Rosetta: protocols::fldsgn::topology::Sheet Class Reference

#include <Sheet.hh>

Inheritance diagram for protocols::fldsgn::topology::Sheet:

Inheritance graph

Public Types
typedef core::Size	Size

typedef core::Real	Real

typedef core::Vector	Vector

typedef core::pose::Pose	Pose

typedef utility::vector1 < core::Size >	VecSize

typedef utility::vector1< int >	VecInt

typedef utility::vector1< Real >	VecReal

typedef protocols::fldsgn::topology::SS_Info2_COP	SS_Info2_COP

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

	Sheet (VecSize const &order_strands, VecInt const &orient_strands, bool is_barrel)
	value constructor More...

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

	~Sheet () override
	default destructor More...

SheetOP	clone ()
	clone this object More...

void	initialize ()
	intialize this class More...

core::Size	num_strands () const
	the number strands inclued in More...

bool	is_barrel () const
	is this barrel ? More...

VecSize	order_strands () const

core::Size	order_strand (core::Size const s) const

VecInt	orient_strands () const

int	orient_strand (core::Size const s) const

core::Size	strand_order (core::Size const s)

VecInt	ca_cb_orients () const

int	ca_cb_orient (core::Size const s) const

int	which_side (Vector const &vec) const

utility::vector1< Real >	calc_sasa_bothsides (Pose const &pose, SS_Info2_COP const ssinfo, Real pore_radius=1.5)
	calc surface areas only with beta-sheet More...

void	calc_geometry (SS_Info2_COP const ssinfo)
	calc geometry of sheet, sheet_plane_, sheet_center_, ca_cb_orients_ More...

bool	is_member (core::Size const s)
	whether the given strand number belongs to this sheet or not More...

Private Attributes
core::Size	num_strands_

bool	is_barrel_

VecSize	order_strands_
	order of strand in sheet -> id of strand More...

VecInt	orient_strands_
	order of strand in sheet -> id of strand More...

std::map< core::Size, core::Size >	strand_order_
	id of strand -> order of strand in sheet More...

Vector	sheet_plane_
	vector defining sheet plane More...

Vector	sheet_center_
	"center" of sheet More...

VecInt	ca_cb_orients_

bool	is_geometry_initialized_
	geometries was calculated or not More...

Friends
std::ostream &	operator<< (std::ostream &out, const Sheet &s)
	return strand pairing More...

Member Typedef Documentation

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

typedef core::Real protocols::fldsgn::topology::Sheet::Real

typedef core::Size protocols::fldsgn::topology::Sheet::Size

typedef protocols::fldsgn::topology::SS_Info2_COP protocols::fldsgn::topology::Sheet::SS_Info2_COP

typedef utility::vector1< int > protocols::fldsgn::topology::Sheet::VecInt

typedef utility::vector1< Real > protocols::fldsgn::topology::Sheet::VecReal

typedef utility::vector1< core::Size > protocols::fldsgn::topology::Sheet::VecSize

typedef core::Vector protocols::fldsgn::topology::Sheet::Vector

Constructor & Destructor Documentation

protocols::fldsgn::topology::Sheet::Sheet ( )

default constructor

References initialize().

protocols::fldsgn::topology::Sheet::Sheet	(	VecSize const &	order_strands,
		VecInt const &	orient_strands,
		bool	is_barrel
	)

value constructor

References initialize().

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

copy constructor

protocols::fldsgn::topology::Sheet::~Sheet ( )

overridedefault

default destructor

Member Function Documentation

int protocols::fldsgn::topology::Sheet::ca_cb_orient ( core::Size const s ) const

inline

References ca_cb_orients_.

Referenced by calc_sasa_bothsides().

VecInt protocols::fldsgn::topology::Sheet::ca_cb_orients ( ) const

inline

References ca_cb_orients_.

void protocols::fldsgn::topology::Sheet::calc_geometry ( SS_Info2_COP const ssinfo )

calc geometry of sheet, sheet_plane_, sheet_center_, ca_cb_orients_

calc geometry

References ca_cb_orients_, core::sequence::end, is_geometry_initialized_, num_strands_, order_strands_, orient_strands_, sheet_center_, and sheet_plane_.

utility::vector1< Real > protocols::fldsgn::topology::Sheet::calc_sasa_bothsides	(	Pose const &	pose,
		SS_Info2_COP const	ssinfo,
		Real	pore_radius = `1.5`
	)

calc surface areas only with beta-sheet

References ca_cb_orient(), core::scoring::calc_per_atom_sasa(), core::sequence::end, core::pose::initialize_atomid_map(), is_geometry_initialized_, order_strands_, core::id::AtomID_Map< T >::set(), and core::pose::Pose::size().

SheetOP protocols::fldsgn::topology::Sheet::clone ( )

inline

clone this object

void protocols::fldsgn::topology::Sheet::initialize ( )

intialize this class

initialize this class

References num_strands_, order_strands_, and strand_order_.

Referenced by Sheet().

bool protocols::fldsgn::topology::Sheet::is_barrel ( ) const

inline

is this barrel ?

References is_barrel_.

bool protocols::fldsgn::topology::Sheet::is_member ( core::Size const s )

whether the given strand number belongs to this sheet or not

References order_strands_.

core::Size protocols::fldsgn::topology::Sheet::num_strands ( ) const

inline

the number strands inclued in

References num_strands_.

core::Size protocols::fldsgn::topology::Sheet::order_strand ( core::Size const s ) const

inline

References order_strands_.

VecSize protocols::fldsgn::topology::Sheet::order_strands ( ) const

inline

References order_strands_.

Referenced by protocols::fldsgn::topology::operator<<().

int protocols::fldsgn::topology::Sheet::orient_strand ( core::Size const s ) const

inline

References orient_strands_.

VecInt protocols::fldsgn::topology::Sheet::orient_strands ( ) const

inline

References orient_strands_.

Referenced by protocols::fldsgn::topology::operator<<().

core::Size protocols::fldsgn::topology::Sheet::strand_order ( core::Size const s )

inline

References strand_order_.

int protocols::fldsgn::topology::Sheet::which_side ( Vector const & vec ) const

References sheet_center_, and sheet_plane_.

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		const Sheet &	s
	)

friend

return strand pairing

Member Data Documentation

VecInt protocols::fldsgn::topology::Sheet::ca_cb_orients_

private

Referenced by ca_cb_orient(), ca_cb_orients(), and calc_geometry().

bool protocols::fldsgn::topology::Sheet::is_barrel_

private

Referenced by is_barrel().

bool protocols::fldsgn::topology::Sheet::is_geometry_initialized_

private

geometries was calculated or not

Referenced by calc_geometry(), and calc_sasa_bothsides().

core::Size protocols::fldsgn::topology::Sheet::num_strands_

private

Referenced by calc_geometry(), initialize(), and num_strands().

VecSize protocols::fldsgn::topology::Sheet::order_strands_

private

order of strand in sheet -> id of strand

Referenced by calc_geometry(), calc_sasa_bothsides(), initialize(), is_member(), order_strand(), and order_strands().

VecInt protocols::fldsgn::topology::Sheet::orient_strands_

private

order of strand in sheet -> id of strand

Referenced by calc_geometry(), orient_strand(), and orient_strands().

Vector protocols::fldsgn::topology::Sheet::sheet_center_

private

"center" of sheet

Referenced by calc_geometry(), and which_side().

Vector protocols::fldsgn::topology::Sheet::sheet_plane_

private

vector defining sheet plane

Referenced by calc_geometry(), and which_side().

std::map< core::Size, core::Size > protocols::fldsgn::topology::Sheet::strand_order_

private

id of strand -> order of strand in sheet

Referenced by initialize(), and strand_order().

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

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