Rosetta 3.4
Public Member Functions
core::fragment::SecondaryStructure Class Reference

tiny helper class that knows the relative fractions of secondary structure L,H,E 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>

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List of all members.

Public Member Functions

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

Detailed Description

tiny helper class that knows the relative fractions of secondary structure L,H,E 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

core::fragment::SecondaryStructure::SecondaryStructure ( ) [inline]
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

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

c'stor compute fractions from fragments

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::total_residue().


Member Function Documentation

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

confidence at position

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().

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

helix fraction at position

Referenced by protocols::loops::define_scorable_core_from_secondary_structure().

core::Real core::fragment::SecondaryStructure::loop_fraction ( core::Size  pos) const [inline]
ObjexxFCL::FArray1D_float const& core::fragment::SecondaryStructure::loop_fraction ( ) const [inline]

return loop fraction - FArray

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

read from file

read from file

References core::fragment::tr().

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

write psipred format

References core::fragment::tr().

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

write psipred format

References core::fragment::tr().

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

read talos+ format

References core::fragment::tr().

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

read talos+ format

References core::fragment::tr().

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

void core::fragment::SecondaryStructure::set_fractions ( core::Size  pos,
core::Real  helix_fraction,
core::Real  sheet_fraction,
core::Real  loop_fraction 
) [inline]

sets secondary structure probabilities at a given position

References sheet_fraction().

core::Real core::fragment::SecondaryStructure::sheet_fraction ( core::Size  pos) const [inline]
void core::fragment::SecondaryStructure::show ( std::ostream &  os) const

write to stream ( opposite from read_from_file )

References protocols::comparative_modeling::features::A.

Referenced by core::fragment::operator<<().

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

return strand fraction at position

Referenced by protocols::abinitio::IterativeBase::IterativeBase().

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

return strand fraction - FArray

Referenced by sheet_fraction().

core::Size core::fragment::SecondaryStructure::total_residue ( ) const [inline]
void core::fragment::SecondaryStructure::write_psipred_ss2 ( std::ostream &  os,
std::string const &  sequence 
) const

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