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core::sequence::SequenceCoupling Class Reference

#include <SequenceCoupling.hh>

Inheritance diagram for core::sequence::SequenceCoupling:
Inheritance graph
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Public Member Functions

 SequenceCoupling ()
 ctors More...
 
void read_from_file (FileName const &fn) override
 Read a SequenceCoupling model in GREMLIN format . More...
 
std::string type () const override
 
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)
 
void insert_char (core::Size pos, char new_char) override
 virtual void generate_from_sequence( Sequence const & seq, std::string matrix="BLOSUM62" ); More...
 
void delete_position (core::Size pos) override
 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)
 
SequenceOP clone () const override
 Returns an owning pointer to a new SequenceProfile object, with data that is a deep copy of the information in this object. More...
 
void read_from_file (FileName const &fn) override
 Read an profile matrix from the given filename using the NCBI PSSM format for a position-specific scoring matrix. 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...
 
void read_from_binary_chk (FileName const &fn)
 Read profile matrix from the given filename in the legacy BLAST binary format. More...
 
utility::vector1
< utility::vector1< Real >
> const & 
profile () const
 Returns the 2D vector1 of Real values representing this profile. More...
 
utility::vector1
< utility::vector1< Real >
> const & 
occurrence_data () const
 Returns the 2D vector1 of Real values of the probabilties of each aa. More...
 
void profile (utility::vector1< utility::vector1< Real > > const &new_profile)
 Sets the 2D vector1 of Real values representing this profile. More...
 
void occurrence_data (utility::vector1< utility::vector1< Real > > const &new_occurrence_data)
 Sets the 2D vector1 of Real values of the probabilties of each aa. More...
 
void insert_char (core::Size pos, char new_char) override
 Inserts a character at the given position. More...
 
void delete_position (core::Size pos) override
 Deletes the given position from the Sequence and shifts everything else back by one. More...
 
std::string type () const override
 
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...
 
utility::vector1< Real > const & probability_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...
 
void probabilty_row (utility::vector1< Real > const &new_prob_row, core::Size pos)
 
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)
 
bool operator== (SequenceProfile const &other) const
 
- Public Member Functions inherited from core::sequence::Sequence
 Sequence ()
 ctor More...
 
 Sequence (std::string const &seq, std::string const &id, core::Size start=1)
 
 Sequence (core::pose::Pose const &pose)
 
 Sequence (Sequence const &src)
 copy constructor. More...
 
 ~Sequence () override
 dtor More...
 
virtual core::Size length () const
 Returns the number of characters in this object. More...
 
virtual void replace_char (core::Size pos, char new_char)
 
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...
 
void spacer_positions (utility::vector1< Size > const &spacer_positions)
 sets spacer_positions 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...
 
utility::vector1< Sizespacer_positions () const
 Returns the spacer positions (chain breaks, e.g., from spaces or commas in original sequence text) 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...
 
Sequenceoperator= (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_
 

Member Typedef Documentation

typedef utility::file::FileName core::sequence::SequenceCoupling::FileName
private
typedef std::string core::sequence::SequenceCoupling::string
private

Constructor & Destructor Documentation

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

ctors

Member Function Documentation

void core::sequence::SequenceCoupling::delete_position ( core::Size  pos)
overridevirtual

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

Reimplemented from core::sequence::Sequence.

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 );.

References edgeList_.

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

References edgeList_.

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

References edgePots_.

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

References edgePots_.

Referenced by delete_position().

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

References edgePots_.

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

References edgeList_.

Referenced by edgePotBetween().

void core::sequence::SequenceCoupling::insert_char ( core::Size  pos,
char  new_char 
)
overridevirtual

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::Sequence.

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

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

References numVerts_.

void core::sequence::SequenceCoupling::read_from_file ( FileName const &  fn)
overridevirtual

Read a SequenceCoupling model in GREMLIN format .

Reimplemented from core::sequence::Sequence.

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; }

core::Real core::sequence::SequenceCoupling::temp ( ) const
inline

References temp_.

void core::sequence::SequenceCoupling::temp ( core::Real const  t)
inline
std::string core::sequence::SequenceCoupling::type ( ) const
inlineoverridevirtual

Reimplemented from core::sequence::Sequence.

Member Data Documentation

utility::vector1< utility::vector1< Size > > core::sequence::SequenceCoupling::edgeList_
private
utility::vector1< utility::vector1< utility::vector1< Real> > > core::sequence::SequenceCoupling::edgePots_
private
Size core::sequence::SequenceCoupling::numEdges_
private

Referenced by delete_position().

Size core::sequence::SequenceCoupling::numVerts_
private

Referenced by delete_position(), insert_char(), and npos().

core::Real core::sequence::SequenceCoupling::temp_
private

Referenced by temp().


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