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>

Inheritance diagram for core::fragment::SecondaryStructure:

[legend]

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
	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 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 ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

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

References compute_fractions().

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

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

private

References core::fragment::FragSet::begin(), core::fragment::FragSet::end(), core::fragment::FragSet::global_offset(), core::fragment::FragSet::max_pos(), and core::fragment::tr().

Referenced by SecondaryStructure().

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

inline

confidence at position

References confidence_, and total_residue_.

Referenced by set_fractions().

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

References loop_fraction_, protocols::mean_field::max(), strand_fraction_, and total_residue_.

Referenced by protocols::abinitio::decide_on_beta_jumping_from_frags(), and protocols::loops::define_scorable_core_from_secondary_structure().

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

inline

return loop fraction at position

References loop_fraction_, and total_residue_.

Referenced by protocols::loops::compute_ss_regions(), protocols::environment::claims::CutBiasClaim::CutBiasClaim(), protocols::topology_broker::CutBiasClaimer::CutBiasClaimer(), protocols::loops::define_scorable_core_from_secondary_structure(), and protocols::jumping::JumpSample::JumpSample().

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

inline

return loop fraction - FArray

References loop_fraction_.

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

read from file

References core::fragment::tr().

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

write psipred format

References protocols::cluster::calibur::aa, protocols::analysis::total, and 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_talos_ss ( std::istream & os )

read talos+ format

References protocols::cluster::calibur::aa, protocols::analysis::total, and 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

References protocols::mean_field::max().

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`
	)