#include <FlexBBDesignMeanField.hh>

Inheritance diagram for protocols::mean_field::FlexBBDesignMeanField:

Public Member Functions
	FlexBBDesignMeanField (core::Size const option, core::pose::PoseOPs &poses, utility::vector1< core::pack::task::PackerTaskOP > tasks, core::scoring::ScoreFunctionOP scfxn)

	FlexBBDesignMeanField (core::Size const 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)

	~FlexBBDesignMeanField () override
	Destructor. More...

void	show (std::ostream &output=std::cout) const
	Generate string representation of FlexBBDesignMeanField for debugging purposes. More...

void	process () override
	overrides process() method in FlexBBMeanField to init AAMatrix for each rot_matrix and average them together More...

void	delete_pose (core::Size pose_ind) override
	deletes a pose from the list of poses More...

void	calc_bb_boltz_probs () override
	overrides FlexBBMeanField::calc_bb_boltz_probs to filter out bb_boltz_probs that aren't designable More...

AAMatrixCOP	aa_matrix () const
	returns averaged AAMatrix More...

void	calc_exp_value_aa_matrix ()
	calculates expected value (averaged) AAMatrix More...

utility::vector1< AAMatrix > const &	aa_matrices () const
	returns a const vector of the AAMatrices constructed from each pose More...

Public Member Functions inherited from protocols::mean_field::FlexBBMeanField
	FlexBBMeanField (core::Size const option, core::pose::PoseOPs &poses, utility::vector1< core::pack::task::PackerTaskOP > tasks, core::scoring::ScoreFunctionOP scfxn)

	FlexBBMeanField (core::Size const 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)

	~FlexBBMeanField () override
	Destructor. More...

void	show (std::ostream &output=std::cout) const
	Generate string representation of FlexBBMeanField for debugging purposes. More...

void	process () override
	overrides process() method in MeanField to add convergence step for each pose and averaging step for all rot_matrices_ More...

void	delete_pose (core::Size pose_ind) override
	deletes a pose from the list of poses More...

RotMatrixCOP	rot_matrix () const override
	returns the expected (averaged) RotMatrix (exp_rot_matrix_) More...

jagged_array< core::Real >	energy_matrix () const
	returns the expected (averaged) EnergyMatrix (exp_energy_matrix_) More...

void	renumber_rotamers ()
	renumbers rotamers with a backbone-independent rotamer numbering scheme More...

void	calc_exp_value_rot_matrix ()
	calculate expected (averaged) RotMatrix More...

jagged_array< core::Real > &	bb_boltz_probs ()
	used by derived classes for write-access to bb_boltz_probs_ More...

utility::vector1< jagged_array < core::Real > > const &	bb_boltz_probs_per_aa ()

utility::vector1< RotMatrix > const &	rot_matrices () const
	returns const references to the utility vector of rot_matrices representing each pose in the backbone ensemble More...

utility::vector1< jagged_array < core::Real > > const &	energy_matrices () const
	returns const references to the utility vector of energy_matrices representing each pose in the backbone ensemble 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...

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
	FlexBBDesignMeanField ()
	no default constructor, uncopyable More...

	FlexBBDesignMeanField (FlexBBDesignMeanField const &object_to_copy)

FlexBBDesignMeanField &	operator= (FlexBBDesignMeanField const &object_to_copy)

Private Attributes
utility::vector1< AAMatrix >	aa_matrices_

AAMatrixOP	exp_aa_matrix_

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

Additional Inherited Members
Protected Attributes inherited from protocols::mean_field::FlexBBMeanField
jagged_array< core::Real >	bb_boltz_probs_

utility::vector1< jagged_array < core::Real > >	bb_boltz_probs_per_aa_

Detailed Description

Remarks

Constructor & Destructor Documentation

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

References aa_matrices_.

protocols::mean_field::FlexBBDesignMeanField::FlexBBDesignMeanField	(	core::Size const	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
	)

References aa_matrices_.

protocols::mean_field::FlexBBDesignMeanField::~FlexBBDesignMeanField ( )

overridedefault

Destructor.

protocols::mean_field::FlexBBDesignMeanField::FlexBBDesignMeanField ( )

private

no default constructor, uncopyable

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

private

Member Function Documentation

utility::vector1< AAMatrix > const& protocols::mean_field::FlexBBDesignMeanField::aa_matrices ( ) const

inline

returns a const vector of the AAMatrices constructed from each pose

References aa_matrices_.

Referenced by protocols::mean_field::GenMeanFieldMover::report_aa_matrix().

AAMatrixCOP protocols::mean_field::FlexBBDesignMeanField::aa_matrix ( ) const

returns averaged AAMatrix

References exp_aa_matrix_.

Referenced by show().

void protocols::mean_field::FlexBBDesignMeanField::calc_bb_boltz_probs ( )

overridevirtual

overrides FlexBBMeanField::calc_bb_boltz_probs to filter out bb_boltz_probs that aren't designable

erases bb_boltz_probs_ for positions that aren't designed

Remarks: this doesn't affect the averaging of the RotMatrix (which is done for positions that are packed; and for positions that are designed) because the RotMatrix is averaged using the bb_boltz_weights_

Reimplemented from protocols::mean_field::FlexBBMeanField.

References protocols::mean_field::FlexBBMeanField::bb_boltz_probs(), protocols::mean_field::FlexBBMeanField::bb_boltz_probs_per_aa_, protocols::mean_field::FlexBBMeanField::calc_bb_boltz_probs(), and protocols::mean_field::FlexBBMeanField::rot_matrices().

void protocols::mean_field::FlexBBDesignMeanField::calc_exp_value_aa_matrix ( )

calculates expected value (averaged) AAMatrix

calculate "expected value" or averaged AAMatrix

weight each position-backbone-aa probability by the Boltzmann probability of that backbone occurring for that position

and then sum them up across all backbones for that position

References protocols::cluster::calibur::aa, aa_matrices_, protocols::mean_field::FlexBBMeanField::bb_boltz_probs(), and exp_aa_matrix_.

Referenced by process().

void protocols::mean_field::FlexBBDesignMeanField::delete_pose ( core::Size pose_ind )

overridevirtual

deletes a pose from the list of poses

resizes the aa_matrices_ vector to allow for the deleted pose

Remarks: called before aa_matrices_ has been fully assigned so simply truncating it is okay

Reimplemented from protocols::mean_field::MeanField.

References aa_matrices_, protocols::mean_field::FlexBBMeanField::delete_pose(), and protocols::mean_field::MeanField::num_poses().

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

private

void protocols::mean_field::FlexBBDesignMeanField::process ( )

overridevirtual

overrides process() method in FlexBBMeanField to init AAMatrix for each rot_matrix and average them together

to implement for design adds step to calculate AAMatrixs

Reimplemented from protocols::mean_field::MeanField.

References aa_matrices_, calc_exp_value_aa_matrix(), protocols::mean_field::FlexBBMeanField::energy_matrices(), protocols::mean_field::MeanField::num_poses(), protocols::mean_field::FlexBBMeanField::process(), protocols::mean_field::FlexBBMeanField::rot_matrices(), and protocols::mean_field::MeanField::temperature().

void protocols::mean_field::FlexBBDesignMeanField::show ( std::ostream & output = std::cout ) const

Generate string representation of FlexBBDesignMeanField for debugging purposes.

References aa_matrix(), and protocols::mean_field::FlexBBMeanField::rot_matrix().

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

Friends And Related Function Documentation

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

friend

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

Member Data Documentation

utility::vector1< AAMatrix > protocols::mean_field::FlexBBDesignMeanField::aa_matrices_

private

Referenced by aa_matrices(), calc_exp_value_aa_matrix(), delete_pose(), FlexBBDesignMeanField(), and process().

AAMatrixOP protocols::mean_field::FlexBBDesignMeanField::exp_aa_matrix_

private

Referenced by aa_matrix(), and calc_exp_value_aa_matrix().

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

src/protocols/mean_field/FlexBBDesignMeanField.hh
src/protocols/mean_field/FlexBBDesignMeanField.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation