#include <SS_Info2.hh>

Inheritance diagram for protocols::fldsgn::topology::SS_Info2:

Public Member Functions
	SS_Info2 ()
	default constructor More...

	SS_Info2 (String const &secstruct)
	value constructor More...

	SS_Info2 (Pose const &pose, String const &secstruct="")
	value constructor More...

basic::datacache::CacheableDataOP	clone () const override
	make clone More...

void	initialize (String const &secstruct)
	initialize parameters of this class More...

void	initialize (Pose const &pose, String const &secstruct="")
	initialize parameters of this class More...

bool	bbpos_is_set () const
	get flag for telling whether bb_pos_ was initiliazed by pose or not More...

String	secstruct () const
	string of secondary structure elements More...

char	secstruct (core::Size ii) const

BB_Pos const &	bb_pos () const
	get xyz-coordinates of backbone structure More...

Strands const &	strands () const
	return strands More...

Helices const &	helices () const
	return helices More...

Loops const &	loops () const
	return loops More...

StrandCOP const	strand (core::Size is) const
	return owning pointer of strand given an index of strands More...

HelixCOP const	helix (core::Size ih) const
	return owning pointer of helix given an index of helices More...

LoopCOP const	loop (core::Size il) const
	return owning pointer of loop given an index of loops More...

core::Size	strand_id (core::Size const nres) const
	return strand index in strands given a residue number More...

core::Size	helix_id (core::Size const nres) const
	return helix index in helices given a residue number More...

core::Size	loop_id (core::Size const nres) const
	return loop index in loops given a residue number More...

core::Size	ss_element_id (core::Size const nres) const
	return the index of secondary structure element given a residue number More...

void	set_SSorient (Pose const &pose)
	set orientation vector of secondary structures given a pose More...

void	set_SSorient ()
	set orientation vector of secondary structures given a pose which is defined in the constructor More...

void	clear_data ()
	clear data More...

Private Types
typedef core::Size	Size

typedef core::pose::Pose	Pose

typedef std::string	String

typedef protocols::fldsgn::topology::BB_Pos	BB_Pos

Private Member Functions
void	resize (core::Size const nres)
	resize vectors More...

void	identify_ss (String const &secstruct)
	identify secondary structures More...

Private Attributes
bool	bbpos_is_set_
	flag for telling whether bb_pos_ was initiliazed by pose or not More...

String	secstruct_
	string of secondary structure elements More...

BB_Pos	bb_pos_
	xyz-coordinates of backbone More...

Strands	strands_
	vector of StrandOP More...

utility::vector1< core::Size >	strand_id_
	vector for storing index of strand id for each residue position More...

Helices	helices_
	vector of HelixOP More...

utility::vector1< core::Size >	helix_id_
	vector for storing index of helix id for each residue position More...

Loops	loops_
	vector of loops More...

utility::vector1< core::Size >	loop_id_

utility::vector1< core::Size >	ss_element_id_
	vector for storing index of secondary structure element for each residue position More...

Friends
std::ostream &	operator<< (std::ostream &out, const SS_Info2 &ssinfo)
	output info of SS_Info2 More...

Member Typedef Documentation

typedef protocols::fldsgn::topology::BB_Pos protocols::fldsgn::topology::SS_Info2::BB_Pos

private

typedef core::pose::Pose protocols::fldsgn::topology::SS_Info2::Pose

private

typedef core::Size protocols::fldsgn::topology::SS_Info2::Size

private

typedef std::string protocols::fldsgn::topology::SS_Info2::String

private

Constructor & Destructor Documentation

protocols::fldsgn::topology::SS_Info2::SS_Info2 ( )

default constructor

protocols::fldsgn::topology::SS_Info2::SS_Info2 ( String const & secstruct )

value constructor

References initialize().

protocols::fldsgn::topology::SS_Info2::SS_Info2	(	Pose const &	pose,
		String const &	secstruct = `""`
	)

value constructor

References initialize().

Member Function Documentation

BB_Pos const& protocols::fldsgn::topology::SS_Info2::bb_pos ( ) const

inline

get xyz-coordinates of backbone structure

References bb_pos_.

Referenced by protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), and protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score().

bool protocols::fldsgn::topology::SS_Info2::bbpos_is_set ( ) const

inline

get flag for telling whether bb_pos_ was initiliazed by pose or not

References bbpos_is_set_.

void protocols::fldsgn::topology::SS_Info2::clear_data ( )

clear data

References bb_pos_, protocols::fldsgn::topology::BB_Pos::clear(), helices_, helix_id_, loop_id_, secstruct_, ss_element_id_, strand_id_, and strands_.

Referenced by initialize().

basic::datacache::CacheableDataOP protocols::fldsgn::topology::SS_Info2::clone ( ) const

override

make clone

Helices const& protocols::fldsgn::topology::SS_Info2::helices ( ) const

inline

return helices

References helices_.

Referenced by protocols::fldsgn::filters::HSSTripletFilter::check_elements(), protocols::fldsgn::filters::HelixPairingFilter::find_missing_helices(), and protocols::fldsgn::potentials::sspot::HSPairPotential::score().

HelixCOP const protocols::fldsgn::topology::SS_Info2::helix ( core::Size ih ) const

inline

return owning pointer of helix given an index of helices

References helices_.

Referenced by protocols::denovo_design::filters::SSShapeComplementarityFilter::setup_sc_hh(), and protocols::denovo_design::filters::SSShapeComplementarityFilter::setup_sc_hss().

core::Size protocols::fldsgn::topology::SS_Info2::helix_id ( core::Size const nres ) const

inline

return helix index in helices given a residue number

References helix_id_.

void protocols::fldsgn::topology::SS_Info2::identify_ss ( String const & secstruct )

private

identify secondary structures

identify the region of each secondary structure element

References helices_, helix_id_, loop_id_, loops_, ss_element_id_, strand_id_, and strands_.

Referenced by initialize().

void protocols::fldsgn::topology::SS_Info2::initialize ( String const & secstruct )

initialize parameters of this class

References clear_data(), identify_ss(), resize(), secstruct(), and secstruct_.

Referenced by SS_Info2().

void protocols::fldsgn::topology::SS_Info2::initialize	(	Pose const &	pose,
		String const &	secstruct = `""`
	)

initialize parameters of this class

References bb_pos_, bbpos_is_set_, clear_data(), identify_ss(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), resize(), secstruct(), core::pose::Pose::secstruct(), secstruct_, set_SSorient(), core::pose::Pose::size(), and protocols::fldsgn::topology::BB_Pos::take_coordinates_from_pose().

LoopCOP const protocols::fldsgn::topology::SS_Info2::loop ( core::Size il ) const

inline

return owning pointer of loop given an index of loops

References loops_.

core::Size protocols::fldsgn::topology::SS_Info2::loop_id ( core::Size const nres ) const

inline

return loop index in loops given a residue number

References loop_id_.

Loops const& protocols::fldsgn::topology::SS_Info2::loops ( ) const

inline

return loops

References loops_.

void protocols::fldsgn::topology::SS_Info2::resize ( core::Size const nres )

private

resize vectors

References bb_pos_, helix_id_, loop_id_, protocols::fldsgn::topology::BB_Pos::resize(), ss_element_id_, and strand_id_.

Referenced by initialize().

String protocols::fldsgn::topology::SS_Info2::secstruct ( ) const

inline

string of secondary structure elements

References secstruct_.

Referenced by initialize().

char protocols::fldsgn::topology::SS_Info2::secstruct ( core::Size ii ) const

inline

References secstruct_.

void protocols::fldsgn::topology::SS_Info2::set_SSorient ( Pose const & pose )

set orientation vector of secondary structures given a pose

References bb_pos_, bbpos_is_set_, set_SSorient(), protocols::fldsgn::topology::BB_Pos::size(), core::pose::Pose::size(), and protocols::fldsgn::topology::BB_Pos::take_coordinates_from_pose().

void protocols::fldsgn::topology::SS_Info2::set_SSorient ( )

set orientation vector of secondary structures given a pose which is defined in the constructor

References bb_pos_, helices_, and strands_.

Referenced by initialize(), and set_SSorient().

core::Size protocols::fldsgn::topology::SS_Info2::ss_element_id ( core::Size const nres ) const

inline

return the index of secondary structure element given a residue number

References ss_element_id_.

StrandCOP const protocols::fldsgn::topology::SS_Info2::strand ( core::Size is ) const

inline

return owning pointer of strand given an index of strands

References strands_.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute_paired_residues(), protocols::denovo_design::components::extract_sheets_from_pose(), protocols::fldsgn::topology::StrandPairingSet::initialize_by_dimer_pairs(), and protocols::denovo_design::filters::SSShapeComplementarityFilter::setup_sc_hss().

core::Size protocols::fldsgn::topology::SS_Info2::strand_id ( core::Size const nres ) const

inline

return strand index in strands given a residue number

References strand_id_.

Referenced by protocols::denovo_design::components::add_paired_residues(), protocols::fldsgn::topology::DimerPairings::finalize(), protocols::fldsgn::topology::StrandPairingSet::initialize_by_dimer_pairs(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), and protocols::fldsgn::potentials::sspot::SSPairPotential::score().

Strands const& protocols::fldsgn::topology::SS_Info2::strands ( ) const

inline

return strands

References strands_.

Referenced by protocols::denovo_design::components::add_paired_residues(), protocols::fldsgn::filters::HSSTripletFilter::check_elements(), protocols::fldsgn::topology::StrandPairingSet::initialize_by_dimer_pairs(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), and protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score().

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		const SS_Info2 &	ssinfo
	)

friend

output info of SS_Info2

Member Data Documentation

BB_Pos protocols::fldsgn::topology::SS_Info2::bb_pos_

private

xyz-coordinates of backbone

Referenced by bb_pos(), clear_data(), initialize(), resize(), and set_SSorient().

bool protocols::fldsgn::topology::SS_Info2::bbpos_is_set_

private

flag for telling whether bb_pos_ was initiliazed by pose or not

Referenced by bbpos_is_set(), initialize(), and set_SSorient().

Helices protocols::fldsgn::topology::SS_Info2::helices_

private

vector of HelixOP

Referenced by clear_data(), helices(), helix(), identify_ss(), protocols::fldsgn::topology::operator<<(), and set_SSorient().

utility::vector1< core::Size > protocols::fldsgn::topology::SS_Info2::helix_id_

private

vector for storing index of helix id for each residue position

Referenced by clear_data(), helix_id(), identify_ss(), and resize().

utility::vector1< core::Size > protocols::fldsgn::topology::SS_Info2::loop_id_

private

Referenced by clear_data(), identify_ss(), loop_id(), and resize().

Loops protocols::fldsgn::topology::SS_Info2::loops_

private

vector of loops

Referenced by identify_ss(), loop(), and loops().

String protocols::fldsgn::topology::SS_Info2::secstruct_

private

string of secondary structure elements

Referenced by clear_data(), initialize(), and secstruct().

utility::vector1< core::Size > protocols::fldsgn::topology::SS_Info2::ss_element_id_

private

vector for storing index of secondary structure element for each residue position

Referenced by clear_data(), identify_ss(), resize(), and ss_element_id().

utility::vector1< core::Size > protocols::fldsgn::topology::SS_Info2::strand_id_

private

vector for storing index of strand id for each residue position

Referenced by clear_data(), identify_ss(), resize(), and strand_id().

Strands protocols::fldsgn::topology::SS_Info2::strands_

private

vector of StrandOP

Referenced by clear_data(), identify_ss(), protocols::fldsgn::topology::operator<<(), set_SSorient(), strand(), and strands().

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

src/protocols/fldsgn/topology/SS_Info2.hh
src/protocols/fldsgn/topology/SS_Info2.cc

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Friends

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation