Rosetta 3.4
Public Member Functions
core::sequence::SequenceCoupling Class Reference

#include <SequenceCoupling.hh>

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List of all members.

Public Member Functions

 SequenceCoupling ()
 ctors
 SequenceCoupling (SequenceCoupling const &src)
 copy ctor
SequenceCouplingoperator= (SequenceCoupling const &rhs)
 assignment operator.
virtual ~SequenceCoupling ()
 dtor
virtual void read_from_file (FileName const &fn)
 Read a SequenceCoupling model in GREMLIN format .
std::string type () const
utility::vector1
< utility::vector1< Size > > 
edgeList () const
 Print this SequenceCoupling object to the given std::ostream. Commenting out to fix PyRosetta build friend std::ostream & operator<<( std::ostream & out, const SequenceCoupling & p );.
utility::vector1
< utility::vector1
< utility::vector1< Real > > > 
edgePots () const
core::Real temp () const
 returns the temperature used in computing profile probabilities
Size npos () const
Size findEdgeId (Size vert1, Size vert2) const
utility::vector1
< utility::vector1< Real >
> const & 
edgePotBetween (Size vert1, Size vert2) const
utility::vector1
< utility::vector1< Real >
> const & 
edgePotBetween (Size edgeId) const
void temp (core::Real const t)
void edgeList (utility::vector1< utility::vector1< Size > > const &eList)
void edgePots (utility::vector1< utility::vector1< utility::vector1< Real > > > const &ePots)
virtual void insert_char (core::Size pos, char new_char)
 virtual void generate_from_sequence( Sequence const & seq, std::string matrix="BLOSUM62" );
virtual void delete_position (core::Size pos)
 Deletes the given position from the Sequence and shifts everything else back by one.
virtual void read_from_file (utility::file::FileName const &fn, Real temp)
 Size width() const;.

Constructor & Destructor Documentation

core::sequence::SequenceCoupling::SequenceCoupling ( ) [inline]

ctors

core::sequence::SequenceCoupling::SequenceCoupling ( SequenceCoupling const &  src) [inline]

copy ctor

virtual core::sequence::SequenceCoupling::~SequenceCoupling ( ) [inline, virtual]

dtor


Member Function Documentation

void core::sequence::SequenceCoupling::delete_position ( core::Size  pos) [virtual]

Deletes the given position from the Sequence and shifts everything else back by one.

Reimplemented from core::sequence::SequenceProfile.

References edgePots().

utility::vector1< utility::vector1< Size> > core::sequence::SequenceCoupling::edgeList ( ) const [inline]

Print this SequenceCoupling object to the given std::ostream. Commenting out to fix PyRosetta build friend std::ostream & operator<<( std::ostream & out, const SequenceCoupling & p );.

Referenced by operator=().

void core::sequence::SequenceCoupling::edgeList ( utility::vector1< utility::vector1< Size > > const &  eList) [inline]
utility::vector1< utility::vector1< Real > > const & core::sequence::SequenceCoupling::edgePotBetween ( Size  vert1,
Size  vert2 
) const
utility::vector1< utility::vector1< Real > > const & core::sequence::SequenceCoupling::edgePotBetween ( Size  edgeId) const
utility::vector1< utility::vector1< utility::vector1< Real > > > core::sequence::SequenceCoupling::edgePots ( ) const [inline]

Referenced by delete_position(), and operator=().

void core::sequence::SequenceCoupling::edgePots ( utility::vector1< utility::vector1< utility::vector1< Real > > > const &  ePots) [inline]
core::Size core::sequence::SequenceCoupling::findEdgeId ( Size  vert1,
Size  vert2 
) const

Referenced by edgePotBetween().

void core::sequence::SequenceCoupling::insert_char ( core::Size  pos,
char  new_char 
) [virtual]

virtual void generate_from_sequence( Sequence const & seq, std::string matrix="BLOSUM62" );

void rescale(core::Real factor=1); void convert_profile_to_probs(); Read profile matrix from the given filename using the NNMAKE .checkpoint format. void read_from_checkpoint( FileName const & fn );

Reimplemented from core::sequence::SequenceProfile.

Size core::sequence::SequenceCoupling::npos ( ) const [inline]
SequenceCoupling& core::sequence::SequenceCoupling::operator= ( SequenceCoupling const &  rhs) [inline]
void core::sequence::SequenceCoupling::read_from_file ( FileName const &  fn) [virtual]
virtual void core::sequence::SequenceCoupling::read_from_file ( utility::file::FileName const &  fn,
Real  temp 
) [virtual]

Size width() const;.

virtual SequenceOP clone() const { SequenceOP new_seq_op( new SequenceProfile( *this ) ); return new_seq_op; }

void core::sequence::SequenceCoupling::temp ( core::Real const  t) [inline]
core::Real core::sequence::SequenceCoupling::temp ( ) const [inline]

returns the temperature used in computing profile probabilities

Reimplemented from core::sequence::SequenceProfile.

Referenced by operator=().

std::string core::sequence::SequenceCoupling::type ( ) const [inline, virtual]

Reimplemented from core::sequence::SequenceProfile.


The documentation for this class was generated from the following files:
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