#include <FlexBBMeanField.hh>

Inheritance diagram for protocols::mean_field::FlexBBMeanField:

Public Member Functions
	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...

virtual void	calc_bb_boltz_probs ()
	calculate Boltzmann weights of each backbone 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...

Protected Attributes
jagged_array< core::Real >	bb_boltz_probs_

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

Private Member Functions
	FlexBBMeanField ()
	no default constructor, uncopyable More...

	FlexBBMeanField (FlexBBMeanField const &object_to_copy)

FlexBBMeanField &	operator= (FlexBBMeanField const &object_to_copy)

Private Attributes
utility::vector1< RotMatrix >	rot_matrices_

RotMatrixOP	exp_rot_matrix_

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

jagged_array< core::Real >	exp_energy_matrix_

jagged_array< core::Real >	bb_boltz_weights_

utility::vector1< core::Size >	nrot_per_pos_

Friends
std::ostream &	operator<< (std::ostream &output, FlexBBMeanField 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 several, non-designable poses to create a single, averaged RotMatrix

Constructor & Destructor Documentation

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

protocols::mean_field::FlexBBMeanField::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
	)

protocols::mean_field::FlexBBMeanField::~FlexBBMeanField ( )

overridedefault

Destructor.

protocols::mean_field::FlexBBMeanField::FlexBBMeanField ( )

private

no default constructor, uncopyable

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

private

Member Function Documentation

jagged_array< core::Real >& protocols::mean_field::FlexBBMeanField::bb_boltz_probs ( )

inline

used by derived classes for write-access to bb_boltz_probs_

Remarks: would prefer for the method to be protected, but disallowed by Rosetta Coding Conventions

References bb_boltz_probs_.

Referenced by protocols::mean_field::FlexBBDesignMeanField::calc_bb_boltz_probs(), and protocols::mean_field::FlexBBDesignMeanField::calc_exp_value_aa_matrix().

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

inline

References bb_boltz_probs_per_aa_.

void protocols::mean_field::FlexBBMeanField::calc_bb_boltz_probs ( )

virtual

calculate Boltzmann weights of each backbone

calculates Boltzmann probabilities of each position in each backbone, relative to the other backbones for that position

uses the sum of energies across all rotamers for each position at a backbone as the E(i) in P(i) = -e^(E(i)/kT)

Remarks: bb_boltz_weights_ = -e^(E(i)/kT); bb_boltz_probs_ = -e^(E(i)/kT) / Z where Z is the sum of -e^(E(i)/kT) for that position at each backbone

Reimplemented in protocols::mean_field::FlexBBDesignMeanField.

References protocols::cluster::calibur::aa, bb_boltz_probs_, bb_boltz_probs_per_aa_, bb_boltz_weights_, energy_matrices_, core::chemical::num_canonical_aas, rot(), rot_matrices_, and protocols::mean_field::MeanField::temperature().

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

void protocols::mean_field::FlexBBMeanField::calc_exp_value_rot_matrix ( )

calculate expected (averaged) RotMatrix

calculate "expected value" or averaged RotMatrix

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

and then sum them up across all backbones for that position

References bb_boltz_weights_, energy_matrices_, exp_energy_matrix_, exp_rot_matrix_, nrot_per_pos_, rot(), and rot_matrices_.

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

overridevirtual

deletes a pose from the list of poses

overrides MeanField::delete_pose to resize appropriate data members

used to delete a pose which does not reach convergence

Remarks: meant to be called before rot_matrices_ and energy_matrices_ have been fully assigned; and before any bb_boltz_weights or nrot_per_pos have been assigned at all

Reimplemented from protocols::mean_field::MeanField.

References protocols::mean_field::jagged_array< T, A >::assign(), bb_boltz_probs_, bb_boltz_probs_per_aa_, bb_boltz_weights_, protocols::mean_field::MeanField::delete_pose(), energy_matrices_, nrot_per_pos_, core::chemical::num_canonical_aas, protocols::mean_field::MeanField::num_packed(), protocols::mean_field::MeanField::num_poses(), and rot_matrices_.

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

utility::vector1< jagged_array < core::Real > > const& protocols::mean_field::FlexBBMeanField::energy_matrices ( ) const

inline

returns const references to the utility vector of energy_matrices representing each pose in the backbone ensemble

References energy_matrices_.

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

jagged_array< core::Real > protocols::mean_field::FlexBBMeanField::energy_matrix ( ) const

inline

returns the expected (averaged) EnergyMatrix (exp_energy_matrix_)

References exp_energy_matrix_.

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

private

void protocols::mean_field::FlexBBMeanField::process ( )

overridevirtual

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

for each pose, tries to build a RotMatrix, converge, and save values of RotMatrix and energy_matrix

to rot_matrices and energy_matrices, then renumbers the rotamers, calculates the Backbone Boltzmann Probabilities

and calculates the averaged RotMatrix

Remarks: if there are errors in building a RotMatrix or if the pose did not converge, that pose is deleted

Reimplemented from protocols::mean_field::MeanField.

References protocols::mean_field::MeanField::build_rot_matrix_for_pose(), calc_bb_boltz_probs(), protocols::mean_field::MeanField::converge(), delete_pose(), protocols::mean_field::MeanField::energies_matrix(), energy_matrices_, protocols::pack_daemon::error_message, protocols::mean_field::MeanField::num_poses(), rot_matrices_, protocols::mean_field::MeanField::rot_matrix(), and protocols::mean_field::TR().

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

void protocols::mean_field::FlexBBMeanField::renumber_rotamers ( )

renumbers rotamers with a backbone-independent rotamer numbering scheme

renumbers the rotamers using a ResHashMap

inserts rotamers into the ResHashMap using a hash function that rounds chi angles down to nearest 10 degrees

before attempting an insert, check if a rotamer has already been inserted and if so, what its rotamer index is

References protocols::mean_field::ResHashMap::attempt_insert(), protocols::mean_field::ResHashMap::last_ind_assigned(), nrot_per_pos_, rot(), and rot_matrices_.

utility::vector1< RotMatrix > const& protocols::mean_field::FlexBBMeanField::rot_matrices ( ) const

inline

returns const references to the utility vector of rot_matrices representing each pose in the backbone ensemble

References rot_matrices_.

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

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

overridevirtual

returns the expected (averaged) RotMatrix (exp_rot_matrix_)

overrides MeanField::rot_matrix to return the averaged RotMatrix

Reimplemented from protocols::mean_field::MeanField.

References exp_rot_matrix_.

Referenced by show(), and protocols::mean_field::FlexBBDesignMeanField::show().

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

Generate string representation of FlexBBMeanField for debugging purposes.

prints out the exp_rot_matrix_

References rot_matrix().

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

Friends And Related Function Documentation

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

friend

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

Member Data Documentation

jagged_array< core::Real > protocols::mean_field::FlexBBMeanField::bb_boltz_probs_

protected

Referenced by bb_boltz_probs(), calc_bb_boltz_probs(), and delete_pose().

utility::vector1< jagged_array < core::Real > > protocols::mean_field::FlexBBMeanField::bb_boltz_probs_per_aa_

protected

Referenced by bb_boltz_probs_per_aa(), calc_bb_boltz_probs(), protocols::mean_field::FlexBBDesignMeanField::calc_bb_boltz_probs(), and delete_pose().

jagged_array< core::Real > protocols::mean_field::FlexBBMeanField::bb_boltz_weights_

private

Referenced by calc_bb_boltz_probs(), calc_exp_value_rot_matrix(), and delete_pose().

utility::vector1< jagged_array < core::Real > > protocols::mean_field::FlexBBMeanField::energy_matrices_

private

Referenced by calc_bb_boltz_probs(), calc_exp_value_rot_matrix(), delete_pose(), energy_matrices(), and process().

jagged_array< core::Real > protocols::mean_field::FlexBBMeanField::exp_energy_matrix_

private

Referenced by calc_exp_value_rot_matrix(), and energy_matrix().

RotMatrixOP protocols::mean_field::FlexBBMeanField::exp_rot_matrix_

private

Referenced by calc_exp_value_rot_matrix(), and rot_matrix().

utility::vector1< core::Size > protocols::mean_field::FlexBBMeanField::nrot_per_pos_

private

Referenced by calc_exp_value_rot_matrix(), delete_pose(), and renumber_rotamers().

utility::vector1< RotMatrix > protocols::mean_field::FlexBBMeanField::rot_matrices_

private

Referenced by calc_bb_boltz_probs(), calc_exp_value_rot_matrix(), delete_pose(), process(), renumber_rotamers(), and rot_matrices().

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

src/protocols/mean_field/FlexBBMeanField.hh
src/protocols/mean_field/FlexBBMeanField.cc

Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation