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core::scoring::MembraneEmbed Class Reference

Whole Pose Membrane Embedding. More...

#include <MembranePotential.hh>

Inheritance diagram for core::scoring::MembraneEmbed:
Inheritance graph

Public Member Functions

 MembraneEmbed ()
 Default Constructor. More...
basic::datacache::CacheableDataOP clone () const override
 Clone Cacheable Data. More...
Size size () const
 Compute Size of MP (??) More...
Realdepth (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...
boolspanning ()
 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...
boolcalculated ()
 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...

Private Attributes

utility::vector1< Realdepth_
Vector normal_
Vector center_
bool calculated_
bool spanning_
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 ( )

Default Constructor.

Member Function Documentation

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

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

References calculated_.

Vector const& core::scoring::MembraneEmbed::center ( ) const
basic::datacache::CacheableDataOP core::scoring::MembraneEmbed::clone ( ) const

Clone Cacheable Data.

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

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

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 center_, depth_, normal_, and core::pose::Pose::size().

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

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

Get MP Penalty.

References penalty_.

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

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)

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)

Set Penalty.

References penalty_.

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

Compute Size of MP (??)

References depth_.

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

Return Ref Spanning Parameter.

References spanning_.

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

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

Return Non_Ref Spanning Parameter.

References spanning_.

Member Data Documentation

bool core::scoring::MembraneEmbed::calculated_

Referenced by calculated().

Vector core::scoring::MembraneEmbed::center_

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

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

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

Vector core::scoring::MembraneEmbed::normal_

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

Real core::scoring::MembraneEmbed::penalty_

Referenced by penalty(), and set_penalty().

bool core::scoring::MembraneEmbed::spanning_

Referenced by spanning().

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