| add_scored_pair(core::Size const res1, core::Size const res2, core::Real const score) | core::sequence::PairScoringScheme | inline |
| clone() const | core::sequence::PairScoringScheme | inlinevirtual |
| gap_extend() const | core::sequence::ScoringScheme | virtual |
| gap_extend(Real const gap_extend) | core::sequence::ScoringScheme | |
| gap_open() const | core::sequence::ScoringScheme | virtual |
| gap_open(Real const gap_open) | core::sequence::ScoringScheme | |
| is_good(Real const &num) | core::sequence::ScoringScheme | |
| pairs() const | core::sequence::PairScoringScheme | inline |
| pairs_ | core::sequence::PairScoringScheme | private |
| PairScoringScheme() | core::sequence::PairScoringScheme | inline |
| PairScoringScheme(Real gap_open_in, Real gap_extend_in, utility::vector1< utility::vector1< core::Real > > pairs) | core::sequence::PairScoringScheme | inline |
| read_data(utility::io::izstream &) | core::sequence::ScoringScheme | virtual |
| read_from_file(utility::file::FileName const &fn) | core::sequence::PairScoringScheme | virtual |
| score(SequenceOP seq1, SequenceOP seq2, core::Size pos1, core::Size pos2) | core::sequence::PairScoringScheme | virtual |
| core::sequence::ScoringScheme::score(SequenceOP seq1, SequenceOP seq2, Size pos1, Size pos2)=0 | core::sequence::ScoringScheme | pure virtual |
| 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 | |
| ~PairScoringScheme() | core::sequence::PairScoringScheme | inlinevirtual |
| ~ScoringScheme() | core::sequence::ScoringScheme | virtual |
1.8.4