| aa_offsets_ | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | protected |
| add(SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2, value_type const val) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| AminoAcidNeighborSparseMatrix(utility::vector1< int > const &first_node_num_states_per_aa, utility::vector1< int > const &second_node_num_states_per_aa) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| blanket_set(value_type val) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| copy_old_data_into_new_table(ObjexxFCL::FArray2D_int const &old_aa_offsets, ObjexxFCL::FArray1D< value_type > const &old_sparse_matrix) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inlineprotected |
| drop_all_submatrices() | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| drop_small_submatrices_where_possible(value_type const epsilon) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| drop_zero_submatrices_where_possible() | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| first_node_num_states_per_aatype_ | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | protected |
| force_aa_neighbors(int node1aa, int node2aa) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| force_all_aa_neighbors() | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| get(SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2) const | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| get(SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2, int ind2num_states_per_aatype, int aa_offset, ObjexxFCL::FArray1< value_type > const &sparse_matrix) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inlinestatic |
| get(SparseMatrixIndex ind2, int ind1_node_state_offset_minus_1, int ind2_num_states_per_aatype, int aa_offset, ObjexxFCL::FArray1< value_type > const &sparse_matrix) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inlinestatic |
| get_aa_submatrix_energies(int node1aa, int node2aa) const | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| get_offset(SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2) const | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inlineprotected |
| get_offset_table_size_in_bytes() const | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| get_sparse_aa_info(int node1aa, int node2aa) const | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| get_submatrix_index(SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2) const | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inlineprotected |
| get_table_size() const | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| getAANeighborOffsets() | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| getMatrixPointer() | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| num_aa_ | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | protected |
| operator[](int index) const | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| operator[](int index) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| scale(SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2, value_type const scaler) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| scale(value_type const scaler) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| second_node_num_states_per_aatype_ | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | protected |
| set(SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2, value_type const val) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| set(SparseMatrixIndex const &ind1, SparseMatrixIndex const &ind2, int ind2num_states_per_aatype, int aa_offset, ObjexxFCL::FArray1< value_type > &sparse_matrix, value_type val) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inlinestatic |
| set(SparseMatrixIndex ind2, int ind1_node_state_offset_minus_1, int ind2_num_states_per_aatype, int aa_offset, ObjexxFCL::FArray1< value_type > &sparse_matrix, value_type val) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inlinestatic |
| set_sparse_aa_info(ObjexxFCL::FArray2_bool const &sparse_conn_info) | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| size() const | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | inline |
| sparse_matrix_ | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | protected |
| table_size_ | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | protected |
| value_type typedef | core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > | |
1.8.7