| alignment_generator() const | protocols::sewing::hashing::BasisMapGenerator | |
| alignment_generator(AlignmentGeneratorOP ag) | protocols::sewing::hashing::BasisMapGenerator | |
| alignment_generator_ | protocols::sewing::hashing::BasisMapGenerator | private |
| alignment_settings() const | protocols::sewing::hashing::BasisMapGenerator | |
| alignment_settings(AlignmentSettings &as) | protocols::sewing::hashing::BasisMapGenerator | |
| alignment_settings_ | protocols::sewing::hashing::BasisMapGenerator | private |
| alignment_settings_from_options() | protocols::sewing::hashing::BasisMapGenerator | |
| basis_map() const | protocols::sewing::hashing::BasisMapGenerator | |
| basis_map(BasisMapOP bm) | protocols::sewing::hashing::BasisMapGenerator | |
| basis_map_ | protocols::sewing::hashing::BasisMapGenerator | private |
| basis_pair_is_valid(data_storage::BasisPair basis_pair, bool first_is_N) | protocols::sewing::hashing::BasisMapGenerator | |
| BasisMapGenerator() | protocols::sewing::hashing::BasisMapGenerator | |
| BasisMapGenerator(BasisMapGenerator const &src) | protocols::sewing::hashing::BasisMapGenerator | |
| BasisMapGenerator(EdgeMapGeneratorOP edge_file_reader, SegmentVectorCOP segments) | protocols::sewing::hashing::BasisMapGenerator | |
| BasisMapGenerator(EdgeMapGeneratorOP edge_file_reader, std::string model_file_name, std::string alignment_file_name) | protocols::sewing::hashing::BasisMapGenerator | |
| BasisMapGenerator(EdgeMapGeneratorOP edge_file_reader, std::string model_file_name) | protocols::sewing::hashing::BasisMapGenerator | |
| BasisMapGenerator(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::BasisMapGenerator | |
| clone() const | protocols::sewing::hashing::BasisMapGenerator | |
| const_pdb_segments() const | protocols::sewing::hashing::BasisMapGenerator | |
| delete_segment_basis_pairs(core::Size) | protocols::sewing::hashing::BasisMapGenerator | |
| edge_file_from_options() | protocols::sewing::hashing::BasisMapGenerator | |
| edge_file_reader() const | protocols::sewing::hashing::BasisMapGenerator | |
| edge_file_reader_ | protocols::sewing::hashing::BasisMapGenerator | private |
| get_alignments(data_storage::SmartSegmentOP query_segment) | protocols::sewing::hashing::BasisMapGenerator | |
| get_basis_pair_for_local_segments(data_storage::SmartSegmentCOP seg1, data_storage::SmartSegmentCOP seg2, bool first_is_N) | protocols::sewing::hashing::BasisMapGenerator | |
| get_basis_pair_for_segment(core::Size segment_id) | protocols::sewing::hashing::BasisMapGenerator | |
| get_basis_pair_for_segment_pair(core::Size seg1, core::Size seg2, bool first_is_N) | protocols::sewing::hashing::BasisMapGenerator | |
| get_basis_res_bounds(data_storage::SmartSegmentCOP seg1, data_storage::SmartSegmentCOP seg2, bool first_is_N) | protocols::sewing::hashing::BasisMapGenerator | |
| hasher_settings() const | protocols::sewing::hashing::BasisMapGenerator | |
| hasher_settings(HasherSettings &hs) | protocols::sewing::hashing::BasisMapGenerator | |
| hasher_settings_ | protocols::sewing::hashing::BasisMapGenerator | private |
| initialize_from_options() | protocols::sewing::hashing::BasisMapGenerator | |
| model_file_from_options() | protocols::sewing::hashing::BasisMapGenerator | |
| pdb_segments() | protocols::sewing::hashing::BasisMapGenerator | |
| pdb_segments(std::map< core::Size, data_storage::SmartSegmentOP >) | protocols::sewing::hashing::BasisMapGenerator | |
| pdb_segments_ | protocols::sewing::hashing::BasisMapGenerator | private |
| read_alignments_from_file(std::string file_name) | protocols::sewing::hashing::BasisMapGenerator | |
| recurse_over_segments(core::Size current_depth, std::set< data_storage::SmartSegmentCOP > segments_to_check) | protocols::sewing::hashing::BasisMapGenerator | |
| segment_vector() const | protocols::sewing::hashing::BasisMapGenerator | |
| segment_vector(SegmentVectorCOP segvec) | protocols::sewing::hashing::BasisMapGenerator | |
| segment_vector_ | protocols::sewing::hashing::BasisMapGenerator | private |
| segs_can_chimerize(data_storage::SmartSegmentCOP seg1, data_storage::SmartSegmentCOP seg2, bool first_is_N) | protocols::sewing::hashing::BasisMapGenerator | |
| set_alignment_settings(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::BasisMapGenerator | |
| set_edge_file(std::string edge_file) | protocols::sewing::hashing::BasisMapGenerator | |
| set_edge_file_reader(EdgeMapGeneratorOP edge_file_reader) | protocols::sewing::hashing::BasisMapGenerator | |
| set_model_file(std::string model_file_name) | protocols::sewing::hashing::BasisMapGenerator | |
| set_private_data(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::BasisMapGenerator | |
| version() const | protocols::sewing::hashing::BasisMapGenerator | |
| version(core::Size ver) | protocols::sewing::hashing::BasisMapGenerator | |
| version_ | protocols::sewing::hashing::BasisMapGenerator | private |
| write_alignments_to_file(std::string file_name) const | protocols::sewing::hashing::BasisMapGenerator | |
| ~BasisMapGenerator() | protocols::sewing::hashing::BasisMapGenerator | virtual |
1.8.7