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protocols::mean_field::DesignMeanField Class Reference

#include <DesignMeanField.hh>

Inheritance diagram for protocols::mean_field::DesignMeanField:
Inheritance graph
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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)
 
DesignMeanFieldoperator= (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().


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