| aa(Size const seqpos) const | core::conformation::Conformation | |
| annotations() const | protocols::environment::ProtectedConformation | inline |
| annotations_ | protocols::environment::ProtectedConformation | private |
| append_polymer_residue_after_seqpos(core::conformation::Residue const &, Size const, bool const ) | protocols::environment::ProtectedConformation | virtual |
| 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(core::conformation::Residue const &, Size const, std::string const &="", std::string const &="", bool const =false) | protocols::environment::ProtectedConformation | virtual |
| atom_is_backbone_norefold(Size const pos, Size const atomno) const | core::conformation::Conformation | |
| atom_tree() const | core::conformation::Conformation | |
| AtomID typedef | core::conformation::Conformation | |
| AtomID_Mask typedef | core::conformation::Conformation | |
| AtomTree typedef | core::conformation::Conformation | |
| AtomTreeOP typedef | core::conformation::Conformation | |
| attach_annotation(SequenceAnnotationCOP) | protocols::environment::ProtectedConformation | private |
| attach_connection_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | |
| attach_general_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | |
| attach_identity_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | |
| attach_length_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | |
| attach_xyz_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | |
| 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< core::PointPosition > const &position) | protocols::environment::ProtectedConformation | virtual |
| core::conformation::Conformation::batch_set_xyz(utility::vector1< AtomID > const &id, utility::vector1< PointPosition > const &position) | core::conformation::Conformation | virtual |
| 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 | |
| bonded_neighbor_all_res(core::id::AtomID atomid, bool virt=false) const | core::conformation::Conformation | |
| buffer_signals() | core::conformation::Conformation | |
| buffering_signals() const | core::conformation::Conformation | |
| chain_begin(Size const chain) const | core::conformation::Conformation | |
| chain_end(Size const chain) const | core::conformation::Conformation | |
| chain_endings(utility::vector1< Size > const &) | protocols::environment::ProtectedConformation | virtual |
| core::conformation::Conformation::chain_endings() const | core::conformation::Conformation | |
| chains_from_termini() | protocols::environment::ProtectedConformation | virtual |
| clear() | protocols::environment::ProtectedConformation | virtual |
| clear_observers() | core::conformation::Conformation | |
| clone() const | protocols::environment::ProtectedConformation | virtual |
| Conformation() | core::conformation::Conformation | |
| Conformation(Conformation const &src) | core::conformation::Conformation | |
| ConnectionEvent typedef | core::conformation::Conformation | |
| const_residues() const | core::conformation::Conformation | |
| contains_carbohydrate_residues(bool const ) | protocols::environment::ProtectedConformation | virtual |
| core::conformation::Conformation::contains_carbohydrate_residues() const | core::conformation::Conformation | |
| copy_segment(Size const size, Conformation const &src, Size const begin, Size const src_begin) | core::conformation::Conformation | |
| debug_pause(bool const 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, std::string const &, Size const, std::string const &) | protocols::environment::ProtectedConformation | virtual |
| delete_chain_ending(Size const ) | protocols::environment::ProtectedConformation | virtual |
| delete_polymer_residue(Size const ) | protocols::environment::ProtectedConformation | virtual |
| delete_residue_range_slow(Size const range_begin, Size const range_end) | protocols::environment::ProtectedConformation | virtual |
| delete_residue_slow(Size const ) | protocols::environment::ProtectedConformation | virtual |
| detach_connection_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | |
| detach_general_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | |
| detach_identity_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | |
| detach_length_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | |
| detach_xyz_obs(MemFn fn, Ptr ptr) const | core::conformation::Conformation | |
| detect_bonds() | core::conformation::Conformation | |
| detect_disulfides() | core::conformation::Conformation | virtual |
| detect_pseudobonds() | core::conformation::Conformation | |
| dof(DOF_ID const &id) const | core::conformation::Conformation | |
| DOF_ID typedef | core::conformation::Conformation | |
| dof_id_from_torsion_id(TorsionID const &id) const | core::conformation::Conformation | |
| DofUnlock class | protocols::environment::ProtectedConformation | friend |
| DomainMap typedef | core::conformation::Conformation | |
| downstream_jump_stub(int const jump_number) const | core::conformation::Conformation | |
| empty() const | core::conformation::Conformation | |
| env_ | protocols::environment::ProtectedConformation | private |
| env_destruction() | protocols::environment::ProtectedConformation | inline |
| EnvClaimBroker class | protocols::environment::ProtectedConformation | friend |
| Environment class | protocols::environment::ProtectedConformation | friend |
| environment() const | protocols::environment::ProtectedConformation | |
| environment_exists_ | protocols::environment::ProtectedConformation | private |
| fail_verification(std::string const &str) | protocols::environment::ProtectedConformation | inlineprivate |
| fill_missing_atoms(core::id::AtomID_Mask missing) | protocols::environment::ProtectedConformation | virtual |
| fix_disulfides(utility::vector1< std::pair< Size, Size > >) | protocols::environment::ProtectedConformation | virtual |
| fold_tree(FoldTree const &) | protocols::environment::ProtectedConformation | virtual |
| core::conformation::Conformation::fold_tree() const | core::conformation::Conformation | virtual |
| FoldTree typedef | core::conformation::Conformation | |
| FoldTreeOP typedef | core::conformation::Conformation | |
| fork_annotation() | protocols::environment::ProtectedConformation | private |
| FragRT typedef | core::conformation::Conformation | |
| FragXYZ typedef | core::conformation::Conformation | |
| GeneralEvent typedef | core::conformation::Conformation | |
| get_residue_mask() const | core::conformation::Conformation | virtual |
| get_residue_weight(core::Size, core::Size) const | core::conformation::Conformation | virtual |
| 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 | |
| has_passport() const | protocols::environment::ProtectedConformation | privatevirtual |
| IdentityEvent typedef | core::conformation::Conformation | |
| insert_chain_ending(Size const ) | protocols::environment::ProtectedConformation | virtual |
| insert_conformation_by_jump(Conformation const &, Size const, Size const, Size const, Size const, std::string const &="", std::string const &="") | protocols::environment::ProtectedConformation | virtual |
| insert_fragment(core::id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz) | protocols::environment::ProtectedConformation | virtual |
| insert_ideal_geometry_at_polymer_bond(Size const seqpos) | protocols::environment::ProtectedConformation | virtual |
| insert_ideal_geometry_at_residue_connection(Size const pos1, Size const connid1) | protocols::environment::ProtectedConformation | virtual |
| insert_residue_by_jump(Residue const &new_rsd_in, Size const 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 const seqpos, int const connection_index) const | core::conformation::Conformation | |
| is_centroid() const | core::conformation::Conformation | |
| is_fullatom() const | core::conformation::Conformation | |
| is_membrane() const | core::conformation::Conformation | |
| is_protected() const | protocols::environment::ProtectedConformation | inlinevirtual |
| is_residue_typeset(std::string tag) const | core::conformation::Conformation | |
| Jump typedef | core::conformation::Conformation | |
| jump(int const jump_number) const | core::conformation::Conformation | |
| jump(AtomID const &id) const | core::conformation::Conformation | |
| jump_atom_id(int const jump_number) const | core::conformation::Conformation | |
| LengthEvent typedef | core::conformation::Conformation | |
| membrane() | core::conformation::Conformation | |
| num_chains() const | core::conformation::Conformation | |
| operator=(Conformation const &src) | protocols::environment::ProtectedConformation | virtual |
| Parent typedef | protocols::environment::ProtectedConformation | private |
| pop_passport() | protocols::environment::ProtectedConformation | privatevirtual |
| prepend_polymer_residue_before_seqpos(core::conformation::Residue const &, Size const, bool const ) | protocols::environment::ProtectedConformation | virtual |
| ProtectedConformation(ProtectedConformation const &src) | protocols::environment::ProtectedConformation | |
| ProtectedConformation(EnvironmentCAP, core::conformation::Conformation const &) | protocols::environment::ProtectedConformation | private |
| push_passport(core::environment::DofPassportCOP) | protocols::environment::ProtectedConformation | privatevirtual |
| rebuild_polymer_bond_dependent_atoms(Size const ) | protocols::environment::ProtectedConformation | virtual |
| rebuild_residue_connection_dependent_atoms(Size const seqpos, Size const connid) | core::conformation::Conformation | |
| receive_observers_from(Conformation const &src) | core::conformation::Conformation | |
| replace_residue(Size const seqpos, core::conformation::Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) | protocols::environment::ProtectedConformation | virtual |
| core::conformation::Conformation::replace_residue(Size const seqpos, Residue const &new_rsd, bool const orient_backbone) | core::conformation::Conformation | virtual |
| reset_chain_endings() | protocols::environment::ProtectedConformation | virtual |
| reset_move_data() | protocols::environment::ProtectedConformation | virtual |
| reset_structure_moved() const | core::conformation::Conformation | |
| residue(Size const seqpos) const | core::conformation::Conformation | |
| residue_type(Size const seqpos) const | core::conformation::Conformation | |
| residues_ | core::conformation::Conformation | protected |
| resolver() const | protocols::environment::ProtectedConformation | |
| safely_append_polymer_residue_after_seqpos(core::conformation::Residue const &, Size const, bool const ) | protocols::environment::ProtectedConformation | virtual |
| safely_prepend_polymer_residue_before_seqpos(core::conformation::Residue const &, Size const, bool const ) | protocols::environment::ProtectedConformation | virtual |
| same_type_as_me(Conformation const &other, bool recurse) const | protocols::environment::ProtectedConformation | virtual |
| secstruct(Size const seqpos) const | core::conformation::Conformation | |
| sequence_matches(Conformation const &other) const | core::conformation::Conformation | |
| SequenceAnnotationCOP typedef | protocols::environment::ProtectedConformation | private |
| set_bond_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, core::Real const setting) | protocols::environment::ProtectedConformation | virtual |
| set_bond_length(AtomID const &atom1, AtomID const &atom2, core::Real const setting) | protocols::environment::ProtectedConformation | virtual |
| set_dof(DOF_ID const &id, core::Real const setting) | protocols::environment::ProtectedConformation | virtual |
| set_environment(EnvironmentCAP) | protocols::environment::ProtectedConformation | private |
| set_jump(AtomID const &, core::kinematics::Jump const &) | protocols::environment::ProtectedConformation | virtual |
| set_jump(int const, core::kinematics::Jump const &) | protocols::environment::ProtectedConformation | virtual |
| set_jump_atom_stub_id(id::StubID const &id) | core::conformation::Conformation | |
| set_polymeric_connection(Size, Size) | protocols::environment::ProtectedConformation | virtual |
| set_secstruct(Size const seqpos, char const setting) | protocols::environment::ProtectedConformation | virtual |
| set_stub_transform(core::id::StubID const &stub_id1, core::id::StubID const &stub_id2, core::kinematics::RT const &target_rt) | protocols::environment::ProtectedConformation | virtual |
| set_torsion(TorsionID const &id, core::Real const setting) | protocols::environment::ProtectedConformation | virtual |
| set_torsion_angle(AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, core::Real const setting, bool quiet=false) | protocols::environment::ProtectedConformation | virtual |
| set_xyz(AtomID const &id, core::PointPosition const &position) | protocols::environment::ProtectedConformation | virtual |
| core::conformation::Conformation::set_xyz(AtomID const &id, PointPosition const &position) | core::conformation::Conformation | virtual |
| setup_membrane(utility::vector1< std::pair< int, int > > embres_map, int membrane) | core::conformation::Conformation | |
| show_residue_connections() const | core::conformation::Conformation | |
| show_residue_connections(std::ostream &os) const | core::conformation::Conformation | |
| size() const | core::conformation::Conformation | |
| structure_moved() const | core::conformation::Conformation | |
| 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 | |
| unblock_signals() | core::conformation::Conformation | |
| unlocks_ | protocols::environment::ProtectedConformation | private |
| update_actcoord(Size resid) | core::conformation::Conformation | |
| update_actcoords() | core::conformation::Conformation | |
| update_domain_map(DomainMap &domain_map) const | core::conformation::Conformation | |
| update_orbital_coords(Residue &rsd) const | core::conformation::Conformation | |
| update_orbital_coords(Size resid) | core::conformation::Conformation | |
| update_polymeric_connection(Size const lower_seqpos) | core::conformation::Conformation | |
| upstream_jump_stub(int const jump_number) const | core::conformation::Conformation | |
| verify(core::id::TorsionID const &) | protocols::environment::ProtectedConformation | inlineprivate |
| verify(core::id::DOF_ID const &) | protocols::environment::ProtectedConformation | inlineprivate |
| verify_backbone(Size const &seqpos) | protocols::environment::ProtectedConformation | inlineprivate |
| verify_jump(core::id::AtomID const &) | protocols::environment::ProtectedConformation | inlineprivate |
| verify_residue(Size const &seqpos) | protocols::environment::ProtectedConformation | inlineprivate |
| xyz(AtomID const &id) const | core::conformation::Conformation | |
| XYZEvent typedef | core::conformation::Conformation | |
| ~Conformation() | core::conformation::Conformation | virtual |
| ~ProtectedConformation() | protocols::environment::ProtectedConformation | virtual |
1.8.7