| add_residue(std::string const &stubmode, std::string const &resname, core::Size const position, bool const jumpmode, std::string const &connecting_atom, core::Size const repeat, core::Size const anchor_rsd, core::select::residue_selector::ResidueSelectorCOP anchor_rsd_selector, std::string const &anchor_atom) | protocols::cyclic_peptide::PeptideStubMover | |
| add_residue(PSM_StubMode const stubmode, std::string const &resname, core::Size const position, bool const jumpmode, std::string const &connecting_atom, core::Size const repeat, core::Size const anchor_rsd, core::select::residue_selector::ResidueSelectorCOP anchor_rsd_selector, std::string const &anchor_atom) | protocols::cyclic_peptide::PeptideStubMover | |
| add_residue_to_empty_pose(core::pose::Pose &pose, core::conformation::Residue &new_rsd, core::Size const istub) | protocols::cyclic_peptide::PeptideStubMover | protected |
| anchor_rsd_selectors_ | protocols::cyclic_peptide::PeptideStubMover | private |
| append_by_bond(core::pose::Pose &pose, core::Size const anchor_rsd, core::conformation::Residue &new_rsd, core::Size const istub) | protocols::cyclic_peptide::PeptideStubMover | protected |
| append_by_jump(core::pose::Pose &pose, core::Size const anchor_rsd, core::conformation::Residue &new_rsd, core::Size const istub) | protocols::cyclic_peptide::PeptideStubMover | protected |
| apply(Pose &) override | protocols::cyclic_peptide::PeptideStubMover | virtual |
| assign_chain_ids(core::pose::Pose &pose) | protocols::cyclic_peptide::PeptideStubMover | static |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const override | protocols::cyclic_peptide::PeptideStubMover | virtual |
| create() | protocols::moves::Mover | virtual |
| default_label() | protocols::cyclic_peptide::PeptideStubMover | inlinestatic |
| fresh_instance() const override | protocols::cyclic_peptide::PeptideStubMover | virtual |
| get_additional_output() | protocols::moves::Mover | virtual |
| get_anchor_rsd(core::pose::Pose const &pose, core::Size const istub) | protocols::cyclic_peptide::PeptideStubMover | protected |
| get_connecting_id_for_append_by_bond(core::conformation::Residue const &new_rsd, core::Size const istub) | protocols::cyclic_peptide::PeptideStubMover | protected |
| get_current_job() const | protocols::moves::Mover | |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_input_pose() const | protocols::moves::Mover | |
| get_last_move_status() const | protocols::moves::Mover | |
| get_name() const override | protocols::cyclic_peptide::PeptideStubMover | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_self_ptr() const | protocols::moves::Mover | inline |
| get_self_ptr() | protocols::moves::Mover | inline |
| get_self_weak_ptr() const | protocols::moves::Mover | inline |
| get_self_weak_ptr() | protocols::moves::Mover | inline |
| get_type() const | protocols::moves::Mover | inline |
| handle_lower_terminus(core::pose::Pose &pose, core::Size const anchor_rsd, core::Real &old_phi, core::Real &old_omega_nminus1, bool &replace_lower_terminal_type) const | protocols::cyclic_peptide::PeptideStubMover | private |
| handle_repeats_in_append_by_bond(core::pose::Pose &pose, core::Size const anchor_rsd, core::conformation::Residue &new_rsd, core::Size const istub) | protocols::cyclic_peptide::PeptideStubMover | protected |
| handle_termini_and_store_terminal_dihedrals(core::pose::Pose &pose, core::Size const anchor_rsd, core::Size const istub, core::Size const connecting_id, core::Size &anchor_connecting_id, core::Real &old_omega_minus1, core::Real &old_phi, core::Real &old_psi, core::Real &old_omega, bool &replace_upper_terminal_type, bool &replace_lower_terminal_type) | protocols::cyclic_peptide::PeptideStubMover | protected |
| handle_upper_terminus(core::pose::Pose &pose, core::Size const anchor_rsd, core::Real &old_psi, core::Real &old_omega, bool &replace_upper_terminal_type) const | protocols::cyclic_peptide::PeptideStubMover | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| init() | protocols::cyclic_peptide::PeptideStubMover | |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| mover_name() | protocols::cyclic_peptide::PeptideStubMover | static |
| name() | protocols::moves::Mover | inlinestatic |
| parse_my_tag(utility::tag::TagCOP, basic::datacache::DataMap &) override | protocols::cyclic_peptide::PeptideStubMover | virtual |
| PeptideStubMover() | protocols::cyclic_peptide::PeptideStubMover | |
| PeptideStubMover(PeptideStubMover const &src) | protocols::cyclic_peptide::PeptideStubMover | |
| perform_single_iteration(core::pose::Pose &pose, core::chemical::ResidueTypeSet const &standard_residues, core::Size istub) | protocols::cyclic_peptide::PeptideStubMover | protected |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| preserve_old_mainchain_torsions(core::pose::Pose &pose, core::Size const anchor_res, core::Real const old_omega_minus1, core::Real const old_phi, core::Real const old_psi, core::Real const old_omega, bool const replace_upper_terminal_type, bool const replace_lower_terminal_type) const | protocols::cyclic_peptide::PeptideStubMover | private |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::cyclic_peptide::PeptideStubMover | static |
| rebuild_atoms(core::pose::Pose &pose, core::Size const residue_index) const | protocols::cyclic_peptide::PeptideStubMover | privatevirtual |
| register_options() | protocols::moves::Mover | inlinestatic |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| reset_ | protocols::cyclic_peptide::PeptideStubMover | private |
| reset_mover_data() | protocols::cyclic_peptide::PeptideStubMover | inline |
| reset_status() | protocols::moves::Mover | |
| residue_label_ | protocols::cyclic_peptide::PeptideStubMover | private |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_reset_mode(bool reset_mode) | protocols::cyclic_peptide::PeptideStubMover | inline |
| set_residue_label(std::string const &label) | protocols::cyclic_peptide::PeptideStubMover | inline |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| set_update_pdb_numbering_mode(bool mode) | protocols::cyclic_peptide::PeptideStubMover | inline |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| Strings typedef | protocols::moves::Mover | |
| stub_anchor_rsd_ | protocols::cyclic_peptide::PeptideStubMover | private |
| stub_anchor_rsd_connecting_atom_ | protocols::cyclic_peptide::PeptideStubMover | private |
| stub_insert_pos_ | protocols::cyclic_peptide::PeptideStubMover | private |
| stub_mode_ | protocols::cyclic_peptide::PeptideStubMover | private |
| stub_rsd_connecting_atom_ | protocols::cyclic_peptide::PeptideStubMover | private |
| stub_rsd_jumping_ | protocols::cyclic_peptide::PeptideStubMover | private |
| stub_rsd_names_ | protocols::cyclic_peptide::PeptideStubMover | private |
| stub_rsd_repeat_ | protocols::cyclic_peptide::PeptideStubMover | private |
| TagCOP typedef | protocols::moves::Mover | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| update_pdb_numbering(core::pose::Pose &pose, utility::vector1< core::Size > &resids_that_we_added) const | protocols::cyclic_peptide::PeptideStubMover | private |
| update_pdb_numbering_ | protocols::cyclic_peptide::PeptideStubMover | private |
| ~PeptideStubMover() override | protocols::cyclic_peptide::PeptideStubMover | |
1.8.7