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core::sequence::ProfSimScoringScheme Member List

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

clone() const overridecore::sequence::ProfSimScoringSchemeinlinevirtual
gap_extend() constcore::sequence::ScoringSchemevirtual
gap_extend(Real const gap_extend)core::sequence::ScoringScheme
gap_extend_core::sequence::ScoringSchemeprivate
gap_open() constcore::sequence::ScoringSchemevirtual
gap_open(Real const gap_open)core::sequence::ScoringScheme
gap_open_core::sequence::ScoringSchemeprivate
initialize_parameters()core::sequence::ProfSimScoringScheme
is_good(Real const &num)core::sequence::ScoringScheme
prior_probs_core::sequence::ProfSimScoringSchemeprivate
ProfSimScoringScheme(Real open=-4, Real extend=-1)core::sequence::ProfSimScoringSchemeinline
read_data(utility::io::izstream &)core::sequence::ScoringSchemevirtual
read_from_file(utility::file::FileName const &)core::sequence::ScoringSchemevirtual
score(SequenceOP seq1, SequenceOP seq2, Size pos1, Size pos2) overridecore::sequence::ProfSimScoringSchemevirtual
ScoringScheme()core::sequence::ScoringScheme
type() constcore::sequence::ScoringScheme
type(std::string new_type)core::sequence::ScoringScheme
type_core::sequence::ScoringSchemeprivate
unimplemented_method_error(std::string const &method_name) constcore::sequence::ScoringScheme
~ProfSimScoringScheme() override=defaultcore::sequence::ProfSimScoringScheme
~ScoringScheme() overridecore::sequence::ScoringScheme
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