#include <SequenceCoupling.hh>

Inheritance diagram for core::sequence::SequenceCoupling:

Collaboration diagram for core::sequence::SequenceCoupling:

Public Member Functions
	SequenceCoupling ()
	ctors More...

	SequenceCoupling (SequenceCoupling const &src)
	copy ctor More...

SequenceCoupling &	operator= (SequenceCoupling const &rhs)
	assignment operator. More...

virtual	~SequenceCoupling ()
	dtor More...

virtual void	read_from_file (FileName const &fn)
	Read a SequenceCoupling model in GREMLIN format . More...

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 );. More...

utility::vector1 < utility::vector1 < utility::vector1< Real > > >	edgePots () const

core::Real	temp () const

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" ); More...

virtual void	delete_position (core::Size pos)
	Deletes the given position from the Sequence and shifts everything else back by one. More...

virtual void	read_from_file (utility::file::FileName const &fn, Real temp)
	Size width() const;. More...

Public Member Functions inherited from core::sequence::SequenceProfile
	SequenceProfile ()
	ctors More...

	SequenceProfile (FileName const &fn)

	SequenceProfile (utility::vector1< utility::vector1< core::Real > > prof, std::string const &sequence, std::string const &id, Size start=1, bool negative_better=false)

	SequenceProfile (SequenceProfile const &src)
	copy ctor More...

SequenceProfile &	operator= (SequenceProfile const &rhs)
	assignment operator. More...

	~SequenceProfile ()
	dtor More...

virtual SequenceOP	clone () const
	Returns an owning pointer to a new SequenceProfile object, with data that is a deep copy of the information in this object. More...

virtual void	generate_from_sequence (Sequence const &seq, std::string matrix="BLOSUM62")
	Generate the profile matrix from a sequence and a given substitution matrix. More...

void	rescale (core::Real factor=1)
	Multiply all profile weights by factor. More...

void	convert_profile_to_probs (core::Real temp=1.0)
	Use boltzman scaling on a per-residue basis to convert the current profile values to probabilities ( range 0.0-1.0 ) More...

void	global_auto_rescale ()
	Use linear rescaling (with a fixed zero) to fit the values within the range -1.0 to 1.0. More...

void	read_from_checkpoint (FileName const &fn, bool negative_better=true)
	Read profile matrix from the given filename using the NNMAKE .checkpoint format. For compatability, negative_better defaults to true. Set manually if necessary. More...

utility::vector1 < utility::vector1< Real > > const &	profile () const
	Returns the 2D vector1 of Real values representing this profile. More...

void	profile (utility::vector1< utility::vector1< Real > > const &new_profile)
	Sets the 2D vector1 of Real values representing this profile. More...

Size	width () const
	Returns the number of distinct values at each position in this profile. More...

utility::vector1< Real > const &	prof_row (Size pos) const
	Returns the vector1 of values at this position. More...

void	prof_row (utility::vector1< Real > const &new_prof_row, core::Size pos)
	Sets the 1D vector1 of Real values representing this profile at pos X. More...

Size	size () const

bool	negative_better () const
	Returns true if negative values are better identities. More...

void	negative_better (bool negbet)
	Set whether negative identities are better. More...

core::Real	temp () const
	returns the temperature used in computing profile probabilities More...

utility::vector1< std::string >	alphabet () const
	Return the alphabet used by this sequence profile. This is an N-dimensional vector1 where N is the width of the profile, and the ith entry of any row in the profile represents the probability of ith character at that row in the sequence. More...

void	alphabet (utility::vector1< std::string > new_alphabet)

Public Member Functions inherited from core::sequence::Sequence
	Sequence ()
	ctor More...

	Sequence (std::string seq, std::string id, core::Size start=1)

	Sequence (core::pose::Pose const &pose)

	Sequence (Sequence const &src)
	copy constructor. More...

virtual	~Sequence ()
	dtor More...

virtual core::Size	length () const
	Returns the number of characters in this object. More...

virtual std::string	to_string () const

void	sequence (std::string sequence)
	sets sequence to the given value. More...

void	id (std::string new_id)
	sets id to the given value. More...

void	start (core::Size new_start)
	sets starting index to the given value. More...

void	gap_char (char gap_char)
	sets gap_char to the given value. More...

core::Size	ungapped_length () const
	Returns the number of characters in this object, ignoring gaps. More...

core::Size	start () const
	Returns the start of this object. More...

std::string	id () const
	Returns the id of this object. More...

char	gap_char () const
	Returns the character used to represent a gap for this object. More...

std::string	ungapped_sequence () const
	Returns the string representing this sequence without gaps. More...

std::string	sequence () const
	Returns the full sequence, which may include gaps. More...

Sequence &	operator= (Sequence const &rhs)
	assignment operator. More...

bool	operator< (const Sequence &s) const
	Returns true if this Sequence object's id is lexicographically less than the given Sequence object's id, returns false otherwise. Uses C++ string < operator to compare this Sequence object's id() to the given Sequence object's id(). More...

bool	operator== (const Sequence &s) const
	Returns true if the given Sequence object is equal to this Sequence object. Tests for string equality of id(), start(), and sequence(), and returns false if any of these are not equal. More...

char	operator[] (core::Size pos) const
	Returns the character at the given sequence position. More...

char	at (core::Size pos) const

void	insert_gap (core::Size pos)
	Inserts a gap at the given position, where insert_gap( 0 ) inserts the character at the beginning of the sequence, and insert_gap( length() ) inserts the character at the end of the sequence. More...

void	append_char (char new_char)
	Append a character. More...

void	append_gap ()
	Append a gap. More...

bool	is_gap (core::Size pos) const
	Returns true if this position in the sequence represents a gap, returns false otherwise. More...

void	read_data (std::istream &in)
	Initializes the information in this sequence from the given std::istream. The istream should yield three pieces of information in the following order: More...

core::Size	resnum (core::Size idx) const
	Returns the index of the given sequence position, which is the position in the sequence minus any gaps that occur earlier in the sequence. For example, if the sequence is —AT, resnum(5) will return 2. Returns 0 for unaligned positions. More...

Private Types
typedef std::string	string

typedef utility::file::FileName	FileName

Private Attributes
core::Real	temp_

Size	numVerts_

Size	numEdges_

utility::vector1 < utility::vector1< Size > >	edgeList_

utility::vector1 < utility::vector1 < utility::vector1< Real > > >	edgePots_

Detailed Description

Definition at line 35 of file SequenceCoupling.hh.

Member Typedef Documentation

typedef utility::file::FileName core::sequence::SequenceCoupling::FileName

private

Definition at line 37 of file SequenceCoupling.hh.

typedef std::string core::sequence::SequenceCoupling::string

private

Definition at line 36 of file SequenceCoupling.hh.

Constructor & Destructor Documentation

core::sequence::SequenceCoupling::SequenceCoupling ( )

inline

ctors

Definition at line 41 of file SequenceCoupling.hh.

core::sequence::SequenceCoupling::SequenceCoupling ( SequenceCoupling const & src)

inline

copy ctor

Definition at line 43 of file SequenceCoupling.hh.

virtual core::sequence::SequenceCoupling::~SequenceCoupling ( )

inlinevirtual

dtor

Definition at line 75 of file SequenceCoupling.hh.

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.

Definition at line 48 of file SequenceCoupling.cc.

References core::sequence::SequenceProfile::delete_position(), edgeList_, edgePots(), edgePots_, numEdges_, and numVerts_.

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 );.

Definition at line 87 of file SequenceCoupling.hh.

References edgeList_.

Referenced by operator=().

void core::sequence::SequenceCoupling::edgeList ( utility::vector1< utility::vector1< Size > > const & eList)

inline

Definition at line 109 of file SequenceCoupling.hh.

References edgeList_.

utility::vector1< utility::vector1< Real > > const & core::sequence::SequenceCoupling::edgePotBetween	(	Size	vert1,
		Size	vert2
	)		const

Definition at line 224 of file SequenceCoupling.cc.

References findEdgeId(), core::sequence::SequenceProfile::profile(), and core::sequence::SequenceProfile::size().

utility::vector1< utility::vector1< Real > > const & core::sequence::SequenceCoupling::edgePotBetween ( Size edgeId) const

Definition at line 229 of file SequenceCoupling.cc.

References edgePots_.

utility::vector1< utility::vector1< utility::vector1< Real > > > core::sequence::SequenceCoupling::edgePots ( ) const

inline

Definition at line 91 of file SequenceCoupling.hh.

References edgePots_.

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

void core::sequence::SequenceCoupling::edgePots ( utility::vector1< utility::vector1< utility::vector1< Real > > > const & ePots)

inline

Definition at line 112 of file SequenceCoupling.hh.

References edgePots_.

core::Size core::sequence::SequenceCoupling::findEdgeId	(	Size	vert1,
		Size	vert2
	)		const

Definition at line 214 of file SequenceCoupling.cc.

References edgeList_.

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.

Definition at line 69 of file SequenceCoupling.cc.

References edgeList_, core::sequence::SequenceProfile::insert_char(), and numVerts_.

Size core::sequence::SequenceCoupling::npos ( ) const

inline

Definition at line 97 of file SequenceCoupling.hh.

References numVerts_.

SequenceCoupling& core::sequence::SequenceCoupling::operator= ( SequenceCoupling const & rhs)

inline

assignment operator.

Definition at line 57 of file SequenceCoupling.hh.

References edgeList(), edgePots(), core::sequence::Sequence::gap_char(), core::sequence::Sequence::id(), core::sequence::SequenceProfile::profile(), core::sequence::Sequence::sequence(), core::sequence::Sequence::start(), and temp().