cctbx.geometry_restraints package

Submodules

• cctbx.geometry_restraints.energies module
  • energies
    • energies.angle_deviations()
    • energies.angle_deviations_weighted()
    • energies.angle_deviations_z()
    • energies.bond_deviations()
    • energies.bond_deviations_weighted()
    • energies.bond_deviations_z()
    • energies.chirality_deviations()
    • energies.dihedral_deviations()
    • energies.get_angle_outliers()
    • energies.get_bond_outliers()
    • energies.get_chirality_outliers()
    • energies.get_dihedral_outliers()
    • energies.get_filtered_n_angle_proxies()
    • energies.get_filtered_n_bond_proxies()
    • energies.get_filtered_n_dihedral_proxies()
    • energies.get_filtered_n_planarity_proxies()
    • energies.nonbonded_deviations()
    • energies.nonbonded_distances()
    • energies.parallelity_deviations()
    • energies.planarity_deviations()
    • energies.reference_dihedral_deviations()
    • energies.show()
• cctbx.geometry_restraints.flags module
  • flags
    • flags.show()
• cctbx.geometry_restraints.lbfgs module
  • empty
  • lbfgs
    • lbfgs.apply_shifts()
    • lbfgs.compute_functional_and_gradients()
    • lbfgs.compute_target()
• cctbx.geometry_restraints.manager module
  • construct_non_crystallographic_conserving_bonds_and_angles()
  • format_distances_for_error_message()
  • manager
    • manager.add_angles_in_place()
    • manager.add_chi_torsion_restraints_in_place()
    • manager.add_dihedrals_in_place()
    • manager.add_new_bond_restraints_in_place()
    • manager.add_new_hbond_restraints_in_place()
    • manager.add_parallelities_in_place()
    • manager.add_planarities_in_place()
    • manager.add_reference_coordinate_restraints_in_place()
    • manager.adopt_den_manager()
    • manager.adopt_reference_coordinate_restraints_in_place()
    • manager.adopt_reference_dihedral_manager()
    • manager.append_reference_coordinate_restraints_in_place()
    • manager.construct_tardy_tree()
    • manager.create_den_manager()
    • manager.discard_symmetry()
    • manager.energies_sites()
    • manager.get_all_angle_proxies()
    • manager.get_all_bond_proxies()
    • manager.get_angle_proxies_without_user_supplied()
    • manager.get_bond_proxies_without_user_supplied()
    • manager.get_c_beta_torsion_proxies()
    • manager.get_chi_torsion_proxies()
    • manager.get_cif_link_entries()
    • manager.get_covalent_angle_proxies()
    • manager.get_covalent_bond_proxies()
    • manager.get_dihedral_proxies()
    • manager.get_dihedral_proxies_without_user_supplied()
    • manager.get_hbond_proxies_iseqs()
    • manager.get_n_angle_proxies()
    • manager.get_n_bond_proxies()
    • manager.get_n_c_beta_torsion_proxies()
    • manager.get_n_chi_torsion_proixes()
    • manager.get_n_den_proxies()
    • manager.get_n_hangle_proxies()
    • manager.get_n_hbond_proxies()
    • manager.get_n_parallelity_bp_proxies()
    • manager.get_n_planarity_bp_proxies()
    • manager.get_n_planarity_proxies()
    • manager.get_n_ramachandran_proxies()
    • manager.get_n_reference_coordinate_proxies()
    • manager.get_n_reference_dihedral_proxies()
    • manager.get_n_stacking_proxies()
    • manager.get_parallelity_proxies_without_user_supplied()
    • manager.get_planarity_proxies_without_user_supplied()
    • manager.get_reference_coordinate_proxies()
    • manager.get_struct_conn_mmcif()
    • manager.get_user_supplied_restraints()
    • manager.harmonic_restraints()
    • manager.is_bonded_atoms()
    • manager.new_included_bonded_atoms()
    • manager.new_including_isolated_sites()
    • manager.nonbonded_model_distances()
    • manager.pair_proxies()
    • manager.reduce_for_tardy()
    • manager.remove_angles_in_place()
    • manager.remove_c_beta_torsion_restraints_in_place()
    • manager.remove_chi_torsion_restraints_in_place()
    • manager.remove_chiralities_in_place()
    • manager.remove_dihedrals_in_place()
    • manager.remove_ncs_dihedrals_in_place()
    • manager.remove_parallelities_in_place()
    • manager.remove_planarities_in_place()
    • manager.remove_ramachandran_in_place()
    • manager.remove_reference_coordinate_restraints_in_place()
    • manager.remove_reference_dihedral_manager()
    • manager.remove_reference_dihedrals_in_place()
    • manager.remove_secondary_structure_restraints()
    • manager.remove_user_supplied_restraints_in_place()
    • manager.replace_site_symmetry()
    • manager.reset_internals()
    • manager.rigid_clusters_due_to_dihedrals_and_planes()
    • manager.select()
    • manager.set_external_energy_function()
    • manager.set_ramachandran_restraints()
    • manager.set_secondary_structure_restraints()
    • manager.shift_sites_cart()
    • manager.show_sorted()
    • manager.simple_edge_list()
    • manager.sites_cart_used_for_pair_proxies()
    • manager.sync_reference_dihedral_with_ncs()
    • manager.ta_harmonic_restraints()
    • manager.update_atom_nonbonded_type()
    • manager.update_dihedral_ncs_restraints()
    • manager.update_plain_pair_sym_table()
    • manager.update_ramachandran_restraints_phi_psi_targets()
    • manager.write_geo_file()

Module contents

cctbx.geometry_restraints.angle_delta_deg(angle_1, angle_2, periodicity=1)

class cctbx.geometry_restraints.angle_proxy_registry(strict_conflict_handling)

Bases: proxy_registry_base

self.table: nested dicts

{ iseq1:

{

(iseq0, iseq2) : Nproxy

}

}

add_if_not_duplicated(proxy, tolerance=1e-06)

expand_with_ncs(nrgl, masters_and_rest_iselection)

lookup_i_proxy(i_seqs)

See also: cctbx::geometry_restraints::angle_proxy::sort_i_seqs()

process(source_info, proxy, tolerance=1e-06)

class cctbx.geometry_restraints.bond_simple_proxy_registry(n_seq, strict_conflict_handling)

Bases: proxy_registry_base

self.table: [ {iseq1: Nproxy} ] , index in this array is iseq0

expand_with_ncs(nrgl, masters_and_rest_iselection)

initialize_table()

is_any_proxy_set(i_seqs, j_seqs)

is_proxy_set(i_seqs)

process(source_info, proxy, tolerance=1e-06)

class cctbx.geometry_restraints.chirality_proxy_registry(strict_conflict_handling)

Bases: proxy_registry_base

self.table - same as dihedral:

{ iseq0:

{

(iseq1, iseq2, iseq3) : Nproxy

}

}

add_if_not_duplicated(proxy, tolerance=1e-06)

expand_with_ncs(nrgl, masters_and_rest_iselection)

process(source_info, proxy, tolerance=1e-06)

class cctbx.geometry_restraints.dihedral_proxy_registry(strict_conflict_handling)

Bases: proxy_registry_base

self.table - similar to angle:

{ iseq0:

{

(iseq1, iseq2, iseq3) : Nproxy

}

}

add_if_not_duplicated(proxy, tolerance=1e-06)

expand_with_ncs(nrgl, masters_and_rest_iselection)

lookup_i_proxy(i_seqs)

See also: cctbx::geometry_restraints::dihedral_proxy::sort_i_seqs()

process(source_info, proxy, tolerance=1e-06)

class cctbx.geometry_restraints.pair_proxies(flags=None, bond_params_table=None, shell_asu_tables=None, model_indices=None, conformer_indices=None, sym_excl_indices=None, donor_acceptor_excl_groups=None, nonbonded_params=None, nonbonded_types=None, nonbonded_charges=None, nonbonded_distance_cutoff_plus_buffer=None, min_cubicle_edge=5)

Bases: object

class cctbx.geometry_restraints.parallelity_proxy_registry(strict_conflict_handling)

Bases: proxy_registry_base

self.table: { ( (iseqs), (jseqs) ) : Nproxy }

add_if_not_duplicated(proxy, tolerance=1e-06)

expand_with_ncs(nrgl, masters_and_rest_iselection)

process(source_info, proxy, tolerance=1e-06)

class cctbx.geometry_restraints.planarity_proxy_registry(strict_conflict_handling)

Bases: proxy_registry_base

self.table:

self.table - similar to dihedral, chiralities, but undefined

number of iseqs in the nested dictionary keys:

{ iseq0:

{

(iseq1, iseq2, iseq3, … ) : Nproxy

}

}

add_if_not_duplicated(proxy, tolerance=1e-06)

expand_with_ncs(nrgl, masters_and_rest_iselection)

process(source_info, proxy, tolerance=1e-06)

class cctbx.geometry_restraints.proxy_registry_base(proxies, strict_conflict_handling)

Bases: object

append_custom_proxy(proxy)

discard_table()

initialize_table()

class cctbx.geometry_restraints.proxy_registry_process_result(tabulated_proxy=None, is_new=False, is_conflicting=False, conflict_source_labels=None)

Bases: object

cctbx.geometry_restraints.resid_to_pymol(resid)

cctbx.geometry_restraints.sigma_as_weight(sigma)

cctbx.geometry_restraints.weight_as_sigma(weight)