| AAMatrix() | protocols::mean_field::AAMatrix | |
| AAMatrix(std::istream &aa_matrix_file) | protocols::mean_field::AAMatrix | |
| AAMatrix(RotMatrix const &rm, protocols::mean_field::jagged_array< core::Real > em, core::Real temp) | protocols::mean_field::AAMatrix | |
| AAMatrix(AAMatrix const &object_to_copy) | protocols::mean_field::AAMatrix | |
| Allocator typedef | protocols::mean_field::jagged_array< AAProb > | |
| allocator_type typedef | protocols::mean_field::jagged_array< AAProb > | |
| apply_func_to_all(typename func_T2< T_2 >::two_param_func func, T_2 operand) | protocols::mean_field::jagged_array< AAProb > | inline |
| apply_func_to_each_col(typename func_T2< T_2 >::two_param_func func, utility::vector1< T_2 > operands) | protocols::mean_field::jagged_array< AAProb > | inline |
| apply_func_to_each_elem(typename func_T2< T_2 >::two_param_func func, jagged_array< T_2 > operands) | protocols::mean_field::jagged_array< AAProb > | inline |
| apply_func_to_each_elem(typename func_T2< T_2 >::three_param_func func, jagged_array< AAProb > operands, T_2 third_oper) | protocols::mean_field::jagged_array< AAProb > | inline |
| assign(utility::vector1< size_type > const &dims) | protocols::mean_field::jagged_array< AAProb > | inline |
| assign(utility::vector1< size_type > const &dims, utility::vector1< AAProb > const &vals) | protocols::mean_field::jagged_array< AAProb > | inline |
| ave_abs_diff(AAMatrix const &aa_matrix) const | protocols::mean_field::AAMatrix | |
| build_aa_matrix(RotMatrix const &rm, protocols::mean_field::jagged_array< core::Real > em, core::Real temp) | protocols::mean_field::AAMatrix | inline |
| build_aa_matrix(std::istream &aa_matrix_file) | protocols::mean_field::AAMatrix | inline |
| const_iterator typedef | protocols::mean_field::jagged_array< AAProb > | |
| const_pointer typedef | protocols::mean_field::jagged_array< AAProb > | |
| const_reference typedef | protocols::mean_field::jagged_array< AAProb > | |
| const_reverse_iterator typedef | protocols::mean_field::jagged_array< AAProb > | |
| ConstIterator typedef | protocols::mean_field::jagged_array< AAProb > | |
| ConstPointer typedef | protocols::mean_field::jagged_array< AAProb > | |
| ConstReference typedef | protocols::mean_field::jagged_array< AAProb > | |
| ConstReverseIterator typedef | protocols::mean_field::jagged_array< AAProb > | |
| copy_data(AAMatrix &object_to_copy_to, AAMatrix const &object_to_copy_from) | protocols::mean_field::AAMatrix | private |
| cosine_distance(AAMatrix const &aa_matrix) const | protocols::mean_field::AAMatrix | |
| curr_aa() const | protocols::mean_field::AAMatrix | inline |
| curr_aa_ | protocols::mean_field::AAMatrix | private |
| curr_aa_prob() const | protocols::mean_field::AAMatrix | |
| Difference typedef | protocols::mean_field::jagged_array< AAProb > | |
| difference_type typedef | protocols::mean_field::jagged_array< AAProb > | |
| dump_transfac(std::string const &filename) const | protocols::mean_field::AAMatrix | |
| empty() const | protocols::mean_field::AAMatrix | |
| equal_size(jagged_array< AAProb > const &other) const | protocols::mean_field::jagged_array< AAProb > | inline |
| equal_size(jagged_array< T_2 > const &other) const | protocols::mean_field::jagged_array< AAProb > | inline |
| frob_distance(AAMatrix const &aa_matrix) const | protocols::mean_field::AAMatrix | |
| get_total() const | protocols::mean_field::jagged_array< AAProb > | inline |
| get_totals_columns() const | protocols::mean_field::jagged_array< AAProb > | inline |
| has_value(AAProbconst &t) const | protocols::mean_field::jagged_array< AAProb > | inline |
| Index typedef | protocols::mean_field::jagged_array< AAProb > | |
| index(AAProbconst &t) const | protocols::mean_field::jagged_array< AAProb > | inline |
| index_type typedef | protocols::mean_field::jagged_array< AAProb > | |
| init(protocols::mean_field::RotMatrix const &rm, protocols::mean_field::jagged_array< core::Real > em, core::Real temp) | protocols::mean_field::AAMatrix | private |
| init(std::istream &aa_matrix_file) | protocols::mean_field::AAMatrix | private |
| Iterator typedef | protocols::mean_field::jagged_array< AAProb > | |
| iterator typedef | protocols::mean_field::jagged_array< AAProb > | |
| jagged_array(allocator_type const &alloc=allocator_type()) | protocols::mean_field::jagged_array< AAProb > | inlineexplicit |
| jagged_array(jagged_array< AAProb > const &v) | protocols::mean_field::jagged_array< AAProb > | inline |
| jagged_array(utility::vector1< utility::vector1< AAProb, A > > const &v) | protocols::mean_field::jagged_array< AAProb > | inline |
| jagged_array(size_type const num) | protocols::mean_field::jagged_array< AAProb > | inlineexplicit |
| jagged_array(size_type const num, utility::vector1< AAProb > const &vals) | protocols::mean_field::jagged_array< AAProb > | inlineexplicit |
| jagged_array(utility::vector1< size_type > const &dims) | protocols::mean_field::jagged_array< AAProb > | inline |
| jagged_array(utility::vector1< size_type > const &dims, utility::vector1< AAProb > const &vals) | protocols::mean_field::jagged_array< AAProb > | inline |
| jagged_array(InputIterator const beg, InputIterator const ending, allocator_type const &alloc=allocator_type()) | protocols::mean_field::jagged_array< AAProb > | inline |
| max_size_col() const | protocols::mean_field::jagged_array< AAProb > | inline |
| operator<<(std::ostream &output, AAMatrix const &object_to_output) | protocols::mean_field::AAMatrix | friend |
| operator=(AAMatrix const &object_to_copy) | protocols::mean_field::AAMatrix | |
| jagged_array< AAProb >::operator=(jagged_array< AAProb > const &v) | protocols::mean_field::jagged_array< AAProb > | inline |
| jagged_array< AAProb >::operator=(utility::vector1< utility::vector1< AAProb, A > > const &v) | protocols::mean_field::jagged_array< AAProb > | inline |
| parse_aa_line(utility::vector1< std::string > const &tokens, utility::vector1< core::chemical::AA > &aa_names) | protocols::mean_field::AAMatrix | private |
| parse_aa_matrix_line(utility::vector1< std::string > const &tokens, utility::vector1< core::chemical::AA > const &aa_names) | protocols::mean_field::AAMatrix | private |
| Pointer typedef | protocols::mean_field::jagged_array< AAProb > | |
| pointer typedef | protocols::mean_field::jagged_array< AAProb > | |
| Reference typedef | protocols::mean_field::jagged_array< AAProb > | |
| reference typedef | protocols::mean_field::jagged_array< AAProb > | |
| reverse_iterator typedef | protocols::mean_field::jagged_array< AAProb > | |
| ReverseIterator typedef | protocols::mean_field::jagged_array< AAProb > | |
| show(std::ostream &output=std::cout) const | protocols::mean_field::AAMatrix | |
| Size typedef | protocols::mean_field::jagged_array< AAProb > | |
| size_col(Size col) const | protocols::mean_field::jagged_array< AAProb > | inline |
| size_type typedef | protocols::mean_field::jagged_array< AAProb > | |
| SSize typedef | protocols::mean_field::jagged_array< AAProb > | |
| ssize_type typedef | protocols::mean_field::jagged_array< AAProb > | |
| Value typedef | protocols::mean_field::jagged_array< AAProb > | |
| value_type typedef | protocols::mean_field::jagged_array< AAProb > | |
| ~AAMatrix() override | protocols::mean_field::AAMatrix | |
| ~jagged_array() override | protocols::mean_field::jagged_array< AAProb > | inline |
1.8.7