#include <SS_Info2.hh>

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

Collaboration 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...

	SS_Info2 (SS_Info2 const &s)
	copy constructor More...

	~SS_Info2 ()
	destructor More...

basic::datacache::CacheableDataOP	clone () const
	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 (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 (Size is) const
	return owning pointer of strand given an index of strands More...

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

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

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

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

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

Size	ss_element_id (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 (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< Size >	strand_id_
	vector for storing index of strand id for each residue position More...

Helices	helices_
	vector of HelixOP More...

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

Loops	loops_
	vector of loops More...

utility::vector1< Size >	loop_id_

utility::vector1< 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...

Detailed Description

Definition at line 272 of file SS_Info2.hh.

Member Typedef Documentation

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

private

Definition at line 278 of file SS_Info2.hh.

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

private

Definition at line 276 of file SS_Info2.hh.

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

private

Definition at line 275 of file SS_Info2.hh.

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

private

Definition at line 277 of file SS_Info2.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 268 of file SS_Info2.cc.

Referenced by clone().

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

value constructor

Definition at line 275 of file SS_Info2.cc.

References initialize().

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

value constructor

Definition at line 283 of file SS_Info2.cc.

References initialize().

protocols::fldsgn::topology::SS_Info2::SS_Info2 ( SS_Info2 const & s)

copy constructor

Definition at line 291 of file SS_Info2.cc.

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

destructor

Definition at line 305 of file SS_Info2.cc.

Member Function Documentation

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

inline

get xyz-coordinates of backbone structure

Definition at line 346 of file SS_Info2.hh.

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

Definition at line 323 of file SS_Info2.hh.

References bbpos_is_set_.

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

clear data

Definition at line 318 of file SS_Info2.cc.

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

make clone

Definition at line 310 of file SS_Info2.cc.

References SS_Info2().

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

inline

return helices

Definition at line 362 of file SS_Info2.hh.

References helices_.

Referenced by protocols::fldsgn::potentials::sspot::HSPairPotential::score().

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

inline

return owning pointer of helix given an index of helices

Definition at line 385 of file SS_Info2.hh.

References helices_.

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

inline

return helix index in helices given a residue number

Definition at line 410 of file SS_Info2.hh.

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

Definition at line 446 of file SS_Info2.cc.

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

Definition at line 381 of file SS_Info2.cc.

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

Definition at line 345 of file SS_Info2.cc.

References bb_pos_, bbpos_is_set_, clear_data(), identify_ss(), core::chemical::ResidueType::is_protein(), core::pose::Pose::residue_type(), resize(), secstruct(), core::pose::Pose::secstruct(), secstruct_, set_SSorient(), protocols::fldsgn::topology::BB_Pos::take_coordinates_from_pose(), and core::pose::Pose::total_residue().

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

inline

return owning pointer of loop given an index of loops

Definition at line 393 of file SS_Info2.hh.

References loops_.

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

inline

return loop index in loops given a residue number

Definition at line 418 of file SS_Info2.hh.

References loop_id_.

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

inline

return loops

Definition at line 370 of file SS_Info2.hh.

References loops_.

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

private

resize vectors

Definition at line 333 of file SS_Info2.cc.

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

Definition at line 331 of file SS_Info2.hh.

References secstruct_.

Referenced by initialize().

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

inline

Definition at line 338 of file SS_Info2.hh.

References secstruct_.

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

set orientation vector of secondary structures given a pose

Definition at line 414 of file SS_Info2.cc.

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

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

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

Definition at line 425 of file SS_Info2.cc.

References bb_pos_, helices_, and strands_.

Referenced by initialize(), and set_SSorient().

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

inline

return the index of secondary structure element given a residue number

Definition at line 426 of file SS_Info2.hh.

References ss_element_id_.

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

inline

return owning pointer of strand given an index of strands

Definition at line 377 of file SS_Info2.hh.

References strands_.

Referenced by protocols::fldsgn::topology::StrandPairingSet::initialize_by_dimer_pairs().

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

inline

return strand index in strands given a residue number

Definition at line 402 of file SS_Info2.hh.

References strand_id_.

Referenced by protocols::fldsgn::topology::DimerPairings::finalize(), 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().

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

inline

return strands

Definition at line 354 of file SS_Info2.hh.

References strands_.

Referenced by 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

Definition at line 393 of file SS_Info2.cc.

Member Data Documentation

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

private

xyz-coordinates of backbone

Definition at line 467 of file SS_Info2.hh.

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

Definition at line 461 of file SS_Info2.hh.

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

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

private

vector of HelixOP

Definition at line 476 of file SS_Info2.hh.

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

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

private

vector for storing index of helix id for each residue position

Definition at line 479 of file SS_Info2.hh.

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

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

private

Definition at line 483 of file SS_Info2.hh.

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

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

private

vector of loops

Definition at line 482 of file SS_Info2.hh.

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

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

private

string of secondary structure elements

Definition at line 464 of file SS_Info2.hh.

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

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

private

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

Definition at line 486 of file SS_Info2.hh.

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

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

private

vector for storing index of strand id for each residue position

Definition at line 473 of file SS_Info2.hh.

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

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

private

vector of StrandOP

Definition at line 470 of file SS_Info2.hh.

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

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation