#include <MeanField.hh>

Inheritance diagram for protocols::mean_field::MeanField:

Public Member Functions
	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...

virtual void	process ()
	simply calls the converge method to find a converged 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
	MeanField ()

	MeanField (MeanField const &object_to_copy)

MeanField &	operator= (MeanField const &object_to_copy)

void	calc_alt_rot_matrix ()
	calculate alt_rot_matrix_ by calculating an energies_matrix_ and then converting energies to Boltzmann probs More...

void	calc_energies_matrix ()
	calculates energies_matrix_ based on the energies in pig_ and the weights in rot_matrix_ More...

void	convert_energies_to_alt_rm ()
	converts the energies_matrix_ to the alt_rot_matrix_ by calculating the Boltzmann probabilities More...

bool	has_converged () const
	returns a bool, based on whether the maximum difference after rmsd-ing rot_matrix_ with alt_rot_matrix_ is < tolerance_ More...

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

Detailed Description

calculator which conducts mean-field algorithm on either a single, non-designable pose or used as base class of other MeanFields

Constructor & Destructor Documentation

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
	)

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,
		core::Real	lambda_mem,
		core::Real	tolerance,
		core::Real	temp,
		core::Real	threshold
	)

protocols::mean_field::MeanField::~MeanField ( )

overridedefault

Destructor.

protocols::mean_field::MeanField::MeanField ( )

private

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

private

Member Function Documentation

RotMatrixCOP protocols::mean_field::MeanField::alt_rot_matrix ( ) const

inline

returns const pointer to alternate RotMatrix

References alt_rot_matrix_.

void protocols::mean_field::MeanField::build_rot_matrix_for_pose ( core::Size pose_ind )

build a RotMatrix for a specific pose in poses_

builds a RotMatrix for a specific pose by initializing RotamerSets and using pack_rotamers_setup

also builds an IG for use in calculating energies_matrix

References alt_rot_matrix_, energies_matrix_, init_option_, core::pack::pack_rotamers_setup(), pig_, poses_, rot_matrix_, scfxn_, tasks_, and protocols::mean_field::TR().

Referenced by protocols::mean_field::FlexBBMeanField::process(), and process().

void protocols::mean_field::MeanField::calc_alt_rot_matrix ( )

private

calculate alt_rot_matrix_ by calculating an energies_matrix_ and then converting energies to Boltzmann probs

used by public methods of algorithm

calculates the next conformational matrix (RM)

i.e. if RotMatrix is RM(i), prints out RM(i+1)

first calculates energies matrix based on RM, then converts energies to Boltzmann weights (RM)

References calc_energies_matrix(), and convert_energies_to_alt_rm().

Referenced by converge().

void protocols::mean_field::MeanField::calc_energies_matrix ( )

private

calculates energies_matrix_ based on the energies in pig_ and the weights in rot_matrix_

calculates energies matrix from RM and IG

uses equation EM[i][j] = one_body_energy[ii][jj] + sum(two_body_energy[jj][n] where:

ii = node (position) of residue

jj = state (rotamer) of residue

n = other rotamers that interact with [ii][jj]

sum is over all rotamers of other residues that interact with [ii][jj]

References energies_matrix_, core::pack::interaction_graph::EdgeBase::get_other_ind(), pig_, rot_matrix_, and threshold_.

Referenced by calc_alt_rot_matrix().

void protocols::mean_field::MeanField::converge ( )

tries to converge to a final RotMatrix

runs mean-field algorithm until convergence is reached or 1000 rounds of convergence has been run

Remarks: 1000 is currently arbitrary - should possibly be changed later

References calc_alt_rot_matrix(), protocols::pack_daemon::error_message, has_converged(), lambda_memory(), rot(), rot_matrix_, and protocols::mean_field::TR().

Referenced by protocols::mean_field::FlexBBMeanField::process(), and process().

void protocols::mean_field::MeanField::convert_energies_to_alt_rm ( )

private

converts the energies_matrix_ to the alt_rot_matrix_ by calculating the Boltzmann probabilities

calculates Boltzmann weights from energies_matrix_ to form alt_rot_matrix_

References alt_rot_matrix_, energies_matrix_, protocols::buns::energy, rot(), temperature_, and threshold_.

Referenced by calc_alt_rot_matrix().

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

virtual

delete a pose

delete pose from the list of poses

Remarks: used if a pose fails to converge

Reimplemented in protocols::mean_field::FlexBBDesignMeanField, and protocols::mean_field::FlexBBMeanField.

References poses_, and tasks_.

Referenced by protocols::mean_field::FlexBBMeanField::delete_pose().

jagged_array< core::Real > const& protocols::mean_field::MeanField::energies_matrix ( ) const

inline

returns const reference to energies_matrix

References energies_matrix_.

Referenced by protocols::mean_field::DesignMeanField::init_aa_matrix(), and protocols::mean_field::FlexBBMeanField::process().

bool protocols::mean_field::MeanField::has_converged ( ) const

private

returns a bool, based on whether the maximum difference after rmsd-ing rot_matrix_ with alt_rot_matrix_ is < tolerance_

checks if algorithm has converged by checking if RMSmat < tolerance

References alt_rot_matrix_, energies_matrix_, protocols::simple_moves::bb_sampler::probability, rot(), rot_matrix_, tolerance_, and protocols::analysis::total.

Referenced by converge().

core::Real protocols::mean_field::MeanField::init_option ( ) const

inline

get init option (used to initialize RotMatrix)

References init_option_.

core::Real protocols::mean_field::MeanField::lambda_memory ( ) const

inline

get lambda memory, used in convergence process

References lambda_memory_.

Referenced by converge().

Size protocols::mean_field::MeanField::num_packed ( ) const

get number of residues that are packable

uses task_ to determine number of residues to be packed

References tasks_.

Referenced by protocols::mean_field::FlexBBMeanField::delete_pose().

core::Size protocols::mean_field::MeanField::num_poses ( ) const

inline

get number of poses

while this is trivial for MeanField (poses_.size() == 1), useful for derived classes with FlexBB

References poses_.

Referenced by protocols::mean_field::FlexBBMeanField::delete_pose(), protocols::mean_field::FlexBBDesignMeanField::delete_pose(), protocols::mean_field::FlexBBMeanField::process(), and protocols::mean_field::FlexBBDesignMeanField::process().

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

private

void protocols::mean_field::MeanField::process ( )

virtual

simply calls the converge method to find a converged RotMatrix

required so that it can be overridden in derived classes which perform many more functions while processing

Reimplemented in protocols::mean_field::FlexBBDesignMeanField, protocols::mean_field::DesignMeanField, and protocols::mean_field::FlexBBMeanField.

References build_rot_matrix_for_pose(), and converge().

Referenced by protocols::mean_field::DesignMeanField::process().

RotMatrixCOP protocols::mean_field::MeanField::rot_matrix ( ) const

virtual

returns const pointer to RotMatrix

Remarks: virtual because can be overridden by FlexBBMeanField

Reimplemented in protocols::mean_field::FlexBBMeanField.

References rot_matrix_.

Referenced by protocols::mean_field::DesignMeanField::init_aa_matrix(), protocols::mean_field::FlexBBMeanField::process(), and show().

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

Generate string representation of MeanField for debugging purposes.

prints out RotMatrix, Energies Matrix, and Alt RotMatrix

References alt_rot_matrix_, energies_matrix_, rot_matrix(), and protocols::mean_field::jagged_array< T, A >::show().

Referenced by protocols::mean_field::operator<<(), and protocols::mean_field::DesignMeanField::show().

core::Real protocols::mean_field::MeanField::temperature ( ) const

inline

get temperature (kT)

References temperature_.

Referenced by protocols::mean_field::FlexBBMeanField::calc_bb_boltz_probs(), protocols::mean_field::DesignMeanField::init_aa_matrix(), and protocols::mean_field::FlexBBDesignMeanField::process().

core::Real protocols::mean_field::MeanField::threshold ( ) const

inline

get threshold

References threshold_.

core::Real protocols::mean_field::MeanField::tolerance ( ) const

inline

get tolerance, used to determine if converged

References tolerance_.

Friends And Related Function Documentation

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

friend

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

Member Data Documentation

RotMatrixOP protocols::mean_field::MeanField::alt_rot_matrix_

private

Referenced by alt_rot_matrix(), build_rot_matrix_for_pose(), convert_energies_to_alt_rm(), has_converged(), and show().

jagged_array< core::Real > protocols::mean_field::MeanField::energies_matrix_

private

Referenced by build_rot_matrix_for_pose(), calc_energies_matrix(), convert_energies_to_alt_rm(), energies_matrix(), has_converged(), and show().

core::Real protocols::mean_field::MeanField::init_option_

private

Referenced by build_rot_matrix_for_pose(), and init_option().

core::Real protocols::mean_field::MeanField::lambda_memory_

private

Referenced by lambda_memory().

core::pack::interaction_graph::FixedBBInteractionGraphOP protocols::mean_field::MeanField::pig_

private

Referenced by build_rot_matrix_for_pose(), and calc_energies_matrix().

core::pose::PoseOPs& protocols::mean_field::MeanField::poses_

private

Referenced by build_rot_matrix_for_pose(), delete_pose(), and num_poses().

RotMatrixOP protocols::mean_field::MeanField::rot_matrix_

private

Referenced by build_rot_matrix_for_pose(), calc_energies_matrix(), converge(), has_converged(), and rot_matrix().

core::scoring::ScoreFunctionOP protocols::mean_field::MeanField::scfxn_

private

Referenced by build_rot_matrix_for_pose().

utility::vector1< core::pack::task::PackerTaskOP > protocols::mean_field::MeanField::tasks_

private

Referenced by build_rot_matrix_for_pose(), delete_pose(), and num_packed().

core::Real protocols::mean_field::MeanField::temperature_

private

Referenced by convert_energies_to_alt_rm(), and temperature().

core::Real protocols::mean_field::MeanField::threshold_

private

Referenced by calc_energies_matrix(), convert_energies_to_alt_rm(), and threshold().

core::Real protocols::mean_field::MeanField::tolerance_

private

Referenced by has_converged(), and tolerance().

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

src/protocols/mean_field/MeanField.hh
src/protocols/mean_field/MeanField.cc

Private Attributes
RotMatrixOP	rot_matrix_

RotMatrixOP	alt_rot_matrix_

jagged_array< core::Real >	energies_matrix_

core::Real	lambda_memory_

core::Real	tolerance_

core::Real	temperature_

core::Real	init_option_

core::Real	threshold_

core::pack::interaction_graph::FixedBBInteractionGraphOP	pig_

core::pose::PoseOPs &	poses_

utility::vector1 < core::pack::task::PackerTaskOP >	tasks_

core::scoring::ScoreFunctionOP	scfxn_

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation