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Rosetta
2021.16
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Rosetta
2021.16
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This is the complete list of members for protocols::motif_grafting::movers::MotifGraftMover, including all inherited members.
| apply(Pose &) override | protocols::motif_grafting::movers::MotifGraftMover | virtual |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const override | protocols::motif_grafting::movers::MotifGraftMover | virtual |
| context_clash_hash_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| count_clashes_between_two_poses(core::pose::Pose const &p_A, core::pose::Pose const &p_B, core::Size clash_cutoff, core::Real clash_atom_scale) | protocols::motif_grafting::movers::MotifGraftMover | |
| create() | protocols::moves::Mover | virtual |
| fragments_permutation_test_by_CA_distances(core::pose::Pose const &p_scaffold, core::pose::PoseOP const &p_motif_, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &vv_scaffold_fragments_indexes, utility::vector1< std::pair< core::Size, core::Size > > const &v_motif_fragments_indexes, core::Real const &RMSD_tol, core::Size const &start_motif_num, utility::vector1< std::pair< core::Size, core::Size > > &buff_combVec, utility::vector1< motif2scaffold_data > &v_m2s_data) | protocols::motif_grafting::movers::MotifGraftMover | |
| fresh_instance() const | protocols::moves::Mover | virtual |
| generate_combinations_of_motif_fragments_by_delta_variation(core::pose::PoseOP const &p_motif_, utility::vector1< std::pair< long int, long int > > const &combinatory_fragment_size_delta, core::Size min_fragment_size, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &vv_resulting_permutations) | protocols::motif_grafting::movers::MotifGraftMover | |
| generate_match_pose(core::pose::Pose &target_pose, core::pose::Pose const &contextStructure, bool b_revert_graft_to_native_sequence, MotifMatch motif_match) | protocols::motif_grafting::movers::MotifGraftMover | |
| generate_scaffold_matches(core::pose::Pose &target_scaffold, core::pose::PoseOP &target_motif_, core::pose::PoseOP &target_contextStructure_) | protocols::motif_grafting::movers::MotifGraftMover | |
| get_additional_output() override | protocols::motif_grafting::movers::MotifGraftMover | virtual |
| get_bb_alignment_and_transformation(core::pose::Pose const &poseA, utility::vector1< core::Size > const &positions_to_alignA, core::pose::Pose const &poseB, utility::vector1< core::Size > const &positions_to_alignB, numeric::xyzMatrix< core::Real > &RotM, numeric::xyzVector< core::Real > &TvecA, numeric::xyzVector< core::Real > &TvecB) | protocols::motif_grafting::movers::MotifGraftMover | |
| get_bb_alignment_and_transformation_wTipsExtraInfo(utility::vector1< bool > const &v_isNorC, core::pose::Pose const &poseA, utility::vector1< core::Size > const &positions_to_alignA, core::pose::Pose const &poseB, utility::vector1< core::Size > const &positions_to_alignB, numeric::xyzMatrix< core::Real > &RotM, numeric::xyzVector< core::Real > &TvecA, numeric::xyzVector< core::Real > &TvecB, utility::vector1< core::Real > &RMSD_tip_elements) | protocols::motif_grafting::movers::MotifGraftMover | |
| get_bb_distance(core::pose::Pose const &poseA, utility::vector1< core::Size > const &positions_to_alignA, core::pose::Pose const &poseB, utility::vector1< core::Size > const &positions_to_alignB) | protocols::motif_grafting::movers::MotifGraftMover | |
| get_clash_score_from_pose(core::pose::Pose &p_input, core::scoring::ScoreFunctionOP const &scorefxn_) | protocols::motif_grafting::movers::MotifGraftMover | |
| get_current_job() const | protocols::moves::Mover | |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_fragments_by_CA_distances_and_NCpoints_restrains(core::pose::Pose const &p_scaffold, core::pose::PoseOP const &p_motif_, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &vv_scaffold_fragments_indexes, utility::vector1< std::pair< core::Size, core::Size > > &v_motif_fragments_indexes, core::Real const &RMSD_tol, utility::vector1< std::pair< long int, long int > > const &max_fragment_replacement_size_delta, utility::vector1< std::pair< core::Size, core::Size > > const &v_motif_fragments_permutation, bool const &b_only_allow_if_N_point_match_aa_identity, bool const &b_only_allow_if_C_point_match_aa_identity, bool const &b_N_point_can_replace_proline, bool const &b_C_point_can_replace_proline) | protocols::motif_grafting::movers::MotifGraftMover | |
| get_input_pose() const | protocols::moves::Mover | |
| get_last_move_status() const | protocols::moves::Mover | |
| get_matching_fragments(core::pose::Pose const &target_scaffold, core::pose::PoseOP const &target_motif_, core::pose::PoseOP const &target_contextStructure_, core::Real const &RMSD_tol, core::Real const &NC_points_RMSD_tol, core::Real const &clash_atom_scale, core::Size const &clash_cutoff, core::Size const &min_fragment_size, std::string const &clash_test_residue, utility::vector1< std::pair< long int, long int > > const &max_fragment_replacement_size_delta_, utility::vector1< std::pair< core::Size, core::Size > > const &combinatory_fragment_size_delta, utility::vector1< utility::vector1< core::Size > > const &vvr_hotspots, bool const &b_full_motif_bb_alignment, bool const &b_allow_independent_alignment_per_fragment, bool const &b_graft_only_hotspots_by_sidechain_replacement, bool const &b_only_allow_if_N_point_match_aa_identity, bool const &b_only_allow_if_C_point_match_aa_identity, std::priority_queue< MotifMatch > &pq) | protocols::motif_grafting::movers::MotifGraftMover | |
| get_mono_aa_pose_copy(core::pose::Pose const &p_input, std::string const &aminoacid_code) | protocols::motif_grafting::movers::MotifGraftMover | |
| get_motif_scaffold_superposition_and_RMSD(core::pose::Pose const &p_scaffold, core::pose::PoseOP const &p_motif_, core::Real const &RMSD_tol, core::Real const &tip_RMSD_tol, utility::vector1< utility::vector1< core::Size > > const &vvr_hotspots, bool const &b_full_motif_bb_alignment, bool const &b_allow_independent_alignment_per_fragment, bool const &b_graft_only_hotspots_by_sidechain_replacement, utility::vector1< motif2scaffold_data > &v_m2s_data) | protocols::motif_grafting::movers::MotifGraftMover | |
| get_name() const override | protocols::motif_grafting::movers::MotifGraftMover | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_next_nonredundant_motifmatch(MotifMatch &match, numeric::HomogeneousTransform< core::Real > &match_xform) | protocols::motif_grafting::movers::MotifGraftMover | |
| get_next_output(core::pose::Pose &work_pose) | protocols::motif_grafting::movers::MotifGraftMover | |
| get_rotated_and_translated_pose(core::pose::Pose const &p_scaffold, numeric::xyzMatrix< core::Real > const &RotM, numeric::xyzVector< core::Real > const &TvecA, numeric::xyzVector< core::Real > const &TvecB) | protocols::motif_grafting::movers::MotifGraftMover | |
| 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 |
| gp_b_allow_independent_alignment_per_fragment_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_b_allow_repeat_same_graft_output_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_b_full_motif_bb_alignment_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_b_graft_only_hotspots_by_sidechain_replacement_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_b_is_first_run_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_b_only_allow_if_C_point_match_aa_identity_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_b_only_allow_if_N_point_match_aa_identity_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_b_reinit_every_apply_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_b_revert_graft_to_native_sequence_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_f_output_filter_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_i_clash_score_cutoff_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_i_min_fragment_size_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_p_contextStructure_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_p_motif_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_p_target_pose_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_r_clash_atom_scale_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_r_NC_points_RMSD_tolerance_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_r_output_cluster_tolerance_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_r_RMSD_tolerance_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_s_clash_test_residue_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_vp_combinatory_fragment_size_delta_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_vp_max_fragment_replacement_size_delta_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| gp_vvr_hotspots_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| init_parameters(std::string const &s_contextStructure, std::string const &s_motif, core::Real const &r_RMSD_tolerance, core::Real const &r_NC_points_RMSD_tolerance, core::Real const &gp_r_clash_atom_scale, core::Size const &i_clash_score_cutoff, core::Size const &i_min_fragment_size, std::string const &s_combinatory_fragment_size_delta, std::string const &s_max_fragment_replacement_size_delta, std::string const &s_clash_test_residue, std::string const &s_hotspots, bool &b_full_motif_bb_alignment, bool const &b_allow_independent_alignment_per_fragment, bool const &b_graft_only_hotspots_by_sidechain_replacement, bool const &b_only_allow_if_N_point_match_aa_identity, bool const &b_only_allow_if_C_point_match_aa_identity, bool const &b_revert_graft_to_native_sequence, bool const &b_allow_repeat_same_graft_output, bool const &b_reinit_every_apply, core::Real const &r_output_cluster_tolerance, filters::FilterCOP const &f_output_filter) | protocols::motif_grafting::movers::MotifGraftMover | |
| join_two_poses_by_jump(core::pose::Pose const &p_A, core::pose::Pose const &p_B) | protocols::motif_grafting::movers::MotifGraftMover | |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| motif_match_results_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| MotifGraftMover() | protocols::motif_grafting::movers::MotifGraftMover | |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| mover_name() | protocols::motif_grafting::movers::MotifGraftMover | static |
| name() | protocols::moves::Mover | inlinestatic |
| output_transforms_ | protocols::motif_grafting::movers::MotifGraftMover | protected |
| parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables(std::string const &s_contextStructure, std::string const &s_motif, core::Real const &r_RMSD_tolerance, core::Real const &r_NC_points_RMSD_tolerance, core::Real const &r_clash_atom_scale, core::Size const &i_clash_score_cutoff, core::Size const &i_min_fragment_size, std::string const &s_combinatory_fragment_size_delta, std::string const &s_max_fragment_replacement_size_delta, std::string const &s_clash_test_residue, std::string const &s_hotspots, bool &b_full_motif_bb_alignment, bool const &b_allow_independent_alignment_per_fragment, bool const &b_graft_only_hotspots_by_sidechain_replacement, bool const &b_only_allow_if_N_point_match_aa_identity, bool const &b_only_allow_if_C_point_match_aa_identity, bool const &b_revert_graft_to_native_sequence, bool const &b_allow_repeat_same_graft_output, bool const &b_reinit_every_apply, core::Real const &r_output_cluster_tolerance, filters::FilterCOP const &f_output_filter) | protocols::motif_grafting::movers::MotifGraftMover | |
| parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &) override | protocols::motif_grafting::movers::MotifGraftMover | virtual |
| permutate_n_vv_of_pairs(utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &vv_of_pairs, utility::vector1< std::pair< core::Size, core::Size > > &buff_combVec, core::Size start_index, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &vv_resulting_permutations) | protocols::motif_grafting::movers::MotifGraftMover | |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::motif_grafting::movers::MotifGraftMover | static |
| 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_status() | protocols::moves::Mover | |
| 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_type(std::string const &setting) | protocols::moves::Mover | inline |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| stich_motif_in_scaffold_by_indexes_rotation_and_translation(core::pose::Pose const &p_scaffold, core::pose::Pose const &p_motif_, motif2scaffold_data &m2s_dat, bool const &skip_motif_extremes) | protocols::motif_grafting::movers::MotifGraftMover | |
| Strings typedef | protocols::moves::Mover | |
| superposition_transform(core::Size natoms, ObjexxFCL::FArray1_double const &weights, ObjexxFCL::FArray2_double &ref_coords, ObjexxFCL::FArray2_double &coords, numeric::xyzMatrix< core::Real > &RotM, numeric::xyzVector< core::Real > &TvecA, numeric::xyzVector< core::Real > &TvecB) | protocols::motif_grafting::movers::MotifGraftMover | |
| TagCOP typedef | protocols::moves::Mover | |
| test_epigraft_and_contextStructure_clashes(core::pose::Pose const &p_scaffold, core::pose::Pose const &p_motif_, core::pose::Pose const &p_contextStructure_, core::Size const &clash_cutoff, utility::vector1< motif2scaffold_data > &v_m2s_data, numeric::geometry::hashing::MinimalClashHash const &context_clash_hash, core::Real clash_atom_scale) | protocols::motif_grafting::movers::MotifGraftMover | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| ~MotifGraftMover() override | protocols::motif_grafting::movers::MotifGraftMover |
1.8.7