Rosetta Core: core::scoring::MembraneEmbed Class Reference

Rosetta Core 2014.16.56682

Whole Pose Membrane Embedding. More...

#include <MembranePotential.hh>

Public Member Functions
	MembraneEmbed ()
	Default Constructor. More...

	MembraneEmbed (MembraneEmbed const &src)
	Copy Constructor. More...

basic::datacache::CacheableDataOP	clone () const
	Clone Cacheable Data. More...

Size	size () const
	Compute Size of MP (??) More...

Real &	depth (Size const seqpos)
	Compute depth of residue in the membrane. More...

void	set_normal (Vector const &v)
	Set Pose Embedding Normal (should not use this method, deprecated 3/11/14) More...

void	set_center (Vector const &v)
	Set Pose Embedding Center (should not use this method, deprecated 3/11/14) More...

void	set_penalty (Real const &p)
	Set Penalty. More...

Real	depth (Size const seqpos) const
	Get NonConst Depth. More...

bool &	spanning ()
	Return Ref Spanning Parameter. More...

bool	spanning () const
	Return Non_Ref Spanning Parameter. More...

bool	calculated () const
	Return Calculated (no idea what this does) More...

bool &	calculated ()
	Return Non_Ref Calculated (no idea what this does - maybe observer) More...

Vector const &	normal () const
	Get Normal Parameter. More...

Vector const &	center () const
	Get Center Parameter. More...

Real const &	penalty () const
	Get MP Penalty. More...

void	initialize (pose::Pose const &pose)
	Initialize Membrane Embedding From Pose?? More...

Public Member Functions inherited from basic::datacache::CacheableData
virtual	~CacheableData ()

Private Attributes
utility::vector1< Real >	depth_

Vector	normal_

Vector	center_

bool	calculated_

bool	spanning_

Size	tm_projection_

Real	penalty_

Detailed Description

Whole Pose Membrane Embedding.

Define the embedding of the membrane pose based on computed normal and center parameters. These are initialzed in the membrane protein framework and then recomputed based upon the structured and stored in MP residues (see MP Framework code)

Constructor & Destructor Documentation

core::scoring::MembraneEmbed::MembraneEmbed ( )

inline

Default Constructor.

Referenced by clone().

core::scoring::MembraneEmbed::MembraneEmbed ( MembraneEmbed const & src )

Copy Constructor.

Copy Constructor for a Membrane Embedding Object.

References calculated_, center_, depth_, normal_, penalty_, and spanning_.

Member Function Documentation

bool core::scoring::MembraneEmbed::calculated ( ) const

inline

Return Calculated (no idea what this does)

References calculated_.

Referenced by core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::Membrane_FAPotential::finalize(), and core::scoring::MembranePotential::finalize().

bool& core::scoring::MembraneEmbed::calculated ( )

inline

Return Non_Ref Calculated (no idea what this does - maybe observer)

References calculated_.

Vector const& core::scoring::MembraneEmbed::center ( ) const

inline

Get Center Parameter.

References center_.

Referenced by core::scoring::hbonds::HBondEnergy::setup_for_packing(), and core::scoring::hbonds::HBondEnergy::setup_for_scoring().

basic::datacache::CacheableDataOP core::scoring::MembraneEmbed::clone ( ) const

inlinevirtual

Clone Cacheable Data.

Implements basic::datacache::CacheableData.

References MembraneEmbed().

Real& core::scoring::MembraneEmbed::depth ( Size const seqpos )

inline

Compute depth of residue in the membrane.

References depth_.

Referenced by core::scoring::MembranePotential::compute_membrane_embedding().

Real core::scoring::MembraneEmbed::depth ( Size const seqpos ) const

inline

Get NonConst Depth.

References depth_.

void core::scoring::MembraneEmbed::initialize ( pose::Pose const & pose )

Initialize Membrane Embedding From Pose??

Initialize a Membrane Embedding Object.

References numeric::xyzVector< class >::assign(), center_, depth_, normal_, nres, and core::pose::Pose::total_residue().

Referenced by core::scoring::MembranePotential::compute_membrane_embedding().

Vector const& core::scoring::MembraneEmbed::normal ( ) const

inline

Get Normal Parameter.

References normal_.

Referenced by core::scoring::ChemicalShiftAnisotropy::compute_csascore(), core::scoring::DipolarCoupling::compute_dcscore(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), and core::scoring::hbonds::HBondEnergy::setup_for_scoring().

Real const& core::scoring::MembraneEmbed::penalty ( ) const

inline

Get MP Penalty.

References penalty_.

void core::scoring::MembraneEmbed::set_center ( Vector const & v )

inline

Set Pose Embedding Center (should not use this method, deprecated 3/11/14)

References center_.

Referenced by core::scoring::MembranePotential::compute_membrane_embedding().

void core::scoring::MembraneEmbed::set_normal ( Vector const & v )

inline

Set Pose Embedding Normal (should not use this method, deprecated 3/11/14)

References normal_.

Referenced by core::scoring::MembranePotential::compute_membrane_embedding().

void core::scoring::MembraneEmbed::set_penalty ( Real const & p )

inline

Set Penalty.

References penalty_.

Size core::scoring::MembraneEmbed::size ( ) const

inline

Compute Size of MP (??)

References depth_.

bool& core::scoring::MembraneEmbed::spanning ( )

inline

Return Ref Spanning Parameter.

References spanning_.

Referenced by core::scoring::MembranePotential::compute_membrane_embedding().

bool core::scoring::MembraneEmbed::spanning ( ) const

inline

Return Non_Ref Spanning Parameter.

References spanning_.

Member Data Documentation

bool core::scoring::MembraneEmbed::calculated_

private

Referenced by calculated(), and MembraneEmbed().

Vector core::scoring::MembraneEmbed::center_

private

Referenced by center(), initialize(), MembraneEmbed(), and set_center().

utility::vector1< Real > core::scoring::MembraneEmbed::depth_

private

Referenced by depth(), initialize(), MembraneEmbed(), and size().

Vector core::scoring::MembraneEmbed::normal_

private

Referenced by initialize(), MembraneEmbed(), normal(), and set_normal().

Real core::scoring::MembraneEmbed::penalty_

private

Referenced by MembraneEmbed(), penalty(), and set_penalty().

bool core::scoring::MembraneEmbed::spanning_

private

Referenced by MembraneEmbed(), and spanning().

Size core::scoring::MembraneEmbed::tm_projection_

private

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

symlinks/rosetta/src/core/scoring/MembranePotential.hh
symlinks/rosetta/src/core/scoring/MembranePotential.cc