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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...
 
Real & fa_proj (Size const seqpos, Size const atom)
 Compute FA Proj to Z Axis. More...
 
Real fa_proj (Size const seqpos, Size const atom) const
 
Real & fa_depth (Size const seqpos, Size const atom)
 Compute Depth of Position in Membrane. More...
 
Real fa_depth (Size const seqpos, Size const atom) const
 
Real & fa_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
 
Vector & fa_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...
 
Real & fa_center ()
 
Real fa_penalty () const
 
Real & fa_penalty ()
 
Real thickness () const
 
Real & thickness ()
 
Real steepness () const
 
Real & steepness ()
 
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

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

Default Constructor.

Member Function Documentation

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().

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

References calculated_.

Referenced by core::scoring::Membrane_FAPotential::fa_projection(), and core::scoring::Membrane_FAPotential::finalize().

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

References calculated_.

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

Cacheable Data base Mehtod - Clone Object.

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

Compute Fullatom Center.

References fa_center_.

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

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

References fa_center_.

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().

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

References fa_depth_.

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

References Fa_Membed_update_.

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

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

References Fa_Membed_update_.

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

References fa_penalty_.

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

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

References fa_penalty_.

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

Compute FA Proj to Z Axis.

References fa_proj_.

Referenced by core::energy_methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::scoring::Membrane_FAPotential::fa_projection(), core::energy_methods::Fa_MbsolvEnergy::get_residue_pair_energy(), and core::energy_methods::Fa_MbenvEnergy::residue_energy().

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

References fa_proj_.

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

Get Coordinates (I think it is storing these)

References fa_proj_coord_.

Referenced by core::energy_methods::Fa_MbenvEnergy::eval_atom_derivative(), and core::scoring::Membrane_FAPotential::fa_projection().

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

References fa_proj_coord_.

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

Compute Derivative of Fa Proj.

References fa_proj_deriv_.

Referenced by core::energy_methods::Fa_MbenvEnergy::eval_atom_derivative(), and core::scoring::Membrane_FAPotential::fa_projection().

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

References fa_proj_deriv_.

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

Initialize Mmebrane Fullatom Embedding from Options.

References allocate_appropriate_memory(), Fa_Membed_update_, steepness_, core::conformation::membrane::thickness, and thickness_.

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

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

References steepness_.

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

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

References steepness_.

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

References thickness_.

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

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

References thickness_.

Member Data Documentation

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

Referenced by calculated().

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

Referenced by allocate_appropriate_memory(), and fa_center().

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

Referenced by allocate_appropriate_memory(), and fa_depth().

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

Referenced by Fa_Membed_update(), and initialize().

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

Referenced by fa_penalty().

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

Referenced by allocate_appropriate_memory(), and fa_proj().

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

Referenced by allocate_appropriate_memory(), and fa_proj_coord().

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

Referenced by allocate_appropriate_memory(), and fa_proj_deriv().

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

Referenced by initialize(), and steepness().

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

Referenced by initialize(), and thickness().

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