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 |