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core::scoring::Membrane_FAEmbed Class Reference

Membrane Fullatom embedding info. More...

#include <Membrane_FAPotential.hh>

Inheritance diagram for core::scoring::Membrane_FAEmbed:
Inheritance graph
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Public Member Functions

 Membrane_FAEmbed ()
 Default Constructor. More...
 
basic::datacache::CacheableDataOP clone () const override
 Cacheable Data base Mehtod - Clone Object. More...
 
Realfa_proj (Size const seqpos, Size const atom)
 Compute FA Proj to Z Axis. More...
 
Real fa_proj (Size const seqpos, Size const atom) const
 
Realfa_depth (Size const seqpos, Size const atom)
 Compute Depth of Position in Membrane. More...
 
Real fa_depth (Size const seqpos, Size const atom) const
 
Realfa_proj_deriv (Size const seqpos, Size const atom)
 Compute Derivative of Fa Proj. More...
 
Real fa_proj_deriv (Size const seqpos, Size const atom) const
 
Vectorfa_proj_coord (Size const seqpos, Size const atom)
 Get Coordinates (I think it is storing these) More...
 
Vector fa_proj_coord (Size const seqpos, Size const atom) const
 
Real fa_center () const
 Compute Fullatom Center. More...
 
Realfa_center ()
 
Real fa_penalty () const
 
Realfa_penalty ()
 
Real thickness () const
 
Realthickness ()
 
Real steepness () const
 
Realsteepness ()
 
bool calculated () const
 
bool & calculated ()
 
bool Fa_Membed_update () const
 
bool & Fa_Membed_update ()
 
void initialize (pose::Pose const &pose)
 Initialize Mmebrane Fullatom Embedding from Options. More...
 

Private Member Functions

void allocate_appropriate_memory (pose::Pose const &pose) const
 Allocate Memory needed in pose cache?? (rebecca thinks we don't need this) More...
 

Private Attributes

utility::vector1< utility::vector1< Real > > fa_proj_
 
utility::vector1< utility::vector1< Real > > fa_depth_
 
utility::vector1< utility::vector1< Vector > > fa_proj_coord_
 
utility::vector1< utility::vector1< Real > > fa_proj_deriv_
 
bool calculated_
 
Real fa_center_
 
Real fa_penalty_
 
Real thickness_
 
Real steepness_
 
bool Fa_Membed_update_
 

Detailed Description

Membrane Fullatom embedding info.

Cacheable Data - Stores Full atom embedding information including projection from z axis, fa depth, center, penalty, membrane thicnkess steepness and normal

Constructor & Destructor Documentation

◆ Membrane_FAEmbed()

core::scoring::Membrane_FAEmbed::Membrane_FAEmbed ( )
inline

Default Constructor.

Member Function Documentation

◆ allocate_appropriate_memory()

void core::scoring::Membrane_FAEmbed::allocate_appropriate_memory ( pose::Pose const &  pose) const
private

Allocate Memory needed in pose cache?? (rebecca thinks we don't need this)

Setup Data Members for Appropriate Sizing.

References fa_center_, fa_depth_, fa_proj_, fa_proj_coord_, fa_proj_deriv_, protocols::mean_field::max(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by initialize().

◆ calculated() [1/2]

bool& core::scoring::Membrane_FAEmbed::calculated ( )
inline

References calculated_.

◆ calculated() [2/2]

bool core::scoring::Membrane_FAEmbed::calculated ( ) const
inline

◆ clone()

basic::datacache::CacheableDataOP core::scoring::Membrane_FAEmbed::clone ( ) const
inlineoverride

Cacheable Data base Mehtod - Clone Object.

◆ fa_center() [1/2]

Real& core::scoring::Membrane_FAEmbed::fa_center ( )
inline

References fa_center_.

◆ fa_center() [2/2]

Real core::scoring::Membrane_FAEmbed::fa_center ( ) const
inline

Compute Fullatom Center.

References fa_center_.

Referenced by core::scoring::Membrane_FAPotential::fa_projection().

◆ fa_depth() [1/2]

Real& core::scoring::Membrane_FAEmbed::fa_depth ( Size const  seqpos,
Size const  atom 
)
inline

Compute Depth of Position in Membrane.

References fa_depth_.

Referenced by core::scoring::Membrane_FAPotential::fa_projection().

◆ fa_depth() [2/2]

Real core::scoring::Membrane_FAEmbed::fa_depth ( Size const  seqpos,
Size const  atom 
) const
inline

References fa_depth_.

◆ Fa_Membed_update() [1/2]

bool& core::scoring::Membrane_FAEmbed::Fa_Membed_update ( )
inline

References Fa_Membed_update_.

◆ Fa_Membed_update() [2/2]

bool core::scoring::Membrane_FAEmbed::Fa_Membed_update ( ) const
inline

◆ fa_penalty() [1/2]

Real& core::scoring::Membrane_FAEmbed::fa_penalty ( )
inline

References fa_penalty_.

◆ fa_penalty() [2/2]

Real core::scoring::Membrane_FAEmbed::fa_penalty ( ) const
inline

◆ fa_proj() [1/2]

Real& core::scoring::Membrane_FAEmbed::fa_proj ( Size const  seqpos,
Size const  atom 
)
inline

◆ fa_proj() [2/2]

Real core::scoring::Membrane_FAEmbed::fa_proj ( Size const  seqpos,
Size const  atom 
) const
inline

References fa_proj_.

◆ fa_proj_coord() [1/2]

Vector& core::scoring::Membrane_FAEmbed::fa_proj_coord ( Size const  seqpos,
Size const  atom 
)
inline

◆ fa_proj_coord() [2/2]

Vector core::scoring::Membrane_FAEmbed::fa_proj_coord ( Size const  seqpos,
Size const  atom 
) const
inline

References fa_proj_coord_.

◆ fa_proj_deriv() [1/2]

Real& core::scoring::Membrane_FAEmbed::fa_proj_deriv ( Size const  seqpos,
Size const  atom 
)
inline

◆ fa_proj_deriv() [2/2]

Real core::scoring::Membrane_FAEmbed::fa_proj_deriv ( Size const  seqpos,
Size const  atom 
) const
inline

References fa_proj_deriv_.

◆ initialize()

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

◆ steepness() [1/2]

Real& core::scoring::Membrane_FAEmbed::steepness ( )
inline

References steepness_.

◆ steepness() [2/2]

Real core::scoring::Membrane_FAEmbed::steepness ( ) const
inline

◆ thickness() [1/2]

Real& core::scoring::Membrane_FAEmbed::thickness ( )
inline

References thickness_.

◆ thickness() [2/2]

Real core::scoring::Membrane_FAEmbed::thickness ( ) const
inline

Member Data Documentation

◆ calculated_

bool core::scoring::Membrane_FAEmbed::calculated_
private

Referenced by calculated().

◆ fa_center_

Real core::scoring::Membrane_FAEmbed::fa_center_
mutableprivate

◆ fa_depth_

utility::vector1< utility::vector1 < Real > > core::scoring::Membrane_FAEmbed::fa_depth_
mutableprivate

◆ Fa_Membed_update_

bool core::scoring::Membrane_FAEmbed::Fa_Membed_update_
private

Referenced by Fa_Membed_update(), and initialize().

◆ fa_penalty_

Real core::scoring::Membrane_FAEmbed::fa_penalty_
mutableprivate

Referenced by fa_penalty().

◆ fa_proj_

utility::vector1< utility::vector1 < Real > > core::scoring::Membrane_FAEmbed::fa_proj_
mutableprivate

◆ fa_proj_coord_

utility::vector1< utility::vector1 < Vector > > core::scoring::Membrane_FAEmbed::fa_proj_coord_
mutableprivate

◆ fa_proj_deriv_

utility::vector1< utility::vector1 < Real > > core::scoring::Membrane_FAEmbed::fa_proj_deriv_
mutableprivate

◆ steepness_

Real core::scoring::Membrane_FAEmbed::steepness_
private

Referenced by initialize(), and steepness().

◆ thickness_

Real core::scoring::Membrane_FAEmbed::thickness_
private

Referenced by initialize(), and thickness().


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