| add_pose_segments_to_segment_vector(core::pose::Pose const &pose, core::pose::PoseOP partner_pose, SegmentVectorCOP segvec, std::map< core::Size, data_storage::SmartSegmentOP > &pdb_segments, std::string pose_segment_starts_string, std::string pose_segment_ends_string, std::string pose_segment_dssp, utility::vector1< data_storage::LigandDescription > &ligands, std::map< core::Size, data_storage::LigandResidueCOP > &partner_ligands, utility::vector1< data_storage::LigandDescription > &expanded_ligands, std::string required_resnums, core::select::residue_selector::ResidueSelectorCOP required_selector, bool strict_dssp_changes) | protocols::sewing::hashing::AlignmentFileGeneratorMover | static |
| add_pose_segments_to_segment_vector(core::pose::Pose const &pose, core::pose::PoseOP partner_pose, BasisMapGeneratorOP bmg, utility::vector1< data_storage::LigandDescription > &ligands, std::map< core::Size, data_storage::LigandResidueCOP > &partner_ligands, utility::vector1< data_storage::LigandDescription > &expanded_ligands, std::string required_resnums, core::select::residue_selector::ResidueSelectorCOP required_selector, bool set_segments_from_dssp) | protocols::sewing::hashing::AlignmentFileGeneratorMover | static |
| align_settings_ | protocols::sewing::hashing::AlignmentFileGeneratorMover | private |
| alignment_settings_from_tag(utility::tag::TagCOP tag) | protocols::sewing::hashing::AlignmentFileGeneratorMover | static |
| AlignmentFileGeneratorMover() | protocols::sewing::hashing::AlignmentFileGeneratorMover | |
| AlignmentFileGeneratorMover(AlignmentFileGeneratorMover const &src) | protocols::sewing::hashing::AlignmentFileGeneratorMover | |
| AlignmentFileGeneratorMover(EdgeMapGeneratorOP edge_file_reader, std::string model_file_name, std::string alignment_file_name) | protocols::sewing::hashing::AlignmentFileGeneratorMover | |
| AlignmentFileGeneratorMover(EdgeMapGeneratorOP edge_file_reader, std::string model_file_name) | protocols::sewing::hashing::AlignmentFileGeneratorMover | |
| AlignmentFileGeneratorMover(std::string model_file_name, std::string edge_file_name, utility::vector1< core::Size > match_segments, utility::vector1< core::Size > pose_segment_starts, utility::vector1< core::Size > pose_segment_ends, core::Size recursive_depth) | protocols::sewing::hashing::AlignmentFileGeneratorMover | |
| AlignmentFileGeneratorMover(BasisMapGeneratorOP bmg) | protocols::sewing::hashing::AlignmentFileGeneratorMover | |
| append_ligands_subelement(utility::tag::XMLSchemaSimpleSubelementList &subs, utility::tag::XMLSchemaDefinition &xsd, bool include_coord) | protocols::sewing::hashing::AlignmentFileGeneratorMover | static |
| apply(core::pose::Pose &pose) override | protocols::sewing::hashing::AlignmentFileGeneratorMover | virtual |
| basis_map_from_alignment(AlignmentFGMSettings const &alignment, core::pose::Pose const &pose, BasisMapGeneratorOP bmg) | protocols::sewing::hashing::AlignmentFileGeneratorMover | static |
| basis_map_generator() const | protocols::sewing::hashing::AlignmentFileGeneratorMover | |
| basis_map_generator(BasisMapGeneratorOP bmg) | protocols::sewing::hashing::AlignmentFileGeneratorMover | |
| basis_map_generator_ | protocols::sewing::hashing::AlignmentFileGeneratorMover | private |
| class_name() | protocols::sewing::hashing::AlignmentFileGeneratorMover | static |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const override | protocols::sewing::hashing::AlignmentFileGeneratorMover | virtual |
| create() | protocols::moves::Mover | virtual |
| fresh_instance() const override | protocols::sewing::hashing::AlignmentFileGeneratorMover | 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::sewing::hashing::AlignmentFileGeneratorMover | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_required_resnums() const | protocols::sewing::hashing::AlignmentFileGeneratorMover | |
| get_required_selector() const | protocols::sewing::hashing::AlignmentFileGeneratorMover | |
| 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 |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| ligands_ | protocols::sewing::hashing::AlignmentFileGeneratorMover | private |
| ligands_subtag_ct_namer(std::string) | protocols::sewing::hashing::AlignmentFileGeneratorMover | static |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| name() | protocols::moves::Mover | inlinestatic |
| parse_ligand_conformers(utility::vector1< data_storage::LigandDescription > &ligands) | protocols::sewing::hashing::AlignmentFileGeneratorMover | static |
| parse_ligands_tag(utility::tag::TagCOP ligands_tag, basic::datacache::DataMap const &data, utility::vector1< data_storage::LigandDescription > &ligands) | protocols::sewing::hashing::AlignmentFileGeneratorMover | static |
| parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &data) override | protocols::sewing::hashing::AlignmentFileGeneratorMover | virtual |
| 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::sewing::hashing::AlignmentFileGeneratorMover | 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 |
| required_resnums_ | protocols::sewing::hashing::AlignmentFileGeneratorMover | private |
| required_selector_ | protocols::sewing::hashing::AlignmentFileGeneratorMover | private |
| 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_required_resnums(std::string) | protocols::sewing::hashing::AlignmentFileGeneratorMover | |
| set_required_selector(core::select::residue_selector::ResidueSelectorCOP) | protocols::sewing::hashing::AlignmentFileGeneratorMover | |
| set_segments_from_dssp_ | protocols::sewing::hashing::AlignmentFileGeneratorMover | private |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| show(std::ostream &output=std::cout) const override | protocols::sewing::hashing::AlignmentFileGeneratorMover | virtual |
| Strings typedef | protocols::moves::Mover | |
| 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 |
| ~AlignmentFileGeneratorMover() override | protocols::sewing::hashing::AlignmentFileGeneratorMover | |
1.8.7