Rosetta  2021.16
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core::sequence::SequenceCoupling Member List

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

alphabet() const core::sequence::SequenceProfileinline
alphabet(utility::vector1< std::string > new_alphabet)core::sequence::SequenceProfileinline
append_char(char new_char)core::sequence::Sequence
append_gap()core::sequence::Sequence
at(core::Size pos) const core::sequence::Sequence
clone() const overridecore::sequence::SequenceProfileinlinevirtual
convert_profile_to_probs(core::Real temp=1.0)core::sequence::SequenceProfile
delete_position(core::Size pos) overridecore::sequence::SequenceCouplingvirtual
edgeList() const core::sequence::SequenceCouplinginline
edgeList(utility::vector1< utility::vector1< Size > > const &eList)core::sequence::SequenceCouplinginline
edgeList_core::sequence::SequenceCouplingprivate
edgePotBetween(Size vert1, Size vert2) const core::sequence::SequenceCoupling
edgePotBetween(Size edgeId) const core::sequence::SequenceCoupling
edgePots() const core::sequence::SequenceCouplinginline
edgePots(utility::vector1< utility::vector1< utility::vector1< Real > > > const &ePots)core::sequence::SequenceCouplinginline
edgePots_core::sequence::SequenceCouplingprivate
FileName typedefcore::sequence::SequenceCouplingprivate
findEdgeId(Size vert1, Size vert2) const core::sequence::SequenceCoupling
gap_char(char gap_char)core::sequence::Sequence
gap_char() const core::sequence::Sequence
generate_from_sequence(Sequence const &seq, std::string matrix="BLOSUM62")core::sequence::SequenceProfilevirtual
global_auto_rescale()core::sequence::SequenceProfile
id(std::string new_id)core::sequence::Sequence
id() const core::sequence::Sequence
insert_char(core::Size pos, char new_char) overridecore::sequence::SequenceCouplingvirtual
insert_gap(core::Size pos)core::sequence::Sequence
is_gap(core::Size pos) const core::sequence::Sequence
length() const core::sequence::Sequencevirtual
negative_better() const core::sequence::SequenceProfileinline
negative_better(bool negbet)core::sequence::SequenceProfileinline
npos() const core::sequence::SequenceCouplinginline
numEdges_core::sequence::SequenceCouplingprivate
numVerts_core::sequence::SequenceCouplingprivate
occurrence_data() const core::sequence::SequenceProfile
occurrence_data(utility::vector1< utility::vector1< Real > > const &new_occurrence_data)core::sequence::SequenceProfile
operator<(const Sequence &s) const core::sequence::Sequenceinline
operator=(Sequence const &rhs)core::sequence::Sequenceinline
operator==(SequenceProfile const &other) const core::sequence::SequenceProfile
core::sequence::Sequence::operator==(const Sequence &s) const core::sequence::Sequenceinline
operator[](core::Size pos) const core::sequence::Sequence
probability_row(Size pos) const core::sequence::SequenceProfile
probabilty_row(utility::vector1< Real > const &new_prob_row, core::Size pos)core::sequence::SequenceProfile
prof_row(Size pos) const core::sequence::SequenceProfile
prof_row(utility::vector1< Real > const &new_prof_row, core::Size pos)core::sequence::SequenceProfile
profile() const core::sequence::SequenceProfile
profile(utility::vector1< utility::vector1< Real > > const &new_profile)core::sequence::SequenceProfile
read_data(std::istream &in)core::sequence::Sequence
read_from_binary_chk(FileName const &fn)core::sequence::SequenceProfile
read_from_checkpoint(FileName const &fn, bool negative_better=true)core::sequence::SequenceProfile
read_from_file(FileName const &fn) overridecore::sequence::SequenceCouplingvirtual
read_from_file(utility::file::FileName const &fn, Real temp)core::sequence::SequenceCouplingvirtual
replace_char(core::Size pos, char new_char)core::sequence::Sequencevirtual
rescale(core::Real factor=1)core::sequence::SequenceProfile
resnum(core::Size idx) const core::sequence::Sequence
Sequence()core::sequence::Sequenceinline
Sequence(std::string const &seq, std::string const &id, core::Size start=1)core::sequence::Sequenceinline
Sequence(core::pose::Pose const &pose)core::sequence::Sequence
Sequence(Sequence const &src)core::sequence::Sequenceinline
sequence(std::string sequence)core::sequence::Sequence
sequence() const core::sequence::Sequence
SequenceCoupling()core::sequence::SequenceCouplinginline
SequenceProfile()core::sequence::SequenceProfile
SequenceProfile(FileName const &fn)core::sequence::SequenceProfileinline
SequenceProfile(FileName const &fn, bool use_occurrence_data)core::sequence::SequenceProfileinline
SequenceProfile(utility::vector1< utility::vector1< core::Real > > prof, std::string const &sequence, std::string const &id, Size start=1, bool negative_better=false, bool use_occurrence_data=false)core::sequence::SequenceProfileinline
size() const core::sequence::SequenceProfileinline
spacer_positions(utility::vector1< Size > const &spacer_positions)core::sequence::Sequence
spacer_positions() const core::sequence::Sequence
start(core::Size new_start)core::sequence::Sequence
start() const core::sequence::Sequence
string typedefcore::sequence::SequenceCouplingprivate
temp() const core::sequence::SequenceCouplinginline
temp(core::Real const t)core::sequence::SequenceCouplinginline
temp_core::sequence::SequenceCouplingprivate
to_string() const core::sequence::Sequencevirtual
type() const overridecore::sequence::SequenceCouplinginlinevirtual
ungapped_length() const core::sequence::Sequence
ungapped_sequence() const core::sequence::Sequence
width() const core::sequence::SequenceProfile
~Sequence() overridecore::sequence::Sequence