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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
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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 ( )
inline

Default Constructor.

Member Function Documentation

bool core::scoring::MembraneEmbed::calculated ( ) const
inline
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
basic::datacache::CacheableDataOP core::scoring::MembraneEmbed::clone ( ) const
inlineoverride

Clone Cacheable Data.

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

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

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

Vector core::scoring::MembraneEmbed::center_
private

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

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

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

Vector core::scoring::MembraneEmbed::normal_
private

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

Real core::scoring::MembraneEmbed::penalty_
private

Referenced by penalty(), and set_penalty().

bool core::scoring::MembraneEmbed::spanning_
private

Referenced by spanning().


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