Rosetta Core  2014.35
core::sequence::MatrixScoringScheme Member List

This is the complete list of members for core::sequence::MatrixScoringScheme, including all inherited members.

clone() const core::sequence::MatrixScoringSchemeinlinevirtual
gap_extend() const core::sequence::ScoringSchemevirtual
gap_extend(Real const gap_extend)core::sequence::ScoringScheme
gap_open() const core::sequence::ScoringSchemevirtual
gap_open(Real const gap_open)core::sequence::ScoringScheme
init_type()core::sequence::MatrixScoringSchemeinlineprivate
is_good(Real const &num)core::sequence::ScoringScheme
MatrixScoringScheme()core::sequence::MatrixScoringSchemeinline
MatrixScoringScheme(Real open, Real extend, utility::file::FileName const &fn)core::sequence::MatrixScoringSchemeinline
MatrixScoringScheme(Real open, Real extend, utility::vector1< utility::vector1< core::Real > > matrix)core::sequence::MatrixScoringSchemeinline
read_data(utility::io::izstream &input)core::sequence::MatrixScoringSchemevirtual
read_from_database(std::string name="BLOSUM62")core::sequence::MatrixScoringScheme
read_from_file(utility::file::FileName const &fn)core::sequence::MatrixScoringSchemevirtual
score(SequenceOP seq1, SequenceOP seq2, Size pos1, Size pos2)core::sequence::MatrixScoringSchemevirtual
scoring_matrix() const core::sequence::MatrixScoringScheme
scoring_matrix_core::sequence::MatrixScoringSchemeprivate
ScoringScheme()core::sequence::ScoringScheme
type() const core::sequence::ScoringScheme
type(std::string new_type)core::sequence::ScoringScheme
unimplemented_method_error(std::string const &method_name) const core::sequence::ScoringScheme
values_for_aa(char aa)core::sequence::MatrixScoringScheme
values_for_aa(core::chemical::AA aa)core::sequence::MatrixScoringScheme
~MatrixScoringScheme()core::sequence::MatrixScoringSchemeinlinevirtual
~ScoringScheme()core::sequence::ScoringSchemevirtual