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protocols::mean_field::FlexBBDesignMeanField Class Reference

#include <FlexBBDesignMeanField.hh>

Inheritance diagram for protocols::mean_field::FlexBBDesignMeanField:
Inheritance graph
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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::Realenergy_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)
 
FlexBBDesignMeanFieldoperator= (FlexBBDesignMeanField const &object_to_copy)
 

Private Attributes

utility::vector1< AAMatrixaa_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::Realbb_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
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
AAMatrixOP protocols::mean_field::FlexBBDesignMeanField::exp_aa_matrix_
private

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