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core::fragment::SecondaryStructure Class Reference

tiny helper class that knows the relative fractions of secondary structure L,H,E @detail so far these fractions can be computed from a FragSet other input strategies are conceivable but not implemented, yet: eg. psipred files, a bunch of poses, More...

#include <SecondaryStructure.hh>

Inheritance diagram for core::fragment::SecondaryStructure:
Inheritance graph
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Public Member Functions

 ~SecondaryStructure () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
 SecondaryStructure ()
 
 SecondaryStructure (utility::vector1< SecondaryStructureOP > &, utility::vector1< Real > &)
 c'ctor that creates a SecondaryStructure as an average of several SecondaryStructure objects More...
 
 SecondaryStructure (core::fragment::FragSet const &frags, core::Size nres=0, bool bJustCenterResidue=false)
 c'stor compute fractions from fragments More...
 
 SecondaryStructure (core::pose::Pose const &)
 c'stor compute fractions from pose ( well it won't be "fractions" ) More...
 
core::Real loop_fraction (core::Size pos) const
 return loop fraction at position More...
 
core::Real strand_fraction (core::Size pos) const
 return strand fraction at position More...
 
core::Real sheet_fraction (core::Size pos) const
 alias for strand-fraction ... More...
 
core::Real helix_fraction (core::Size pos) const
 helix fraction at position More...
 
core::Real confidence (core::Size pos) const
 confidence at position More...
 
void set_fractions (core::Size pos, core::Real helix_fraction, core::Real sheet_fraction, core::Real loop_fraction, core::Real confidence=0)
 sets secondary structure probabilities at a given position More...
 
ObjexxFCL::FArray1D_float const & loop_fraction () const
 return loop fraction - FArray More...
 
ObjexxFCL::FArray1D_float const & strand_fraction () const
 return strand fraction - FArray More...
 
core::Size total_residue () const
 returns regions (in loop-class format) that belong to contiguous pieces of ss-structure More...
 
char secstruct (core::Size pos) const
 returns the most probably secstruct at that position More...
 
void extend (core::Size)
 extends with pure 'L' at end until requested size is reached. More...
 
void read_from_file (std::string fn)
 read from file More...
 
void show (std::ostream &) const
 @detail write to stream ( opposite from read_from_file ) More...
 
void write_psipred_ss2 (std::ostream &os, std::string const &sequence) const
 write psipred format More...
 
void read_psipred_ss2 (std::istream &os)
 write psipred format More...
 
void read_psipred_ss2 (std::string filename)
 write psipred format More...
 
void read_talos_ss (std::istream &os)
 read talos+ format More...
 
void read_talos_ss (std::string filename)
 read talos+ format More...
 

Private Member Functions

void compute_fractions (core::fragment::FragSet const &, bool bJustCenterResidue)
 

Private Attributes

ObjexxFCL::FArray1D_float loop_fraction_
 store loop/strand fractions More...
 
ObjexxFCL::FArray1D_float strand_fraction_
 
ObjexxFCL::FArray1D_float confidence_
 store confidence values: used by talos, but not by psipred More...
 
core::Size total_residue_
 length of FArrays More...
 

Detailed Description

tiny helper class that knows the relative fractions of secondary structure L,H,E @detail so far these fractions can be computed from a FragSet other input strategies are conceivable but not implemented, yet: eg. psipred files, a bunch of poses,

Constructor & Destructor Documentation

◆ ~SecondaryStructure()

core::fragment::SecondaryStructure::~SecondaryStructure ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

◆ SecondaryStructure() [1/4]

core::fragment::SecondaryStructure::SecondaryStructure ( )
inline

◆ SecondaryStructure() [2/4]

core::fragment::SecondaryStructure::SecondaryStructure ( utility::vector1< SecondaryStructureOP > &  components,
utility::vector1< Real > &  weights 
)

c'ctor that creates a SecondaryStructure as an average of several SecondaryStructure objects

◆ SecondaryStructure() [3/4]

core::fragment::SecondaryStructure::SecondaryStructure ( core::fragment::FragSet const &  frags,
core::Size  nres = 0,
bool  bJustCenterResidue = false 
)
inline

c'stor compute fractions from fragments

References compute_fractions().

◆ SecondaryStructure() [4/4]

core::fragment::SecondaryStructure::SecondaryStructure ( core::pose::Pose const &  pose)

c'stor compute fractions from pose ( well it won't be "fractions" )

References core::pose::Pose::secstruct(), and core::pose::Pose::size().

Member Function Documentation

◆ compute_fractions()

void core::fragment::SecondaryStructure::compute_fractions ( core::fragment::FragSet const &  frags,
bool  bJustCenterResidue 
)
private

◆ confidence()

core::Real core::fragment::SecondaryStructure::confidence ( core::Size  pos) const
inline

confidence at position

References confidence_, and total_residue_.

Referenced by set_fractions().

◆ extend()

void core::fragment::SecondaryStructure::extend ( core::Size  nres)

extends with pure 'L' at end until requested size is reached.

Referenced by protocols::jumping::JumpSample::JumpSample().

◆ helix_fraction()

core::Real core::fragment::SecondaryStructure::helix_fraction ( core::Size  pos) const
inline

◆ loop_fraction() [1/2]

ObjexxFCL::FArray1D_float const& core::fragment::SecondaryStructure::loop_fraction ( ) const
inline

return loop fraction - FArray

References loop_fraction_.

Referenced by set_fractions().

◆ loop_fraction() [2/2]

core::Real core::fragment::SecondaryStructure::loop_fraction ( core::Size  pos) const
inline

◆ read_from_file()

void core::fragment::SecondaryStructure::read_from_file ( std::string  fn)

read from file

@detail read from file

References core::fragment::tr().

◆ read_psipred_ss2() [1/2]

void core::fragment::SecondaryStructure::read_psipred_ss2 ( std::istream &  os)

◆ read_psipred_ss2() [2/2]

void core::fragment::SecondaryStructure::read_psipred_ss2 ( std::string  filename)

write psipred format

References protocols::abinitio::filename(), and core::fragment::tr().

◆ read_talos_ss() [1/2]

void core::fragment::SecondaryStructure::read_talos_ss ( std::istream &  os)

◆ read_talos_ss() [2/2]

void core::fragment::SecondaryStructure::read_talos_ss ( std::string  filename)

read talos+ format

References protocols::abinitio::filename(), and core::fragment::tr().

◆ secstruct()

char core::fragment::SecondaryStructure::secstruct ( core::Size  pos) const

returns the most probably secstruct at that position

returns regions (in loop-class format) that belong to contiguous pieces of ss-structure

References protocols::mean_field::max().

◆ set_fractions()

void core::fragment::SecondaryStructure::set_fractions ( core::Size  pos,
core::Real  helix_fraction,
core::Real  sheet_fraction,
core::Real  loop_fraction,
core::Real  confidence = 0 
)
inline

sets secondary structure probabilities at a given position

References confidence(), confidence_, helix_fraction(), loop_fraction(), loop_fraction_, sheet_fraction(), strand_fraction_, and total_residue_.

◆ sheet_fraction()

core::Real core::fragment::SecondaryStructure::sheet_fraction ( core::Size  pos) const
inline

◆ show()

void core::fragment::SecondaryStructure::show ( std::ostream &  os) const

@detail write to stream ( opposite from read_from_file )

References protocols::comparative_modeling::features::A, core::chemical::element::F, and core::chemical::element::I.

◆ strand_fraction() [1/2]

ObjexxFCL::FArray1D_float const& core::fragment::SecondaryStructure::strand_fraction ( ) const
inline

return strand fraction - FArray

References strand_fraction_.

Referenced by sheet_fraction().

◆ strand_fraction() [2/2]

core::Real core::fragment::SecondaryStructure::strand_fraction ( core::Size  pos) const
inline

◆ total_residue()

core::Size core::fragment::SecondaryStructure::total_residue ( ) const
inline

◆ write_psipred_ss2()

void core::fragment::SecondaryStructure::write_psipred_ss2 ( std::ostream &  os,
std::string const &  sequence 
) const

Member Data Documentation

◆ confidence_

ObjexxFCL::FArray1D_float core::fragment::SecondaryStructure::confidence_
private

store confidence values: used by talos, but not by psipred

Referenced by confidence(), and set_fractions().

◆ loop_fraction_

ObjexxFCL::FArray1D_float core::fragment::SecondaryStructure::loop_fraction_
private

store loop/strand fractions

Referenced by helix_fraction(), loop_fraction(), and set_fractions().

◆ strand_fraction_

ObjexxFCL::FArray1D_float core::fragment::SecondaryStructure::strand_fraction_
private

◆ total_residue_

core::Size core::fragment::SecondaryStructure::total_residue_
private

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