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protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD Class Reference

#include <Pool_ConvergenceCheck.hh>

Inheritance diagram for protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD:
Inheritance graph
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Public Member Functions

 Pool_RMSD (std::string silent_file)
 
 Pool_RMSD ()
 
 ~Pool_RMSD () override
 
core::Size evaluate (core::pose::Pose const &, std::string &best_decoy, core::Real &best_rmsd) const
 return position in pool for the best_decoy More...
 
core::Size evaluate (core::io::silent::SilentStruct const &, std::string &best_decoy, core::Real &best_rmsd) const
 
virtual core::Size evaluate_and_add (core::pose::Pose const &pose, std::string &cluster_center, core::Real &best_rmsd, core::Real transition_threshold)
 
core::Size size () const
 
void add (core::io::silent::SilentStruct const &, std::string new_tag="keep_silent_tag")
 
void add (core::pose::Pose const &, std::string new_tag)
 
virtual void finalize ()
 
void get (core::Size index, ObjexxFCL::FArray2D_double &result)
 
std::string & get_tag (core::Size index)
 
void pop_back ()
 
void clear ()
 
void set_reserve_size (int max_size)
 
core::Size evaluate_and_add (ObjexxFCL::FArray2D_double &coords, std::string &best_decoy, core::Real &best_rmsd, core::Real transition_threshold)
 
core::Size evaluate (ObjexxFCL::FArray2D_double &, std::string &best_decoy, core::Real &best_rmsd) const
 
core::Size evaluate (ObjexxFCL::FArray2D_double &, std::string &best_decoy, core::Real &best_rmsd, core::Size index) const
 
void add (ObjexxFCL::FArray2D_double const &, core::Size nres, std::string new_tag)
 
void set_excluded_residues (utility::vector1< core::Size > const &excluded_residues)
 

Protected Member Functions

core::Size natom () const
 
ObjexxFCL::FArray3D_double const & coords () const
 
std::string const & tag (core::Size index) const
 

Private Types

typedef utility::vector1
< std::string > 
Tags
 

Private Member Functions

void fill_pool (std::string const &silentfile)
 

Private Attributes

toolbox::DecoySetEvaluation pool_
 
ObjexxFCL::FArray1D_double weights_
 
Tags tags_
 
core::Size reserve_size_
 
utility::vector1< core::Sizeexcluded_residues_
 

Member Typedef Documentation

typedef utility::vector1< std::string > protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::Tags
private

Constructor & Destructor Documentation

protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::Pool_RMSD ( std::string  silent_file)
inline

References fill_pool().

protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::Pool_RMSD ( )
inline
protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::~Pool_RMSD ( )
overridedefault

Member Function Documentation

void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add ( core::io::silent::SilentStruct const &  pss,
std::string  new_tag = "keep_silent_tag" 
)
void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add ( core::pose::Pose const &  pose,
std::string  new_tag 
)
void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add ( ObjexxFCL::FArray2D_double const &  xyz,
core::Size  nres,
std::string  new_tag 
)
void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::clear ( )
ObjexxFCL::FArray3D_double const& protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::coords ( ) const
inlineprotected
core::Size protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate ( core::pose::Pose const &  fit_pose,
std::string &  best_decoy,
core::Real best_rmsd 
) const

return position in pool for the best_decoy

References protocols::simple_filters::coords(), protocols::toolbox::fill_CA_coords(), and core::pose::Pose::size().

core::Size protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate ( core::io::silent::SilentStruct const &  pss,
std::string &  best_decoy,
core::Real best_rmsd 
) const
core::Size protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate ( ObjexxFCL::FArray2D_double &  ,
std::string &  best_decoy,
core::Real best_rmsd 
) const
core::Size protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate ( ObjexxFCL::FArray2D_double &  ,
std::string &  best_decoy,
core::Real best_rmsd,
core::Size  index 
) const
core::Size protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate_and_add ( core::pose::Pose const &  pose,
std::string &  cluster_center,
core::Real best_rmsd,
core::Real  transition_threshold 
)
virtual
core::Size protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate_and_add ( ObjexxFCL::FArray2D_double &  coords,
std::string &  best_decoy,
core::Real best_rmsd,
core::Real  transition_threshold 
)
void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::fill_pool ( std::string const &  silentfile)
private
virtual void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::finalize ( )
inlinevirtual
void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::get ( core::Size  index,
ObjexxFCL::FArray2D_double &  result 
)
std::string & protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::get_tag ( core::Size  index)
core::Size protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::natom ( ) const
inlineprotected
void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::pop_back ( )
void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::set_excluded_residues ( utility::vector1< core::Size > const &  excluded_residues)
void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::set_reserve_size ( int  max_size)
core::Size protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::size ( ) const
inline
std::string const& protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::tag ( core::Size  index) const
inlineprotected

Member Data Documentation

utility::vector1< core::Size > protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::excluded_residues_
private
toolbox::DecoySetEvaluation protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::pool_
private
core::Size protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::reserve_size_
private
Tags protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::tags_
private

Referenced by tag().

ObjexxFCL::FArray1D_double protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::weights_
private

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