def _nonbonded_pair_objects( max_bonded_cutoff=3., i_seqs=None, ): if i_seqs is None: atoms = self.pdb_hierarchy.atoms() i_seqs = flex.size_t() for atom in atoms: i_seqs.append(atom.i_seq) if (self.model_indices is not None): model_indices = self.model_indices.select(i_seqs) conformer_indices = self.conformer_indices.select(i_seqs) sym_excl_indices = self.sym_excl_indices.select(i_seqs) donor_acceptor_excl_groups = self.donor_acceptor_excl_groups.select( i_seqs) asu_mappings = self.special_position_settings.asu_mappings( buffer_thickness=max_bonded_cutoff) sites_cart = self.sites_cart.select(i_seqs) asu_mappings.process_sites_cart( original_sites=sites_cart, site_symmetry_table=self.site_symmetry_table().select(i_seqs)) pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings) nonbonded_proxies = geometry_restraints.nonbonded_sorted_asu_proxies( model_indices=model_indices, conformer_indices=conformer_indices, sym_excl_indices=sym_excl_indices, donor_acceptor_excl_groups=donor_acceptor_excl_groups, nonbonded_params=geometry_restraints.nonbonded_params( default_distance=1), nonbonded_types=flex.std_string(conformer_indices.size()), nonbonded_charges=flex.int(conformer_indices.size(), 0), nonbonded_distance_cutoff_plus_buffer=max_bonded_cutoff, min_cubicle_edge=5, shell_asu_tables=[pair_asu_table]) return nonbonded_proxies, sites_cart, pair_asu_table, asu_mappings, i_seqs
def _nonbonded_pair_objects(max_bonded_cutoff=3., i_seqs=None, ): if i_seqs is None: atoms = self.pdb_hierarchy.atoms() i_seqs = flex.size_t() for atom in atoms: i_seqs.append(atom.i_seq) if (self.model_indices is not None): model_indices = self.model_indices.select(i_seqs) conformer_indices = self.conformer_indices.select(i_seqs) sym_excl_indices = self.sym_excl_indices.select(i_seqs) donor_acceptor_excl_groups = self.donor_acceptor_excl_groups.select(i_seqs) asu_mappings = self.special_position_settings.asu_mappings( buffer_thickness=max_bonded_cutoff) sites_cart = self.sites_cart.select(i_seqs) asu_mappings.process_sites_cart( original_sites=sites_cart, site_symmetry_table=self.site_symmetry_table().select(i_seqs)) pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings) nonbonded_proxies = geometry_restraints.nonbonded_sorted_asu_proxies( model_indices=model_indices, conformer_indices=conformer_indices, sym_excl_indices=sym_excl_indices, donor_acceptor_excl_groups=donor_acceptor_excl_groups, nonbonded_params=geometry_restraints.nonbonded_params( default_distance=1), nonbonded_types=flex.std_string(conformer_indices.size()), nonbonded_charges=flex.int(conformer_indices.size(), 0), nonbonded_distance_cutoff_plus_buffer=max_bonded_cutoff, min_cubicle_edge=5, shell_asu_tables=[pair_asu_table]) return nonbonded_proxies, sites_cart, pair_asu_table, asu_mappings, i_seqs
def exercise_with_zeolite(verbose): if (not libtbx.env.has_module("iotbx")): print("Skipping exercise_with_zeolite(): iotbx not available") return from iotbx.kriber import strudat atlas_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/misc/strudat_zeolite_atlas", test=os.path.isfile) if (atlas_file is None): print("Skipping exercise_with_zeolite(): input file not available") return strudat_contents = strudat.read_all_entries(open(atlas_file)) strudat_entry = strudat_contents.get("YUG") si_structure = strudat_entry.as_xray_structure() if (verbose): out = sys.stdout else: out = StringIO() drls = distance_and_repulsion_least_squares( si_structure=si_structure, distance_cutoff=3.5, nonbonded_repulsion_function_type="prolsq", n_macro_cycles=2, out=out) # nbp = drls.geometry_restraints_manager.pair_proxies().nonbonded_proxies assert nbp.n_total() > 50 # expected is 60, but the exact number depends on the minimizer # site_labels = drls.minimized_structure.scatterers().extract_labels() sites_cart = drls.start_structure.sites_cart() pair_proxies = drls.geometry_restraints_manager.pair_proxies() out = StringIO() pair_proxies.bond_proxies.show_sorted(by_value="residual", sites_cart=sites_cart, site_labels=site_labels, f=out) if (verbose): sys.stdout.write(out.getvalue()) assert len(out.getvalue().splitlines()) == 48 * 4 + 2 assert out.getvalue().splitlines()[-1].find("remaining") < 0 out = StringIO() pair_proxies.bond_proxies.show_sorted(by_value="residual", sites_cart=sites_cart, site_labels=site_labels, f=out, prefix="0^", max_items=28) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\ 0^Bond restraints: 48 0^Sorted by residual: 0^bond O3 0^ O4 0^ ideal model delta sigma weight residual 0^ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01 ... 0^bond SI1 0^ SI1 0^ ideal model delta sigma weight residual sym.op. 0^ 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1 0^... (remaining 20 not shown) """, selections=[range(6), range(-5, 0)]) out = StringIO() pair_proxies.bond_proxies.show_sorted(by_value="delta", sites_cart=sites_cart, site_labels=site_labels, f=out, prefix="0^", max_items=28) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\ 0^Bond restraints: 48 0^Sorted by delta: 0^bond O3 0^ O4 0^ ideal model delta sigma weight residual 0^ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01 ... 0^... (remaining 20 not shown) """, selections=[range(6), [-1]]) site_labels_long = ["abc" + label + "def" for label in site_labels] out = StringIO() pair_proxies.bond_proxies.show_sorted(by_value="residual", sites_cart=sites_cart, site_labels=site_labels_long, f=out, prefix="^0", max_items=28) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\ ^0Bond restraints: 48 ^0Sorted by residual: ^0bond abcO3def ^0 abcO4def ^0 ideal model delta sigma weight residual ^0 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01 ... ^0bond abcSI1def ^0 abcSI1def ^0 ideal model delta sigma weight residual sym.op. ^0 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1 ^0... (remaining 20 not shown) """, selections=[range(6), range(-5, 0)]) out = StringIO() pair_proxies.bond_proxies.show_sorted(by_value="residual", sites_cart=sites_cart, f=out, prefix=".=", max_items=28) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\ .=Bond restraints: 48 .=Sorted by residual: .=bond 4 .= 5 .= ideal model delta sigma weight residual .= 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01 ... .=bond 0 .= 0 .= ideal model delta sigma weight residual sym.op. .= 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1 .=... (remaining 20 not shown) """, selections=[range(6), range(-5, 0)]) out = StringIO() pair_proxies.bond_proxies.show_sorted(by_value="residual", sites_cart=sites_cart, f=out, prefix="-+", max_items=1) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff( out.getvalue().replace("e-00", "e-0"), """\ -+Bond restraints: 48 -+Sorted by residual: -+bond 4 -+ 5 -+ ideal model delta sigma weight residual -+ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01 -+... (remaining 47 not shown) """) out = StringIO() pair_proxies.bond_proxies.show_sorted(by_value="residual", sites_cart=sites_cart, f=out, prefix="=+", max_items=0) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff( out.getvalue(), """\ =+Bond restraints: 48 =+Sorted by residual: =+... (remaining 48 not shown) """) # sites_cart = si_structure.sites_cart() site_labels = [sc.label for sc in si_structure.scatterers()] asu_mappings = si_structure.asu_mappings(buffer_thickness=3.5) for min_cubicle_edge in [0, 5]: pair_generator = crystal.neighbors_fast_pair_generator( asu_mappings=asu_mappings, distance_cutoff=asu_mappings.buffer_thickness(), minimal=False, min_cubicle_edge=min_cubicle_edge) sorted_asu_proxies = geometry_restraints.nonbonded_sorted_asu_proxies( asu_mappings=asu_mappings) while (not pair_generator.at_end()): p = geometry_restraints.nonbonded_asu_proxy( pair=next(pair_generator), vdw_distance=3) sorted_asu_proxies.process(p) out = StringIO() sorted_asu_proxies.show_sorted(by_value="delta", sites_cart=sites_cart, site_labels=site_labels, f=out, prefix="d%") if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff( out.getvalue(), """\ d%Nonbonded interactions: 7 d%Sorted by model distance: ... d%nonbonded SI2 d% SI2 d% model vdw sym.op. d% 3.092 3.000 -x+1,y,-z ... d%nonbonded SI1 d% SI1 d% model vdw sym.op. d% 3.216 3.000 -x+1/2,-y+1/2,-z+1 """, selections=[range(2), range(10, 14), range(26, 30)]) out = StringIO() sorted_asu_proxies.show_sorted(by_value="delta", sites_cart=sites_cart, f=out, prefix="*j", max_items=5) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue(), """\ *jNonbonded interactions: 7 *jSorted by model distance: ... *jnonbonded 0 *j 1 *j model vdw *j 3.107 3.000 *jnonbonded 0 *j 0 *j model vdw sym.op. *j 3.130 3.000 -x+1,y,-z+1 *j... (remaining 2 not shown) """, selections=[range(2), range(-9, 0)]) out = StringIO() sorted_asu_proxies.show_sorted(by_value="delta", sites_cart=sites_cart, f=out, prefix="@r", max_items=0) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue(), """\ @rNonbonded interactions: 7 """)
def exercise_with_zeolite(verbose): if (not libtbx.env.has_module("iotbx")): print "Skipping exercise_with_zeolite(): iotbx not available" return from iotbx.kriber import strudat atlas_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/misc/strudat_zeolite_atlas", test=os.path.isfile) if (atlas_file is None): print "Skipping exercise_with_zeolite(): input file not available" return strudat_contents = strudat.read_all_entries(open(atlas_file)) strudat_entry = strudat_contents.get("YUG") si_structure = strudat_entry.as_xray_structure() if (verbose): out = sys.stdout else: out = StringIO() drls = distance_and_repulsion_least_squares( si_structure=si_structure, distance_cutoff=3.5, nonbonded_repulsion_function_type="prolsq", n_macro_cycles=2, out=out) # nbp = drls.geometry_restraints_manager.pair_proxies().nonbonded_proxies assert nbp.n_total() > 50 # expected is 60, but the exact number depends on the minimizer # site_labels = drls.minimized_structure.scatterers().extract_labels() sites_cart = drls.start_structure.sites_cart() pair_proxies = drls.geometry_restraints_manager.pair_proxies() out = StringIO() pair_proxies.bond_proxies.show_sorted( by_value="residual", sites_cart=sites_cart, site_labels=site_labels, f=out) if (verbose): sys.stdout.write(out.getvalue()) assert len(out.getvalue().splitlines()) == 48*4+2 assert out.getvalue().splitlines()[-1].find("remaining") < 0 out = StringIO() pair_proxies.bond_proxies.show_sorted( by_value="residual", sites_cart=sites_cart, site_labels=site_labels, f=out, prefix="0^", max_items=28) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\ 0^Bond restraints: 48 0^Sorted by residual: 0^bond O3 0^ O4 0^ ideal model delta sigma weight residual 0^ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01 ... 0^bond SI1 0^ SI1 0^ ideal model delta sigma weight residual sym.op. 0^ 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1 0^... (remaining 20 not shown) """, selections=[range(6), range(-5,0)]) out = StringIO() pair_proxies.bond_proxies.show_sorted( by_value="delta", sites_cart=sites_cart, site_labels=site_labels, f=out, prefix="0^", max_items=28) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\ 0^Bond restraints: 48 0^Sorted by delta: 0^bond O3 0^ O4 0^ ideal model delta sigma weight residual 0^ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01 ... 0^... (remaining 20 not shown) """, selections=[range(6), [-1]]) site_labels_long = ["abc"+label+"def" for label in site_labels] out = StringIO() pair_proxies.bond_proxies.show_sorted( by_value="residual", sites_cart=sites_cart, site_labels=site_labels_long, f=out, prefix="^0", max_items=28) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\ ^0Bond restraints: 48 ^0Sorted by residual: ^0bond abcO3def ^0 abcO4def ^0 ideal model delta sigma weight residual ^0 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01 ... ^0bond abcSI1def ^0 abcSI1def ^0 ideal model delta sigma weight residual sym.op. ^0 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1 ^0... (remaining 20 not shown) """, selections=[range(6), range(-5,0)]) out = StringIO() pair_proxies.bond_proxies.show_sorted( by_value="residual", sites_cart=sites_cart, f=out, prefix=".=", max_items=28) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\ .=Bond restraints: 48 .=Sorted by residual: .=bond 4 .= 5 .= ideal model delta sigma weight residual .= 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01 ... .=bond 0 .= 0 .= ideal model delta sigma weight residual sym.op. .= 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1 .=... (remaining 20 not shown) """, selections=[range(6), range(-5,0)]) out = StringIO() pair_proxies.bond_proxies.show_sorted( by_value="residual", sites_cart=sites_cart, f=out, prefix="-+", max_items=1) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\ -+Bond restraints: 48 -+Sorted by residual: -+bond 4 -+ 5 -+ ideal model delta sigma weight residual -+ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01 -+... (remaining 47 not shown) """) out = StringIO() pair_proxies.bond_proxies.show_sorted( by_value="residual", sites_cart=sites_cart, f=out, prefix="=+", max_items=0) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue(), """\ =+Bond restraints: 48 =+Sorted by residual: =+... (remaining 48 not shown) """) # sites_cart = si_structure.sites_cart() site_labels = [sc.label for sc in si_structure.scatterers()] asu_mappings = si_structure.asu_mappings(buffer_thickness=3.5) for min_cubicle_edge in [0, 5]: pair_generator = crystal.neighbors_fast_pair_generator( asu_mappings=asu_mappings, distance_cutoff=asu_mappings.buffer_thickness(), minimal=False, min_cubicle_edge=min_cubicle_edge) sorted_asu_proxies = geometry_restraints.nonbonded_sorted_asu_proxies( asu_mappings=asu_mappings) while (not pair_generator.at_end()): p = geometry_restraints.nonbonded_asu_proxy( pair=pair_generator.next(), vdw_distance=3) sorted_asu_proxies.process(p) out = StringIO() sorted_asu_proxies.show_sorted( by_value="delta", sites_cart=sites_cart, site_labels=site_labels, f=out, prefix="d%") if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue(), """\ d%Nonbonded interactions: 7 d%Sorted by model distance: ... d%nonbonded SI2 d% SI2 d% model vdw sym.op. d% 3.092 3.000 -x+1,y,-z ... d%nonbonded SI1 d% SI1 d% model vdw sym.op. d% 3.216 3.000 -x+1/2,-y+1/2,-z+1 """, selections=[range(2), range(10,14), range(26,30)]) out = StringIO() sorted_asu_proxies.show_sorted( by_value="delta", sites_cart=sites_cart, f=out, prefix="*j", max_items=5) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue(), """\ *jNonbonded interactions: 7 *jSorted by model distance: ... *jnonbonded 0 *j 1 *j model vdw *j 3.107 3.000 *jnonbonded 0 *j 0 *j model vdw sym.op. *j 3.130 3.000 -x+1,y,-z+1 *j... (remaining 2 not shown) """, selections=[range(2), range(-9,0)]) out = StringIO() sorted_asu_proxies.show_sorted( by_value="delta", sites_cart=sites_cart, f=out, prefix="@r", max_items=0) if (verbose): sys.stdout.write(out.getvalue()) assert not show_diff(out.getvalue(), """\ @rNonbonded interactions: 7 """)