protocols::mean_field::DesignMeanField Class Reference

#include <DesignMeanField.hh>

Inheritance diagram for protocols::mean_field::DesignMeanField:

Public Member Functions
	DesignMeanField (core::Size option, core::pose::PoseOPs &poses, utility::vector1< core::pack::task::PackerTaskOP > tasks, core::scoring::ScoreFunctionOP scfxn)
	DesignMeanField (core::Size option, core::pose::PoseOPs &poses, utility::vector1< core::pack::task::PackerTaskOP > tasks, core::scoring::ScoreFunctionOP scfxn, core::Real lambda_mem, core::Real tolerance, core::Real temp, core::Real threshold)
	~DesignMeanField () override
	Destructor. More...
void	show (std::ostream &output=std::cout) const
	Generate string representation of DesignMeanField for debugging purposes. More...
void	process () override
	overrides process() method in MeanField to initialize AAMatrix from RotMatrix More...
AAMatrixCOP	aa_matrix () const
	returns const reference to AAMatrix More...
Public Member Functions inherited from protocols::mean_field::MeanField
	MeanField (core::Size const option, core::pose::PoseOPs &poses, utility::vector1< core::pack::task::PackerTaskOP > const &tasks, core::scoring::ScoreFunctionOP scfxn)
	MeanField (core::Size const option, core::pose::PoseOPs &poses, utility::vector1< core::pack::task::PackerTaskOP > const &tasks, core::scoring::ScoreFunctionOP scfxn, core::Real lambda_mem, core::Real tolerance, core::Real temp, core::Real threshold)
	~MeanField () override
	Destructor. More...
void	show (std::ostream &output=std::cout) const
	Generate string representation of MeanField for debugging purposes. More...
void	converge ()
	tries to converge to a final RotMatrix More...
void	build_rot_matrix_for_pose (core::Size pose_ind)
	build a RotMatrix for a specific pose in poses_ More...
virtual void	delete_pose (core::Size pose_ind)
	delete a pose More...
virtual RotMatrixCOP	rot_matrix () const
	returns const pointer to RotMatrix More...
RotMatrixCOP	alt_rot_matrix () const
	returns const pointer to alternate RotMatrix More...
jagged_array< core::Real > const &	energies_matrix () const
	returns const reference to energies_matrix More...
core::Real	lambda_memory () const
	get lambda memory, used in convergence process More...
core::Real	tolerance () const
	get tolerance, used to determine if converged More...
core::Real	temperature () const
	get temperature (kT) More...
core::Real	threshold () const
	get threshold More...
core::Real	init_option () const
	get init option (used to initialize RotMatrix) More...
core::Size	num_poses () const
	get number of poses More...
core::Size	num_packed () const
	get number of residues that are packable More...

Private Member Functions
	DesignMeanField ()
	no default constructor, uncopyable More...
	DesignMeanField (DesignMeanField const &object_to_copy)
DesignMeanField &	operator= (DesignMeanField const &object_to_copy)
void	init_aa_matrix ()
	initialize the aa_matrix. More...

Private Attributes
AAMatrixOP	aa_matrix_

Friends
std::ostream &	operator<< (std::ostream &output, DesignMeanField const &object_to_output)
	Insertion operator (overloaded so that FlexBBMeanField can be "printed" in PyRosetta). More...

Detailed Description

calculator which conducts mean-field algorithm on one, designable pose to create a RotMatrix and AAMatrix

Constructor & Destructor Documentation

protocols::mean_field::DesignMeanField::DesignMeanField	(	core::Size	option,
		core::pose::PoseOPs &	poses,
		utility::vector1< core::pack::task::PackerTaskOP >	tasks,
		core::scoring::ScoreFunctionOP	scfxn
	)

protocols::mean_field::DesignMeanField::DesignMeanField	(	core::Size	option,
		core::pose::PoseOPs &	poses,
		utility::vector1< core::pack::task::PackerTaskOP >	tasks,
		core::scoring::ScoreFunctionOP	scfxn,
		core::Real	lambda_mem,
		core::Real	tolerance,
		core::Real	temp,
		core::Real	threshold
	)

protocols::mean_field::DesignMeanField::~DesignMeanField ( )

overridedefault

Destructor.

protocols::mean_field::DesignMeanField::DesignMeanField ( )

private

no default constructor, uncopyable

protocols::mean_field::DesignMeanField::DesignMeanField ( DesignMeanField const &  object_to_copy )

private

Member Function Documentation

AAMatrixCOP protocols::mean_field::DesignMeanField::aa_matrix

(

)

const

returns const reference to AAMatrix

References aa_matrix_.

void protocols::mean_field::DesignMeanField::init_aa_matrix ( )

private

initialize the aa_matrix.

Remarks

This can theoretically be called at any time but should only be called after the RotMatrix has converged

initalize a AAMatrix from the rot_matrix

References aa_matrix_, protocols::mean_field::MeanField::energies_matrix(), protocols::mean_field::MeanField::rot_matrix(), and protocols::mean_field::MeanField::temperature().

Referenced by process().

DesignMeanField& protocols::mean_field::DesignMeanField::operator= ( DesignMeanField const &  object_to_copy )

private

void protocols::mean_field::DesignMeanField::process ( )

overridevirtual

overrides process() method in MeanField to initialize AAMatrix from RotMatrix

Reimplemented from protocols::mean_field::MeanField.

References init_aa_matrix(), and protocols::mean_field::MeanField::process().

void protocols::mean_field::DesignMeanField::show

(

std::ostream &

output = std::cout

)

const

Generate string representation of DesignMeanField for debugging purposes.

References aa_matrix_, and protocols::mean_field::MeanField::show().

Referenced by protocols::mean_field::operator<<().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  output, DesignMeanField const &  object_to_output  )

friend

Insertion operator (overloaded so that FlexBBMeanField can be "printed" in PyRosetta).

Member Data Documentation

AAMatrixOP protocols::mean_field::DesignMeanField::aa_matrix_

private

Referenced by aa_matrix(), init_aa_matrix(), and show().

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

• src/protocols/mean_field/DesignMeanField.hh
• src/protocols/mean_field/DesignMeanField.cc