core::scoring::Membrane_FAEmbed Class Reference

Membrane Fullatom embedding info. More...

#include <Membrane_FAPotential.hh>

Public Member Functions
	Membrane_FAEmbed ()
	Default Constructor. More...
	Membrane_FAEmbed (Membrane_FAEmbed const &src)
	Copy Constructor. More...
basic::datacache::CacheableDataOP	clone () const
	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...
Public Member Functions inherited from basic::datacache::CacheableData
virtual	~CacheableData ()

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.

Referenced by clone().

core::scoring::Membrane_FAEmbed::Membrane_FAEmbed

(

Membrane_FAEmbed const &

src

)

Copy Constructor.

Copy Constructor for Membrane Fullatom Embedding.

References calculated_, fa_center_, fa_depth_, Fa_Membed_update_, fa_proj_, fa_proj_coord_, and fa_proj_deriv_.

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_, core::conformation::Residue::nheavyatoms(), nres, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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

inlinevirtual

Cacheable Data base Mehtod - Clone Object.

Implements basic::datacache::CacheableData.

References Membrane_FAEmbed().

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::scoring::methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::scoring::Membrane_FAPotential::fa_projection(), core::scoring::methods::Fa_MbsolvEnergy::get_residue_pair_energy(), and core::scoring::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::scoring::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::scoring::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(), basic::options::OptionKeys::membrane::Fa_Membed_update, Fa_Membed_update_, basic::options::option, steepness_, basic::options::OptionKeys::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::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::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(), and Membrane_FAEmbed().

Real core::scoring::Membrane_FAEmbed::fa_center_

mutableprivate

Referenced by allocate_appropriate_memory(), fa_center(), and Membrane_FAEmbed().

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

mutableprivate

Referenced by allocate_appropriate_memory(), fa_depth(), and Membrane_FAEmbed().

bool core::scoring::Membrane_FAEmbed::Fa_Membed_update_

private

Referenced by Fa_Membed_update(), initialize(), and Membrane_FAEmbed().

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(), fa_proj(), and Membrane_FAEmbed().

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

mutableprivate

Referenced by allocate_appropriate_memory(), fa_proj_coord(), and Membrane_FAEmbed().

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

mutableprivate

Referenced by allocate_appropriate_memory(), fa_proj_deriv(), and Membrane_FAEmbed().

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:

• src/core/scoring/Membrane_FAPotential.hh
• src/core/scoring/Membrane_FAPotential.cc