| ::ConformationTests class | core::conformation::Conformation | friend |
| aa(Size seqpos) const | core::conformation::Conformation | inline |
| add_parameters_set(ParametersSetOP newset) | core::conformation::Conformation | |
| add_pseudobond(Size lr, Size lr_connid, Size ur, Size ur_connid, Size nbonds) | core::conformation::Conformation | private |
| align_virtual_atoms_in_carbohydrate_residue(uint const sequence_position) | core::conformation::Conformation | |
| annotated_sequence(bool show_all_variants) const | core::conformation::Conformation | |
| append_polymer_residue_after_seqpos(Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry) | core::conformation::Conformation | virtual |
| append_residue(Residue const &new_rsd_in, bool const attach_by_jump, std::string const &root_atom, id::NamedAtomID anchor_id, bool const start_new_chain) | core::conformation::Conformation | private |
| append_residue_by_bond(conformation::Residue const &new_rsd, bool const build_ideal_geometry=false, int connection_index=0, Size anchor_residue=0, int anchor_connection_index=0, bool const start_new_chain=false, bool const lookup_bond_length=false) | core::conformation::Conformation | |
| append_residue_by_jump(conformation::Residue const &new_rsd, Size const anchor_residue, std::string const &anchor_atom="", std::string const &root_atom="", bool const start_new_chain=false) | core::conformation::Conformation | virtual |
| apply_transform_Rx_plus_v(numeric::xyzMatrix< Real > const &R, Vector const &v) | core::conformation::Conformation | virtual |
| atom_is_backbone_norefold(Size pos, Size atomno) const | core::conformation::Conformation | |
| atom_tree() const | core::conformation::Conformation | inline |
| atom_tree_ | core::conformation::Conformation | private |
| atom_tree_torsion(TorsionID const &tor_id) const | core::conformation::Conformation | private |
| AtomID typedef | core::conformation::Conformation | |
| AtomID_Mask typedef | core::conformation::Conformation | |
| atoms_are_bonded(AtomID const &id1, AtomID const &id2) const | core::conformation::Conformation | |
| AtomTree typedef | core::conformation::Conformation | |
| AtomTreeOP typedef | core::conformation::Conformation | |
| attach_connection_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
| attach_general_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
| attach_identity_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
| attach_length_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
| attach_xyz_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
| backbone_torsion_angle_atoms(TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const | core::conformation::Conformation | |
| backbone_torsion_angle_atoms_meta_aramid(TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const | core::conformation::Conformation | private |
| backbone_torsion_angle_atoms_oligourea(TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const | core::conformation::Conformation | private |
| backbone_torsion_angle_atoms_ortho_aramid(TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const | core::conformation::Conformation | private |
| backbone_torsion_angle_atoms_para_aramid(TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const | core::conformation::Conformation | private |
| batch_get_xyz(utility::vector1< AtomID > const &id, utility::vector1< PointPosition > &position) const | core::conformation::Conformation | virtual |
| batch_set_xyz(utility::vector1< AtomID > const &id, utility::vector1< PointPosition > const &position) | core::conformation::Conformation | virtual |
| begin() noexcept | core::conformation::Conformation | inline |
| begin() const noexcept | core::conformation::Conformation | inline |
| block_signals() | core::conformation::Conformation | |
| blocking_signals() const | core::conformation::Conformation | |
| bond_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3) const | core::conformation::Conformation | |
| bond_length(AtomID const &atom1, AtomID const &atom2) const | core::conformation::Conformation | |
| bond_orientation(AtomID const &atom1, AtomID const &atom2) const | core::conformation::Conformation | |
| bond_orientation(core::id::TorsionID const torsion) const | core::conformation::Conformation | |
| bonded_neighbor_all_res(core::id::AtomID const &atomid, bool virt=false, bool skip_canonical_and_solvent=false, bool intra_res=true, bool inter_res=true) const | core::conformation::Conformation | |
| branch_connection_torsion_angle_atoms(TorsionID const &torsion, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const | core::conformation::Conformation | private |
| buffer_signals() | core::conformation::Conformation | |
| buffering_signals() const | core::conformation::Conformation | |
| chain_begin(Size chain) const | core::conformation::Conformation | inline |
| chain_end(Size chain) const | core::conformation::Conformation | inline |
| chain_endings() const | core::conformation::Conformation | |
| chain_endings(utility::vector1< Size > const &endings) | core::conformation::Conformation | virtual |
| chain_endings_ | core::conformation::Conformation | private |
| chains_from_termini() | core::conformation::Conformation | virtual |
| check_valid_membrane() const | core::conformation::Conformation | |
| clear() | core::conformation::Conformation | |
| clear_glycan_trees() | core::conformation::Conformation | |
| clear_observers() | core::conformation::Conformation | |
| clear_parameters_set_list() | core::conformation::Conformation | |
| clone() const | core::conformation::Conformation | virtual |
| Conformation() | core::conformation::Conformation | |
| Conformation(Conformation const &src) | core::conformation::Conformation | |
| connection_obs_hub_ | core::conformation::Conformation | mutableprivate |
| ConnectionEvent typedef | core::conformation::Conformation | |
| const_iterator typedef | core::conformation::Conformation | |
| const_residue_(Size seqpos) const | core::conformation::Conformation | inlineprotected |
| const_residues() const | core::conformation::Conformation | |
| contains_carbohydrate_residues() const | core::conformation::Conformation | inline |
| contains_carbohydrate_residues(bool setting) | core::conformation::Conformation | inline |
| contains_carbohydrate_residues_ | core::conformation::Conformation | private |
| copy_segment(Size size, Conformation const &src, Size begin, Size src_begin) | core::conformation::Conformation | |
| create_new_parameters_set() | core::conformation::Conformation | |
| debug_pause(bool flag) const | core::conformation::Conformation | |
| debug_pause() const | core::conformation::Conformation | |
| debug_residue_torsions(bool verbose=false) const | core::conformation::Conformation | |
| declare_chemical_bond(Size const seqpos1, std::string const &atom_name1, Size const seqpos2, std::string const &atom_name2) | core::conformation::Conformation | virtual |
| delete_chain_ending(Size const seqpos) | core::conformation::Conformation | virtual |
| delete_polymer_residue(Size const seqpos) | core::conformation::Conformation | virtual |
| delete_residue_range_slow(Size const range_begin, Size const range_end) | core::conformation::Conformation | virtual |
| delete_residue_slow(Size const seqpos) | core::conformation::Conformation | virtual |
| detach_connection_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
| detach_general_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
| detach_identity_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
| detach_length_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
| detach_xyz_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | inline |
| detached_copy(Conformation const &src) | core::conformation::Conformation | virtual |
| detect_bonds() | core::conformation::Conformation | |
| detect_disulfides(utility::vector1< Size > const &disulf_one=utility::vector1< core::Size >(), utility::vector1< Size > const &disulf_two=utility::vector1< core::Size >()) | core::conformation::Conformation | virtual |
| detect_pseudobonds() | core::conformation::Conformation | |
| difference_type typedef | core::conformation::Conformation | |
| dof(DOF_ID const &id) const | core::conformation::Conformation | |
| DOF_ID typedef | core::conformation::Conformation | |
| dof_id_from_atom_ids(id::AtomID const &id1, id::AtomID const &id2, id::AtomID const &id3, id::AtomID const &id4) const | core::conformation::Conformation | |
| dof_id_from_atom_ids(id::AtomID const &id1, id::AtomID const &id2, id::AtomID const &id3) const | core::conformation::Conformation | |
| dof_id_from_atom_ids(id::AtomID const &id1, id::AtomID const &id2) const | core::conformation::Conformation | |
| dof_id_from_atom_ids(utility::vector1< id::AtomID > const &ids) const | core::conformation::Conformation | |
| dof_id_from_torsion_id(TorsionID const &id) const | core::conformation::Conformation | |
| dof_moved_ | core::conformation::Conformation | private |
| DomainMap typedef | core::conformation::Conformation | |
| downstream_jump_stub(int jump_number) const | core::conformation::Conformation | |
| empty() const | core::conformation::Conformation | inline |
| end() noexcept | core::conformation::Conformation | inline |
| end() const noexcept | core::conformation::Conformation | inline |
| fill_missing_atoms(id::AtomID_Mask missing) | core::conformation::Conformation | virtual |
| fix_disulfides(utility::vector1< std::pair< Size, Size > > const &disulf_bonds) | core::conformation::Conformation | virtual |
| fold_tree() const | core::conformation::Conformation | inlinevirtual |
| fold_tree(FoldTree const &fold_tree_in) | core::conformation::Conformation | virtual |
| fold_tree_ | core::conformation::Conformation | private |
| FoldTree typedef | core::conformation::Conformation | |
| FoldTreeOP typedef | core::conformation::Conformation | |
| force_update_residue_coordinates() const | core::conformation::Conformation | protected |
| force_update_residue_torsions() const | core::conformation::Conformation | protected |
| FragRT typedef | core::conformation::Conformation | |
| FragXYZ typedef | core::conformation::Conformation | |
| general_obs_hub_ | core::conformation::Conformation | mutableprivate |
| GeneralEvent typedef | core::conformation::Conformation | |
| get_jump_atom_ids(core::Size jump_number, AtomID &upstream_id, AtomID &downstream_id) const | core::conformation::Conformation | |
| get_residue_mask() const | core::conformation::Conformation | virtual |
| get_residue_weight(core::Size, core::Size) const | core::conformation::Conformation | virtual |
| get_self_ptr() const | core::conformation::Conformation | inline |
| get_self_ptr() | core::conformation::Conformation | inline |
| get_self_weak_ptr() const | core::conformation::Conformation | inline |
| get_self_weak_ptr() | core::conformation::Conformation | inline |
| get_stub_transform(id::StubID const &stub_id1, id::StubID const &stub_id2) const | core::conformation::Conformation | |
| get_torsion_angle_atom_ids(TorsionID const &tor_id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const | core::conformation::Conformation | |
| glycan_tree_set() const | core::conformation::Conformation | |
| has_passport() const | core::conformation::Conformation | inlinevirtual |
| identity_obs_hub_ | core::conformation::Conformation | mutableprivate |
| IdentityEvent typedef | core::conformation::Conformation | |
| in_place_copy(Conformation const &src) | core::conformation::Conformation | private |
| insert_chain_ending(Size const seqpos) | core::conformation::Conformation | virtual |
| insert_conformation_by_jump(Conformation const &conf, Size const insert_seqpos, Size const insert_jumppos, Size const anchor_pos, Size const anchor_jump_number=0, std::string const &anchor_atom="", std::string const &root_atom="") | core::conformation::Conformation | virtual |
| insert_fragment(id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz) | core::conformation::Conformation | virtual |
| insert_ideal_geometry_at_polymer_bond(Size const seqpos) | core::conformation::Conformation | virtual |
| insert_ideal_geometry_at_residue_connection(Size const pos1, Size const connid1) | core::conformation::Conformation | virtual |
| insert_polymer_residue(Residue const &new_rsd_in, Size const seqpos, bool const join_lower, bool const join_upper) | core::conformation::Conformation | private |
| insert_residue_by_bond(Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, bool const build_ideal_geometry=false, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false, bool const lookup_bond_length=false) | core::conformation::Conformation | |
| insert_residue_by_jump(Residue const &new_rsd_in, Size seqpos, Size anchor_pos, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false) | core::conformation::Conformation | |
| inter_residue_connection_partner(Size seqpos, int connection_index) const | core::conformation::Conformation | |
| is_bonded(core::id::AtomID const &atomid1, core::id::AtomID const &atomid2, bool virt=false, bool skip_canonical_and_solvent=false) const | core::conformation::Conformation | |
| is_centroid() const | core::conformation::Conformation | |
| is_fullatom() const | core::conformation::Conformation | |
| is_membrane() const | core::conformation::Conformation | inline |
| is_mixed_mode() const | core::conformation::Conformation | |
| is_protected() const | core::conformation::Conformation | inlinevirtual |
| iterator typedef | core::conformation::Conformation | |
| Jump typedef | core::conformation::Conformation | |
| jump(int jump_number) const | core::conformation::Conformation | |
| jump(AtomID const &id) const | core::conformation::Conformation | |
| jump_atom_id(int jump_number) const | core::conformation::Conformation | |
| length_obs_hub_ | core::conformation::Conformation | mutableprivate |
| LengthEvent typedef | core::conformation::Conformation | |
| membrane_info() | core::conformation::Conformation | |
| membrane_info() const | core::conformation::Conformation | |
| membrane_info_ | core::conformation::Conformation | private |
| modifiable_residue_type_set_for_conf(core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const | core::conformation::Conformation | |
| n_parameters_sets() const | core::conformation::Conformation | |
| notify_connection_obs(ConnectionEvent const &e) const | core::conformation::Conformation | private |
| notify_general_obs(GeneralEvent const &e) const | core::conformation::Conformation | private |
| notify_identity_obs(IdentityEvent const &e, bool fire_general=true) const | core::conformation::Conformation | private |
| notify_length_obs(LengthEvent const &e, bool fire_general=true) const | core::conformation::Conformation | private |
| notify_xyz_obs(XYZEvent const &e, bool fire_general=true) const | core::conformation::Conformation | private |
| num_chains() const | core::conformation::Conformation | inline |
| operator=(Conformation const &src) | core::conformation::Conformation | virtual |
| Parameters typedef | core::conformation::Conformation | |
| parameters_set(core::Size const index) | core::conformation::Conformation | |
| parameters_set(core::Size const index) const | core::conformation::Conformation | |
| parameters_set_ | core::conformation::Conformation | private |
| ParametersCOP typedef | core::conformation::Conformation | |
| ParametersOP typedef | core::conformation::Conformation | |
| ParametersSet typedef | core::conformation::Conformation | |
| ParametersSetCOP typedef | core::conformation::Conformation | |
| ParametersSetOP typedef | core::conformation::Conformation | |
| PartialAtomID typedef | core::conformation::Conformation | |
| pop_passport() | core::conformation::Conformation | inlinevirtual |
| pre_nresidue_change() | core::conformation::Conformation | private |
| prepend_polymer_residue_before_seqpos(Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry) | core::conformation::Conformation | virtual |
| push_passport(core::environment::DofPassportCOP) | core::conformation::Conformation | inlinevirtual |
| rebuild_polymer_bond_dependent_atoms(Size const seqpos) | core::conformation::Conformation | virtual |
| rebuild_polymer_bond_dependent_atoms(Size const seqpos, int const upper_lower) | core::conformation::Conformation | private |
| rebuild_polymer_bond_dependent_atoms_this_residue_only(Size const seqpos) | core::conformation::Conformation | |
| rebuild_residue_connection_dependent_atoms(Size seqpos, Size connid) | core::conformation::Conformation | |
| receive_observers_from(Conformation const &src) | core::conformation::Conformation | |
| rederive_chain_endings() | core::conformation::Conformation | private |
| rederive_chain_ids() | core::conformation::Conformation | private |
| replace_residue(Size const seqpos, Residue const &new_rsd, bool const orient_backbone) | core::conformation::Conformation | virtual |
| replace_residue(Size const seqpos, Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) | core::conformation::Conformation | virtual |
| reset_chain_endings() | core::conformation::Conformation | virtual |
| reset_move_data() | core::conformation::Conformation | virtual |
| reset_residue_type_set_for_conf(core::chemical::PoseResidueTypeSetCOP new_set, core::chemical::TypeSetMode mode=core::chemical::INVALID_t) | core::conformation::Conformation | |
| reset_structure_moved() const | core::conformation::Conformation | inline |
| residue(Size seqpos) const | core::conformation::Conformation | inline |
| residue_(Size seqpos) | core::conformation::Conformation | inlineprivate |
| residue_coordinates_need_updating_ | core::conformation::Conformation | mutableprivate |
| residue_cop(Size seqpos) const | core::conformation::Conformation | inline |
| residue_data(Size seqpos) const | core::conformation::Conformation | inline |
| residue_data(Size seqpos) | core::conformation::Conformation | inline |
| residue_torsions_need_updating_ | core::conformation::Conformation | mutableprivate |
| residue_type(Size seqpos) const | core::conformation::Conformation | inline |
| residue_type_ptr(Size seqpos) const | core::conformation::Conformation | inline |
| residue_type_set_for_conf(core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const | core::conformation::Conformation | |
| residue_type_sets_ | core::conformation::Conformation | private |
| residue_typeset_mode(bool majority=true) const | core::conformation::Conformation | |
| residues_ | core::conformation::Conformation | private |
| residues_append(Residue const &new_rsd, bool start_new_chain, bool by_jump=false, std::string const &root_atom="", id::NamedAtomID anchor_id=id::NamedAtomID::BOGUS_NAMED_ATOM_ID()) | core::conformation::Conformation | private |
| residues_delete(Size seqpos) | core::conformation::Conformation | private |
| residues_insert(Size seqpos, Residue const &new_rsd, bool use_lower_chain=false, bool new_chain=false) | core::conformation::Conformation | private |
| residues_replace(Size seqpos, Residue const &new_rsd) | core::conformation::Conformation | private |
| resolve_partial_atom_id(PartialAtomID const &partial_id) const | core::conformation::Conformation | |
| safely_append_polymer_residue_after_seqpos(Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry) | core::conformation::Conformation | virtual |
| safely_prepend_polymer_residue_before_seqpos(Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry) | core::conformation::Conformation | virtual |
| same_type_as_me(Conformation const &other, bool const recurse=true) const | core::conformation::Conformation | virtual |
| secstruct(Size seqpos) const | core::conformation::Conformation | inline |
| secstruct_ | core::conformation::Conformation | private |
| sequence_matches(Conformation const &other) const | core::conformation::Conformation | |
| set_bond_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, Real const setting) | core::conformation::Conformation | virtual |
| set_bond_length(AtomID const &atom1, AtomID const &atom2, Real const setting) | core::conformation::Conformation | virtual |
| set_dof(DOF_ID const &id, Real const setting) | core::conformation::Conformation | virtual |
| set_dof_moved(AtomID const &id) | core::conformation::Conformation | inlineprivate |
| set_dof_moved(DOF_ID const &id) | core::conformation::Conformation | inlineprivate |
| set_jump(int const jump_number, Jump const &new_jump) | core::conformation::Conformation | virtual |
| set_jump(AtomID const &id, Jump const &new_jump) | core::conformation::Conformation | virtual |
| set_jump_atom_stub_id(id::StubID const &id) | core::conformation::Conformation | |
| set_membrane_info(membrane::MembraneInfoOP mem_info) | core::conformation::Conformation | |
| set_noncanonical_connection(Size res_id_lower, Size lr_conn_id, Size res_id_upper, Size ur_conn_id) | core::conformation::Conformation | |
| set_polymeric_connection(Size res_id_lower, Size res_id_upper) | core::conformation::Conformation | virtual |
| set_secstruct(Size const seqpos, char const setting) | core::conformation::Conformation | inlinevirtual |
| set_stub_transform(id::StubID const &stub_id1, id::StubID const &stub_id2, kinematics::RT const &target_rt) | core::conformation::Conformation | virtual |
| set_torsion(TorsionID const &id, Real const setting) | core::conformation::Conformation | virtual |
| set_torsion_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, Real const setting, bool const quiet=false) | core::conformation::Conformation | virtual |
| set_xyz(AtomID const &id, PointPosition const &position) | core::conformation::Conformation | virtual |
| set_xyz_moved(AtomID const &id) | core::conformation::Conformation | inlineprivate |
| set_xyz_moved(utility::vector1< AtomID > const &ids) | core::conformation::Conformation | inlineprivate |
| setup_atom_tree() | core::conformation::Conformation | private |
| setup_glycan_trees() | core::conformation::Conformation | |
| sever_chemical_bond(Size seqpos1, Size res1_resconn_index, Size seqpos2, Size res2_resconn_index) | core::conformation::Conformation | virtual |
| show_residue_connections() const | core::conformation::Conformation | |
| show_residue_connections(std::ostream &os) const | core::conformation::Conformation | |
| size() const | core::conformation::Conformation | inline |
| size_type typedef | core::conformation::Conformation | |
| structure_moved() const | core::conformation::Conformation | inline |
| structure_moved_ | core::conformation::Conformation | mutableprivate |
| stub_from_id(id::StubID const &id) const | core::conformation::Conformation | |
| torsion(TorsionID const &id) const | core::conformation::Conformation | |
| torsion_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4) const | core::conformation::Conformation | |
| TorsionID typedef | core::conformation::Conformation | |
| tree_set_observer_ | core::conformation::Conformation | private |
| unblock_signals() | core::conformation::Conformation | |
| update_actcoord(Size resid) | core::conformation::Conformation | |
| update_actcoords() | core::conformation::Conformation | |
| update_domain_map(DomainMap &domain_map) const | core::conformation::Conformation | |
| update_membrane_position(Vector center, Vector normal) | core::conformation::Conformation | |
| update_noncanonical_connection(Size lower_seqpos, Size lr_conn_id, Size upper_seqpos, Size ur_conn_id) | core::conformation::Conformation | virtual |
| update_orbital_coords(Residue &rsd) const | core::conformation::Conformation | |
| update_orbital_coords(Size resid) | core::conformation::Conformation | |
| update_polymeric_connection(Size lower_seqpos, bool update_connection_dep_atoms=false) | core::conformation::Conformation | |
| update_residue_coordinates() const | core::conformation::Conformation | private |
| update_residue_coordinates(Size seqpos, bool fire_signal=true) const | core::conformation::Conformation | private |
| update_residue_torsions() const | core::conformation::Conformation | private |
| update_residue_torsions(Size seqpos, bool fire_signal=true) const | core::conformation::Conformation | private |
| update_sequence_numbering(Size new_size, utility::vector1< Size > const &old2new) | core::conformation::Conformation | private |
| upstream_jump_stub(int jump_number) const | core::conformation::Conformation | |
| xyz(AtomID const &id) const | core::conformation::Conformation | |
| xyz_moved_ | core::conformation::Conformation | private |
| xyz_obs_hub_ | core::conformation::Conformation | mutableprivate |
| XYZEvent typedef | core::conformation::Conformation | |
| ~Conformation() override | core::conformation::Conformation | |
1.8.7