(fft_map.n_real(), minfrac)] gridding_last = [iceil(n * b) for n, b in zip(fft_map.n_real(), maxfrac)] data = maptbx.copy(real_map, gridding_first, gridding_last) # basic_map = maptbx.basic_map( maptbx.basic_map_asu_flag(), data, crystal_symmetry.space_group(), crystal_symmetry.direct_space_asu().as_float_asu(), real_map.focus(), crystal_symmetry.unit_cell().orthogonalization_matrix(), out_of_bounds_clamp.as_handle(), crystal_symmetry.unit_cell(), 0.5, True) testing_function_for_rsfit(basic_map, delta_h, xray_structure, out)
def test_direction(): from cctbx.array_family import flex from cctbx import uctbx, xray, crystal from smtbx.refinement import constraints from scitbx.matrix import col, row from libtbx.test_utils import approx_equal uc = uctbx.unit_cell((1, 2, 3)) xs = xray.structure(crystal_symmetry=crystal.symmetry( unit_cell=uc, space_group_symbol='hall: P 2x 2y'), scatterers=flex.xray_scatterer(( xray.scatterer('C0', site=(0, 0, 0)), xray.scatterer('C1', site=(0, 2, 0)), xray.scatterer('C2', site=(1, 1, 0)), xray.scatterer('C3', site=(3, 1, 0)), ))) r = constraints.ext.reparametrisation(xs.unit_cell()) sc = xs.scatterers() site_0 = r.add(constraints.independent_site_parameter, sc[0]) site_1 = r.add(constraints.independent_site_parameter, sc[1]) site_2 = r.add(constraints.independent_site_parameter, sc[2]) site_3 = r.add(constraints.independent_site_parameter, sc[3]) d = constraints.vector_direction((site_0, site_1, site_2)).direction(uc) sd = constraints.static_direction.calc_best_line(uc, (site_0, site_1, site_2)) assert approx_equal(d, sd, eps=1e-15) d = constraints.vector_direction((site_0, site_1)).direction(uc) assert approx_equal( d, row(uc.orthogonalize(col(sc[1].site) - col(sc[0].site))).normalize(), eps=1e-15) n = constraints.static_direction.calc_best_plane_normal( uc, (site_0, site_1, site_2)) n1 = constraints.static_direction.calc_best_plane_normal( uc, (site_0, site_1, site_2, site_3)) v01 = uc.orthogonalize(col(sc[0].site) - col(sc[1].site)) v21 = uc.orthogonalize(col(sc[2].site) - col(sc[1].site)) nc = row(v01).cross(row(v21)).normalize() assert approx_equal(n, n1, eps=1e-15) assert approx_equal(n, nc, eps=1e-15)
def exercise_u_iso_proportional_to_pivot_u_eq(): xs = xray.structure(crystal_symmetry=crystal.symmetry( unit_cell=(), space_group_symbol='hall: P 2x 2y'), scatterers=flex.xray_scatterer(( xray.scatterer('C0', u=(1, 1, 1, 0, 0, 0)), xray.scatterer('C1'), xray.scatterer('C2', site=(0.1, 0.2, 0.3), u=(1, 2, 3, 0, 0, 0)), xray.scatterer('C3'), ))) r = constraints.ext.reparametrisation(xs.unit_cell()) sc = xs.scatterers() sc[0].flags.set_grad_u_aniso(True) sc[2].flags.set_grad_u_aniso(True) u_0 = r.add(constraints.special_position_u_star_parameter, site_symmetry=xs.site_symmetry_table().get(0), scatterer=sc[0]) u_iso_1 = r.add(constraints.u_iso_proportional_to_pivot_u_eq, pivot_u=u_0, multiplier=3, scatterer=sc[1]) u_2 = r.add(constraints.independent_u_star_parameter, sc[2]) u_iso_3 = r.add(constraints.u_iso_proportional_to_pivot_u_eq, pivot_u=u_2, multiplier=2, scatterer=sc[3]) r.finalise() m = 3 + 6 n = m + 6 + 1 + 1 r.linearise() assert approx_equal(u_iso_1.value, 3, eps=1e-15) assert approx_equal(u_iso_3.value, 4, eps=1e-15) jt0 = sparse.matrix(m, n) for i in xrange(m): jt0[i, i] = 1 p, q = u_0.argument(0).index, u_0.index jt0[p, q] = jt0[p + 1, q + 1] = jt0[p + 2, q + 2] = 1 q = u_iso_1.index jt0[p, q] = jt0[p + 1, q] = jt0[p + 2, q] = 1 p, q = u_2.index, u_iso_3.index jt0[p, q] = jt0[p + 1, q] = jt0[p + 2, q] = 2 / 3 assert sparse.approx_equal(tolerance=1e-15)(r.jacobian_transpose, jt0)
def __init__(self, staggered, verbose=False): self.staggered = staggered self.verbose = verbose self.cs = crystal.symmetry(uctbx.unit_cell((1, 1, 2, 90, 90, 80)), "hall: P 2z") self.o = xray.scatterer('O', site=(0, 0, 0)) self.o.flags.set_grad_site(True) self.c1 = xray.scatterer('C1', site=(1.5, 0, 0)) self.c2 = xray.scatterer('C2', site=(2.5, 1, 0)) self.h = xray.scatterer('H') self.reparam = constraints.ext.reparametrisation(self.cs.unit_cell()) xo = self.reparam.add(constraints.independent_site_parameter, self.o) x1 = self.reparam.add(constraints.independent_site_parameter, self.c1) x2 = self.reparam.add(constraints.independent_site_parameter, self.c2) l = self.reparam.add(constraints.independent_scalar_parameter, value=self.bond_length, variable=False) phi = self.reparam.add(constraints.independent_scalar_parameter, value=0, variable=False) uc = self.cs.unit_cell() _ = mat.col if staggered: xh = self.reparam.add( constraints.staggered_terminal_tetrahedral_xh_site, pivot=xo, pivot_neighbour=x1, stagger_on=x2, length=l, hydrogen=(self.h, )) else: xh = self.reparam.add(constraints.terminal_tetrahedral_xh_site, pivot=xo, pivot_neighbour=x1, azimuth=phi, length=l, e_zero_azimuth=uc.orthogonalize( _(self.c2.site) - _(self.c1.site)), hydrogen=(self.h, )) self.reparam.finalise() self.xh, self.xo, self.x1, self.x2 = [ x.index for x in (xh, xo, x1, x2) ] self.l, self.phi = l.index, phi.index
def as_xray_structure(self, scatterer=None): from cctbx import xray if (scatterer is None): scatterer = xray.scatterer(scattering_type="const") result = xray.structure(special_position_settings=self) for position in self.positions(): result.add_scatterer( scatterer.customized_copy(label=position.label, site=position.site)) return result
def exercise_u_iso_proportional_to_pivot_u_eq(): xs = xray.structure( crystal_symmetry=crystal.symmetry( unit_cell=(), space_group_symbol='hall: P 2x 2y'), scatterers=flex.xray_scatterer(( xray.scatterer('C0', u=(1, 1, 1, 0, 0, 0)), xray.scatterer('C1'), xray.scatterer('C2', site=(0.1, 0.2, 0.3), u=(1, 2, 3, 0, 0, 0)), xray.scatterer('C3'), ))) r = constraints.ext.reparametrisation(xs.unit_cell()) sc = xs.scatterers() sc[0].flags.set_grad_u_aniso(True) sc[2].flags.set_grad_u_aniso(True) u_0 = r.add(constraints.special_position_u_star_parameter, site_symmetry=xs.site_symmetry_table().get(0), scatterer=sc[0]) u_iso_1 = r.add(constraints.u_iso_proportional_to_pivot_u_eq, pivot_u=u_0, multiplier=3, scatterer=sc[1]) u_2 = r.add(constraints.independent_u_star_parameter, sc[2]) u_iso_3 = r.add(constraints.u_iso_proportional_to_pivot_u_eq, pivot_u=u_2, multiplier=2, scatterer=sc[3]) r.finalise() m = 3 + 6 n = m + 6 + 1 + 1 r.linearise() assert approx_equal(u_iso_1.value, 3, eps=1e-15) assert approx_equal(u_iso_3.value, 4, eps=1e-15) jt0 = sparse.matrix(m, n) for i in xrange(m): jt0[i, i] = 1 p, q = u_0.argument(0).index, u_0.index jt0[p, q] = jt0[p+1, q+1] = jt0[p+2, q+2] = 1 q = u_iso_1.index jt0[p, q] = jt0[p+1, q] = jt0[p+2, q] = 1 p, q = u_2.index, u_iso_3.index jt0[p, q] = jt0[p+1, q] = jt0[p+2, q] = 2/3 assert sparse.approx_equal(tolerance=1e-15)(r.jacobian_transpose, jt0)
def as_xray_structure(self, scatterer=None): from cctbx import xray if (scatterer is None): scatterer = xray.scatterer(scattering_type="const") result = xray.structure(special_position_settings=self) for position in self.positions(): result.add_scatterer(scatterer.customized_copy( label=position.label, site=position.site)) return result
def exercise_lbfgs(test_case, use_geo, out, d_min=2): sites_cart, geo_manager = cctbx.geometry_restraints.manager.\ construct_non_crystallographic_conserving_bonds_and_angles( sites_cart=flex.vec3_double(test_case.sites), edge_list_bonds=test_case.bonds, edge_list_angles=test_case.angles()) scatterers = flex.xray_scatterer(sites_cart.size(), xray.scatterer(scattering_type="C", b=20)) for sc, lbl in zip(scatterers, test_case.labels): sc.label = lbl structure = xray.structure(crystal_symmetry=geo_manager.crystal_symmetry, scatterers=scatterers) structure.set_sites_cart(sites_cart=sites_cart) f_calc = structure.structure_factors(d_min=d_min, anomalous_flag=False).f_calc() fft_map = f_calc.fft_map() fft_map.apply_sigma_scaling() if (use_geo): axis = matrix.col(flex.random_double_point_on_sphere()) rot = scitbx.math.r3_rotation_axis_and_angle_as_matrix(axis=axis, angle=25, deg=True) trans = matrix.col(flex.random_double_point_on_sphere()) * 1.0 structure.apply_rigid_body_shift(rot=rot, trans=trans) geo_manager.energies_sites(sites_cart=structure.sites_cart()).show( f=out) minimized = real_space_refinement_simple.lbfgs( sites_cart=structure.sites_cart(), density_map=fft_map.real_map(), geometry_restraints_manager=geo_manager, gradients_method="fd", real_space_target_weight=1, real_space_gradients_delta=d_min / 3) geo_manager.energies_sites(sites_cart=minimized.sites_cart).show(f=out) else: minimized = real_space_refinement_simple.lbfgs( sites_cart=structure.sites_cart(), density_map=fft_map.real_map(), unit_cell=structure.unit_cell(), gradients_method="fd", real_space_gradients_delta=d_min / 3) rmsd_start = sites_cart.rms_difference(structure.sites_cart()) rmsd_final = sites_cart.rms_difference(minimized.sites_cart) print("RMSD start, final:", rmsd_start, rmsd_final, file=out) if (use_geo): assert rmsd_start >= 1 - 1e-6 assert rmsd_final < 0.2 def show_f_g(label, f, g): print(label, "f, |g|:", f, flex.mean_sq(g)**0.5, file=out) show_f_g(label="start", f=minimized.f_start, g=minimized.g_start) show_f_g(label="final", f=minimized.f_final, g=minimized.g_final) assert minimized.f_final <= minimized.f_start return minimized
def quartz_p1(metrical_matrix=None): if metrical_matrix is not None: unit_cell = uctbx.unit_cell(metrical_matrix=metrical_matrix) else: unit_cell = uctbx.unit_cell(parameters=(5.01,5.01,5.47,90,90,120)) return xray.structure( crystal_symmetry=crystal.symmetry( unit_cell=unit_cell, space_group_symbol='hall: P 1'), scatterers=flex.xray_scatterer(( xray.scatterer( #0 label='Si', site=(0.500000, 0.500000, 0.333333), u=0.000000), xray.scatterer( #1 label='Si', site=(0.000000, 0.500000, 0.666667), u=0.000000), xray.scatterer( #2 label='Si', site=(0.500000, 0.000000, 0.000000), u=0.000000), xray.scatterer( #3 label='O', site=(0.197000, 0.803000, 0.833333), u=0.000000), xray.scatterer( #4 label='O', site=(0.394000, 0.197000, 0.166667), u=0.000000), xray.scatterer( #5 label='O', site=(0.803000, 0.606000, 0.500000), u=0.000000), xray.scatterer( #6 label='O', site=(0.197000, 0.394000, 0.500000), u=0.000000), xray.scatterer( #7 label='O', site=(0.606000, 0.803000, 0.166667), u=0.000000), xray.scatterer( #8 label='O', site=(0.803000, 0.197000, 0.833333), u=0.000000) )))
def exercise_u_iso_proportional_to_pivot_u_iso(): # Test working constraint xs = xray.structure( crystal_symmetry=crystal.symmetry( unit_cell=(), space_group_symbol='hall: P 2x 2y'), scatterers=flex.xray_scatterer(( xray.scatterer('C0', u=0.12), xray.scatterer('C1'), ))) r = constraints.ext.reparametrisation(xs.unit_cell()) sc = xs.scatterers() u_iso = r.add(constraints.independent_u_iso_parameter, sc[0]) u_iso_1 = r.add(constraints.u_iso_proportional_to_pivot_u_iso, pivot_u_iso=u_iso, multiplier=2, scatterer=sc[1]) r.finalise() r.linearise() assert approx_equal(u_iso_1.value, 0.24, eps=1e-15) # Test conflicting constraints xs = xray.structure( crystal_symmetry=crystal.symmetry( unit_cell=(), space_group_symbol='hall: P 2x 2y'), scatterers=flex.xray_scatterer(( xray.scatterer('C0', u=0.12), xray.scatterer('C1', u=0.21), xray.scatterer('C2') ))) with warnings.catch_warnings(record=True) as w: warnings.simplefilter("always") r = constraints.reparametrisation( structure=xs, constraints=[constraints.adp.shared_u((0, 2)), constraints.adp.shared_u((1, 2))], connectivity_table=smtbx.utils.connectivity_table(xs)) assert len(w) == 1 assert w[-1].category == constraints.ConflictingConstraintWarning assert w[-1].message.conflicts == set(((2, 'U'),))
def pdb_atoms_as_xray_structure(pdb_atoms, crystal_symmetry): xray_structure = xray.structure(crystal_symmetry=crystal_symmetry) unit_cell = xray_structure.unit_cell() for atom in pdb_atoms: scatterer = xray.scatterer(label=atom.name, site=unit_cell.fractionalize(atom.xyz), b=atom.b, occupancy=atom.occ, scattering_type=atom.element) xray_structure.add_scatterer(scatterer) return xray_structure
def debug_write_reciprocal_lattice_points_as_pdb(self, file_name='reciprocal_lattice.pdb'): from cctbx import crystal, xray cs = crystal.symmetry(unit_cell=(1000,1000,1000,90,90,90), space_group="P1") xs = xray.structure(crystal_symmetry=cs) for site in self.trial_sites: xs.add_scatterer(xray.scatterer("C", site=site)) xs.sites_mod_short() with open(file_name, 'wb') as f: print >> f, xs.as_pdb_file()
def tst_pdb_output(): print("Testing pdb-output option") xray_scatterer = xray.scatterer( scattering_type = 'SE') for sg,target_list in zip( ['p1','p43212'], [ [target_p1,target_p1_inverse,target_p1_partial, target_p1_inverse_partial], [target_p43212,target_p43212_inverse,target_p43212_half, target_p43212_inverse_half] ] ): print("Testing group of targets in %s" %(sg)) for t1 in target_list: e1=get_emma_model_from_pdb(pdb_records=t1) for t2 in target_list: e2=get_emma_model_from_pdb(pdb_records=t2) match_list=e1.best_superpositions_on_other( e2) match=match_list[0] assert match offset_e2=match.get_transformed_model2() # make sure that offset_i2 is pretty much the same as e1 now. new_match_list=e1.best_superpositions_on_other( offset_e2) new_match=new_match_list[0] assert new_match assert approx_equal(new_match.rms,0.,eps=0.01) assert len(new_match.pairs)==12 assert approx_equal( new_match.rt.r,matrix.sqr((1, 0, 0, 0, 1, 0, 0, 0, 1))) assert approx_equal(new_match.rt.t.transpose(),matrix.col((0, 0, 0))) print("Testing pdb-output option with different-sized entries") e1=get_emma_model_from_pdb(pdb_records=pdb6) e2=get_emma_model_from_pdb(pdb_records=pdb5) pdb_inp_e2=iotbx.pdb.input(source_info=None, lines=pdb5) match_list=e1.best_superpositions_on_other(e2) match=match_list[0] assert match output_pdb="output.pdb" offset_e2=match.get_transformed_model2(output_pdb=output_pdb, template_pdb_inp=pdb_inp_e2) with open(output_pdb) as f: offset_e2_text_lines=f.readlines() for o,e in zip(offset_e2_text_lines, pdb5_out.splitlines()): o=o.strip() e=e.strip() if o != e: print(o) print(e) assert o==e
def get_transformed_model2(self,output_pdb=None, scattering_type="SE",f=sys.stdout, return_superposed_model2=True,template_pdb_inp=None): # tt 2013-01-25; 2016-10-31 from cctbx import xray xray_scatterer = xray.scatterer( scattering_type = scattering_type) model2=self.ref_model2.as_xray_structure(xray_scatterer) from cctbx.array_family import flex new_coords=flex.vec3_double() for i_model2 in xrange(self.ref_model2.size()): c2 = matrix.col(self.eucl_symop * self.ref_model2[i_model2].site) c2 += self.adjusted_shift c2=inside_zero_one(c2) new_coords.append(c2) model2.set_sites_frac(new_coords) if output_pdb is not None: assert template_pdb_inp is not None # Set up new xrs with these sites and with scattering types, occ, b, # labels from original 2nd model xrs=xray.structure(model2.xray_structure()) assert len(model2.scatterers())==len(template_pdb_inp.atoms()) b_iso_values=flex.double() for scatterer,atom in zip(model2.scatterers(),template_pdb_inp.atoms()): b_iso_values.append(atom.b) new_scatterer = xray.scatterer( scattering_type = atom.element, label=atom.name, occupancy=atom.occ, site=scatterer.site) xrs.add_scatterer(new_scatterer) xrs.set_b_iso(values = b_iso_values) pdb_string=xrs.as_pdb_file() ff=open(output_pdb,'w') print >>ff, pdb_string ff.close() print >>f,"\nWrote model 2 mapped to model 1 to file %s " %(output_pdb) if return_superposed_model2: return model2.as_emma_model()
def structure_init2(site, site2, sg, cell): symmetry = crystal.symmetry(unit_cell=cell, space_group_symbol=sg) structure = xray.structure(crystal_symmetry=symmetry) scatterer = xray.scatterer(site=site, u=0.1, occupancy=1.0, scattering_type="C") scatterer2 = xray.scatterer(site=site2, u=0.1, occupancy=1.0, scattering_type="C") structure.add_scatterer(scatterer) structure.add_scatterer(scatterer2) xyzf = flex.vec3_double() atmrad = flex.double() for scatterer in structure.scatterers(): xyzf.append(list(scatterer.site)) atmrad.append( van_der_waals_radii.vdw.table[scatterer.element_symbol()]) assert xyzf.size() == atmrad.size() return structure, xyzf, atmrad
def pdb_atoms_as_xray_structure(pdb_atoms, crystal_symmetry): xray_structure = xray.structure(crystal_symmetry = crystal_symmetry) unit_cell = xray_structure.unit_cell() for atom in pdb_atoms: scatterer = xray.scatterer( label = atom.name, site = unit_cell.fractionalize(atom.xyz), b = atom.b, occupancy = atom.occ, scattering_type = atom.element) xray_structure.add_scatterer(scatterer) return xray_structure
def scatterers(self): yield xray.scatterer('Ba', (0.500000, 0.369879, 0.431121)) yield xray.scatterer('Mg', (-0.000000, 0.385261, -0.084062)) yield xray.scatterer('F1', (0.000000, 0.291730, 0.783213)) yield xray.scatterer('F2', (0.000000, 0.328018, 0.303193)) yield xray.scatterer('F3', (0.000000, 0.506766, 0.591744)) yield xray.scatterer('F4', (0.500000, 0.414262, 1.002902))
def __init__(self, staggered, verbose=False): self.staggered = staggered self.verbose = verbose self.cs = crystal.symmetry(uctbx.unit_cell((1, 1, 2, 90, 90, 80)), "hall: P 2z") self.o = xray.scatterer('O', site=(0,0,0)) self.o.flags.set_grad_site(True) self.c1 = xray.scatterer('C1', site=(1.5, 0, 0)) self.c2 = xray.scatterer('C2', site=(2.5, 1, 0)) self.h = xray.scatterer('H') self.reparam = constraints.ext.reparametrisation(self.cs.unit_cell()) xo = self.reparam.add(constraints.independent_site_parameter, self.o) x1 = self.reparam.add(constraints.independent_site_parameter, self.c1) x2 = self.reparam.add(constraints.independent_site_parameter, self.c2) l = self.reparam.add(constraints.independent_scalar_parameter, value=self.bond_length, variable=False) phi = self.reparam.add(constraints.independent_scalar_parameter, value=0, variable=False) uc = self.cs.unit_cell() _ = mat.col if staggered: xh = self.reparam.add( constraints.staggered_terminal_tetrahedral_xh_site, pivot=xo, pivot_neighbour=x1, stagger_on=x2, length=l, hydrogen=(self.h,)) else: xh = self.reparam.add( constraints.terminal_tetrahedral_xh_site, pivot=xo, pivot_neighbour=x1, azimuth=phi, length=l, e_zero_azimuth=uc.orthogonalize(_(self.c2.site) - _(self.c1.site)), hydrogen=(self.h,)) self.reparam.finalise() self.xh, self.xo, self.x1, self.x2 = [ x.index for x in (xh, xo, x1, x2) ] self.l, self.phi = l.index, phi.index
def dummy_structure(space_group_info, volume, n_scatterers): structure = xray.structure( special_position_settings=crystal.special_position_settings( crystal_symmetry=crystal.symmetry( unit_cell=space_group_info.any_compatible_unit_cell(volume=volume), space_group_info=space_group_info))) b_iso = 20 u_iso = adptbx.b_as_u(b_iso) u_star = adptbx.u_iso_as_u_star(structure.unit_cell(), u_iso) scatterer = xray.scatterer(label="C", site=(0.123,0.234,0.345), u=u_star) for i in xrange(n_scatterers): structure.add_scatterer(scatterer) return structure
def build_xray_structure_with_carbon_along_x(a, b_iso, x=[0]): result = xray.structure( crystal_symmetry=crystal.symmetry( unit_cell=(a,a,a,90,90,90), space_group_symbol="P1")) for i,v in enumerate(x): result.add_scatterer(xray.scatterer( label="C%d" % (i+1), scattering_type="C", site=(v,0,0), b=b_iso)) reg = result.scattering_type_registry(table="n_gaussian", d_min=1/12) g = reg.as_type_gaussian_dict()["C"] assert g.n_terms() == 5 assert not g.use_c() return result
def __init__(self, n_runs, **kwds): libtbx.adopt_optional_init_args(self, kwds) self.n_runs = n_runs self.crystal_symmetry = crystal.symmetry( unit_cell=uctbx.unit_cell((5.1534, 5.1534, 8.6522, 90, 90, 120)), space_group_symbol='Hall: P 6c') self.structure = xray.structure( self.crystal_symmetry.special_position_settings(), flex.xray_scatterer( (xray.scatterer('K1', site=(0, 0, -0.00195), u=self.u_cif_as_u_star( (0.02427, 0.02427, 0.02379, 0.01214, 0.00000, 0.00000))), xray.scatterer('S1', site=(1 / 3, 2 / 3, 0.204215), u=self.u_cif_as_u_star( (0.01423, 0.01423, 0.01496, 0.00712, 0.00000, 0.00000))), xray.scatterer('Li1', site=(1 / 3, 2 / 3, 0.815681), u=self.u_cif_as_u_star( (0.02132, 0.02132, 0.02256, 0.01066, 0.00000, 0.00000))), xray.scatterer('O1', site=(1 / 3, 2 / 3, 0.035931), u=self.u_cif_as_u_star( (0.06532, 0.06532, 0.01669, 0.03266, 0.00000, 0.00000))), xray.scatterer('O2', site=(0.343810, 0.941658, 0.258405), u=self.u_cif_as_u_star( (0.02639, 0.02079, 0.05284, 0.01194, -0.00053, -0.01180)))))) mi = self.crystal_symmetry.build_miller_set(anomalous_flag=False, d_min=0.5) fo_sq = mi.structure_factors_from_scatterers( self.structure, algorithm="direct").f_calc().norm() self.fo_sq = fo_sq.customized_copy(sigmas=flex.double(fo_sq.size(), 1))
def exercise_u_iso_proportional_to_pivot_u_iso(): # Test working constraint xs = xray.structure(crystal_symmetry=crystal.symmetry( unit_cell=(), space_group_symbol='hall: P 2x 2y'), scatterers=flex.xray_scatterer(( xray.scatterer('C0', u=0.12), xray.scatterer('C1'), ))) r = constraints.ext.reparametrisation(xs.unit_cell()) sc = xs.scatterers() u_iso = r.add(constraints.independent_u_iso_parameter, sc[0]) u_iso_1 = r.add(constraints.u_iso_proportional_to_pivot_u_iso, pivot_u_iso=u_iso, multiplier=2, scatterer=sc[1]) r.finalise() r.linearise() assert approx_equal(u_iso_1.value, 0.24, eps=1e-15) # Test conflicting constraints xs = xray.structure( crystal_symmetry=crystal.symmetry(unit_cell=(), space_group_symbol='hall: P 2x 2y'), scatterers=flex.xray_scatterer( (xray.scatterer('C0', u=0.12), xray.scatterer('C1', u=0.21), xray.scatterer('C2')))) with warnings.catch_warnings(record=True) as w: warnings.simplefilter("always") r = constraints.reparametrisation( structure=xs, constraints=[ constraints.adp.shared_u((0, 2)), constraints.adp.shared_u((1, 2)) ], connectivity_table=smtbx.utils.connectivity_table(xs)) assert len(w) == 1 assert w[-1].category == constraints.ConflictingConstraintWarning assert w[-1].message.conflicts == set(((2, 'U'), ))
def __init__(self): self.size_value = 9 self.rx = pi self.ry = pi/2 self.rz = pi/3 self.sites = ((0,0,0), (1,0,0), (0,1,0), (0,0,1)) self.uc = uctbx.unit_cell((1, 1, 1)) self.xs = xray.structure( crystal_symmetry=crystal.symmetry( unit_cell=self.uc, space_group_symbol='hall: P 2x 2y'), scatterers=flex.xray_scatterer(( #triangle xray.scatterer('C0'), xray.scatterer('C1'), xray.scatterer('C2'), xray.scatterer('C3'), ))) self.center = col((0,0,0)) for s in self.sites: self.center = self.center + col(s) self.center = self.center / len(self.sites) self.reset_sites()
def exercise_2(): symmetry = crystal.symmetry(unit_cell=(5.67, 10.37, 10.37, 90, 135.49, 90), space_group_symbol="C2") structure = xray.structure(crystal_symmetry=symmetry) atmrad = flex.double() xyzf = flex.vec3_double() for k in xrange(100): scatterer = xray.scatterer(site=((1. + k * abs(math.sin(k))) / 1000.0, (1. + k * abs(math.cos(k))) / 1000.0, (1. + k) / 1000.0), scattering_type="C") structure.add_scatterer(scatterer) atmrad.append( van_der_waals_radii.vdw.table[scatterer.element_symbol()]) xyzf.append(scatterer.site) miller_set = miller.build_set(crystal_symmetry=structure, d_min=1.0, anomalous_flag=False) step = 0.5 crystal_gridding = maptbx.crystal_gridding(unit_cell=structure.unit_cell(), step=step) nxyz = crystal_gridding.n_real() shrink_truncation_radius = 1.0 solvent_radius = 1.0 m1 = around_atoms(structure.unit_cell(), structure.space_group().order_z(), structure.sites_frac(), atmrad, nxyz, solvent_radius, shrink_truncation_radius) assert m1.solvent_radius == 1 assert m1.shrink_truncation_radius == 1 assert flex.max(m1.data) == 1 assert flex.min(m1.data) == 0 assert m1.data.size() == m1.data.count(1) + m1.data.count(0) m2 = mmtbx.masks.bulk_solvent( xray_structure=structure, gridding_n_real=nxyz, ignore_zero_occupancy_atoms=False, solvent_radius=solvent_radius, shrink_truncation_radius=shrink_truncation_radius) assert m2.data.all_eq(m1.data) m3 = mmtbx.masks.bulk_solvent( xray_structure=structure, grid_step=step, ignore_zero_occupancy_atoms=False, solvent_radius=solvent_radius, shrink_truncation_radius=shrink_truncation_radius) assert m3.data.all_eq(m1.data) f_mask2 = m2.structure_factors(miller_set=miller_set) f_mask3 = m3.structure_factors(miller_set=miller_set) assert approx_equal(f_mask2.data(), f_mask3.data()) assert approx_equal(flex.sum(flex.abs(f_mask3.data())), 1095.17999134)
def exercise_extract_u_cart_plus_u_iso(): from cctbx import uctbx, sgtbx, xray uc = uctbx.unit_cell((1,1,1)) sg = sgtbx.space_group_info("P 1") a = flex.xray_scatterer() assert a.size() == 0 s1 = xray.scatterer(label = "C", u = 0.1) s2 = xray.scatterer(label = "C", u = 0.1) s2.flags.set_use_u_iso(False) s3 = xray.scatterer(label = "C", u = (1,1,1,1,1,1)) s4 = xray.scatterer(label = "C", u = (1,1,1,1,1,1)) s4.flags.set_use_u_aniso(False) s5 = xray.scatterer(label = "C", u = 0.1) s5.u_star=(1,1,1,1,1,1) s5.flags.set_use_u_aniso(True) s6 = xray.scatterer(label = "C", u = 0.1) s6.u_star=(1,1,1,1,1,1) s7 = xray.scatterer(label = "C", u = (1,1,1,1,1,1)) s7.u_iso=0.1 s8 = xray.scatterer(label = "C", u = (1,1,1,1,1,1)) s8.u_iso=0.1 s8.flags.set_use_u_iso(True) s9 = xray.scatterer(label = "C") s10 = xray.scatterer(label = "C") s10.flags.set_use_u_iso(False) a = flex.xray_scatterer((s1,s2,s3,s4,s5,s6,s7,s8,s9,s10)) u_cart_total = a.extract_u_cart_plus_u_iso(uc) assert approx_equal(u_cart_total, [(0.1,0.1,0.1,0,0,0), (0,0,0,0,0,0), (1,1,1,1,1,1), (0,0,0,0,0,0), (1.1,1.1,1.1,1,1,1), (0.1,0.1,0.1,0,0,0), (1,1,1,1,1,1), (1.1,1.1,1.1,1,1,1), (0,0,0,0,0,0), (0,0,0,0,0,0)])
def expand_cell(scatterers, direction, number): for atom in scatterers: print atom.label, number site = list(atom.site) coord = site[direction] for n in range(number): n = float(n) new = (coord / number) + (n / number) site[direction] = new label = atom.label+chr(97+int(n)) # 97 => a yield xray.scatterer(label=label, site=site, u=atom.u_iso, occupancy=atom.occupancy)
def as_xray_scatterer(self, unit_cell=None): scattering_type = eltbx.xray_scattering.get_standard_label( label=self.type, exact=False, optional=True) if (scattering_type is None): scattering_type = eltbx.xray_scattering.get_standard_label( label=self.segid, exact=False, optional=True) if (scattering_type is None): scattering_type = "unknown" site = (self.x, self.y, self.z) if (unit_cell is not None): site = unit_cell.fractionalize(site) return xray.scatterer(label="_".join((self.segid, self.type)), site=site, u=adptbx.b_as_u(self.b), occupancy=self.q, scattering_type=scattering_type)
def debug_write_reciprocal_lattice_points_as_pdb( self, file_name="reciprocal_lattice.pdb" ): from cctbx import crystal, xray cs = crystal.symmetry( unit_cell=(1000, 1000, 1000, 90, 90, 90), space_group="P1" ) xs = xray.structure(crystal_symmetry=cs) for site in self.trial_sites: xs.add_scatterer(xray.scatterer("C", site=site)) xs.sites_mod_short() with open(file_name, "wb") as f: print(xs.as_pdb_file(), file=f)
def debug_write_reciprocal_lattice_points_as_pdb( points, file_name="reciprocal_lattice.pdb" ): from cctbx import crystal, xray cs = crystal.symmetry(unit_cell=(1000, 1000, 1000, 90, 90, 90), space_group="P1") xs = xray.structure(crystal_symmetry=cs) sel = flex.random_selection(points.size(), min(20000, points.size())) rsp = points.select(sel) for site in rsp: xs.add_scatterer(xray.scatterer("C", site=site)) xs.sites_mod_short() with open(file_name, "wb") as f: print(xs.as_pdb_file(), file=f)
def test_rigid_pivoted_rotatable(): uc = uctbx.unit_cell((1, 1, 1)) xs = xray.structure( crystal_symmetry=crystal.symmetry(unit_cell=uc, space_group_symbol='hall: P 2x 2y'), scatterers=flex.xray_scatterer(( #triangle xray.scatterer('C0', site=(0, 0, 0)), xray.scatterer('C1', site=(0, 2, 0)), xray.scatterer('C2', site=(1, 1, 0)), ))) r = constraints.ext.reparametrisation(xs.unit_cell()) sc = xs.scatterers() pivot = r.add(constraints.independent_site_parameter, sc[0]) pivot_neighbour = r.add(constraints.independent_site_parameter, sc[1]) azimuth = r.add(constraints.independent_scalar_parameter, value=math.pi / 2, variable=True) size = r.add(constraints.independent_scalar_parameter, value=1, variable=False) rg = r.add(constraints.rigid_pivoted_rotatable_group, pivot=pivot, pivot_neighbour=pivot_neighbour, azimuth=azimuth, size=size, scatterers=(sc[1], sc[2])) site_proxy = r.add(constraints.rigid_site_proxy, rg, 1) r.finalise() r.linearise() r.store() #check that proxy and the final results are the same... assert uc.distance(col(site_proxy.value), col(sc[2].site)) == pytest.approx(0, abs=1e-15) #rotation happens around the center of gravity assert uc.distance(col((0, 1, 1)), col(sc[2].site)) == pytest.approx(0, abs=1e-15)
def scatterers(O, u_iso=0): assert O.types is not None from cctbx import xray from cctbx.array_family import flex result = flex.xray_scatterer() sites = iter(O.sites) for type,count in zip(O.types, O.type_counts): for _ in range(count): result.append(xray.scatterer( label="%s%d"%(type, len(result)+1), scattering_type=type, site=next(sites), u=u_iso)) assert len(result) == len(O.sites) return result