| add_aa_virt_rsd_as_root(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| add_peptide_plane_variants_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| add_terminal_res_repulsion(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| add_virt_res_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| align_file_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| align_pose(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| align_poses(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| alignment_atom_id_map_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| already_connected(std::pair< core::Size, core::Size > const &potential_chain_partner, utility::vector1< std::pair< core::Size, core::Size > > const &chain_partners) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| already_connected(core::Size const start_chain, core::Size const stop_chain, utility::vector1< std::pair< core::Size, core::Size > > const &chain_partners, utility::vector1< bool > already_checked) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| apply(core::pose::Pose &pose_to_visualize) override | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | virtual |
| apply_bulge_variants(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| apply_cutpoint_variants(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| apply_full_to_sub_mapping(utility::vector1< core::Size > &res_vector) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| apply_peptide_plane_variants(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| apply_peptide_plane_variants_OLD(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| apply_terminus_variants_at_protein_rna_boundaries(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| apply_virtual_phosphate_variants(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| apply_virtual_res_variant(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| bridge_res_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| bulge_res_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| calc_rms_res_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| check_close_chain_break(core::pose::Pose const &pose) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| check_moving_res_in_chain(core::Size const &start_chain, core::Size const &end_chain, core::Size const &num_chains, core::Size &which_chain_has_moving_res) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| check_superimpose_res(core::pose::Pose const &pose) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::moves::Mover | virtual |
| copy_rna_chi(core::pose::Pose &pose, core::pose::Pose const &import_pose, utility::vector1< core::Size > const &input_res, utility::vector1< core::Size > const &slice_res) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| create() | protocols::moves::Mover | virtual |
| cst_file_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| cst_set_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| cutpoint_closed_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| cutpoint_open_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| cuts_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| desired_sequence_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| disulfide_file_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| dump_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| extra_minimize_res_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| figure_out_cuts() | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| figure_out_gap_size_and_first_chain_break_res() | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| figure_out_jump_partners() | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| figure_out_partition_definition(core::pose::Pose const &pose) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| figure_out_Prepend_Internal(core::pose::Pose const &pose) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| figure_out_working_sequence_and_mapping() | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| fix_phi_psi_offsets(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| fixed_res_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| fresh_instance() const | protocols::moves::Mover | virtual |
| get_additional_output() | protocols::moves::Mover | virtual |
| 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::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | 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_stepwise_jump_atom(core::chemical::ResidueType const &rsd) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| get_type() const | protocols::moves::Mover | inline |
| get_working_pose(core::pose::Pose const &pose, core::pose::Pose &working_pose) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| Import_pose(core::pose::Pose &import_pose, protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP &stream) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| initialize_phi_psi_offsets(core::pose::Pose const &pose) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| initialize_pose_from_streams(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| input_streams_with_residue_info_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| is_cutpoint_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| is_working_cutpoint_closed(core::Size const res, std::map< core::Size, core::Size > &full_to_sub) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| jump_partners_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| jump_res_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| make_full_pose(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| make_pose(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| moving_res_list_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| name() | protocols::moves::Mover | inlinestatic |
| parin_favorite_output_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| parse_my_tag(TagCOP tag, basic::datacache::DataMap &data) | protocols::moves::Mover | virtual |
| phi_offsets_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| psi_offsets_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| ready_to_align() const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| ready_to_align_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| register_options() | protocols::moves::Mover | inlinestatic |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| remove_cterminus_variant_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| remove_nterminus_variant_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| reroot_fold_tree(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| reset_status() | protocols::moves::Mover | |
| rsd_set_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| save_phi_psi_offsets(core::pose::Pose const &start_pose, utility::vector1< core::Size > const &input_res, utility::vector1< core::Size > const &slice_res) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| secstruct_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| set_add_peptide_plane_variants(bool const &setting) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_add_virt_res(bool const setting) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_align_file(std::string const &align_file) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_bridge_res(utility::vector1< core::Size > const &bridge_res) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_bulge_res(utility::vector1< core::Size > const &bulge_res) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_calc_rms_res(utility::vector1< core::Size > const &calc_rms_res) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_cst_file(std::string const &cst_file) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_disulfide_file(std::string const &disulfide_file) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_dump(bool const dump) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_extra_minimize_res(utility::vector1< core::Size > const &setting) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | inline |
| set_fixed_res(utility::vector1< core::Size > const &fixed_res) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_jump_res(utility::vector1< core::Size > const &jump_res) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_parin_favorite_output(bool const &setting) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | inline |
| set_remove_cterminus_variant(bool const &setting) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | inline |
| set_remove_nterminus_variant(bool const &setting) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | inline |
| set_rsd_set(core::chemical::ResidueTypeSetCAP &rsd_set) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_secstruct(std::string const &secstruct) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_superimpose_res(utility::vector1< core::Size > const &superimpose_res) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_terminal_res(utility::vector1< core::Size > const &terminal_res) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| set_virtual_res(utility::vector1< core::Size > const &set_virtual_res_list) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| setup_constraints(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| setup_disulfides(core::pose::Pose &pose) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| setup_full_model_info(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| setup_secstruct(core::pose::Pose &pose) const | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| setup_working_native_pose() | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| StepWiseProteinPoseSetup(utility::vector1< core::Size > const &moving_res_list, std::string const &desired_sequence, utility::vector1< protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP > &input_streams_with_residue_info, utility::vector1< core::Size > const &cutpoint_open, utility::vector1< core::Size > const &cutpoint_closed) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| Strings typedef | protocols::moves::Mover | |
| superimpose_res_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| TagCOP typedef | protocols::moves::Mover | |
| terminal_res_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| virtual_res_list_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| virtualize_5prime_phosphates_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| which_chain(core::Size const &i) | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| working_align_pose_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| working_native_pose | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| working_parameters() | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
| working_parameters_ | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | private |
| ~StepWiseProteinPoseSetup() override | protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup | |
1.8.7