Rosetta  2020.46
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD Class Reference

#include <HPool.hh>

Inheritance diagram for protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD:
Inheritance graph
[legend]

Public Member Functions

 HPool_RMSD (std::string silent_file, core::Size lv=1)
 
core::Size evaluate (core::pose::Pose &pose, core::Real resolution, std::string &best_decoy, core::Real &best_rmsd)
 
core::Size evaluate (core::io::silent::SilentStruct &pss, core::Real resolution, std::string &best_decoy, core::Real &best_rmsd)
 
bool load_lib (const core::Size)
 
void clear_lib (const core::Size)
 
core::Size get_size (core::Size nsubc)
 
void debug ()
 
- Public Member Functions inherited from protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
 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 evaluate (ObjexxFCL::FArray2D_double &coord, core::Real resolution, std::string &best_decoy, core::Real &best_rmsd)
 
core::Size evaluate_core (ObjexxFCL::FArray2D_double &coord, std::string &best_decoy, core::Real &best_rmsd, core::Size index) const
 
void add (ObjexxFCL::FArray2D_double &, std::string &)
 
- Protected Member Functions inherited from protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
core::Size natom () const
 
ObjexxFCL::FArray3D_double const & coords () const
 
std::string const & tag (core::Size index) const
 

Private Member Functions

void build_pair_dis_matrix ()
 
core::Real get_pair_dist (core::Size, core::Size) const
 
core::Real dist_square (ObjexxFCL::FArray2_double &, ObjexxFCL::FArray2_double &)
 
core::Real dist_square (core::Size, core::Size)
 

Private Attributes

utility::vector1< HPool_RMSD_OPsubpools_
 
utility::vector1< core::Realpair_dis_
 
std::string silent_file_
 
std::string tag_prefix_
 
core::Size old_size_
 
core::Size level_
 
core::Size n_extra_
 
core::Real radius_
 
bool has_child_
 
std::deque< core::Sizesub_ndx_deque_
 

Constructor & Destructor Documentation

protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::HPool_RMSD ( std::string  silent_file,
core::Size  lv = 1 
)

Member Function Documentation

void protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::add ( ObjexxFCL::FArray2D_double &  coord,
std::string &  tag 
)
protected
void protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::build_pair_dis_matrix ( )
private
void protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::clear_lib ( const core::Size  nc)

References subpools_.

Referenced by load_lib().

void protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::debug ( )
core::Real protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::dist_square ( ObjexxFCL::FArray2_double &  conf1,
ObjexxFCL::FArray2_double &  conf2 
)
private
core::Real protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::dist_square ( core::Size  ndx1,
core::Size  ndx2 
)
private
core::Size protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate ( core::pose::Pose pose,
core::Real  resolution,
std::string &  best_decoy,
core::Real best_rmsd 
)
core::Size protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate ( core::io::silent::SilentStruct pss,
core::Real  resolution,
std::string &  best_decoy,
core::Real best_rmsd 
)
core::Size protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate ( ObjexxFCL::FArray2D_double &  coord,
core::Real  resolution,
std::string &  best_decoy,
core::Real best_rmsd 
)
protected
core::Size protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate_core ( ObjexxFCL::FArray2D_double &  coord,
std::string &  best_decoy,
core::Real best_rmsd,
core::Size  index 
) const
protected
core::Real protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::get_pair_dist ( core::Size  i,
core::Size  j 
) const
private
core::Size protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::get_size ( core::Size  nsubc)
inline

References subpools_.

bool protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::load_lib ( const core::Size  nc)

Member Data Documentation

bool protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::has_child_
private

Referenced by add(), evaluate(), HPool_RMSD(), and load_lib().

core::Size protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::level_
private

Referenced by HPool_RMSD(), and load_lib().

core::Size protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::n_extra_
private

Referenced by evaluate().

core::Size protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::old_size_
private

Referenced by evaluate(), and HPool_RMSD().

utility::vector1< core::Real > protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::pair_dis_
private
core::Real protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::radius_
private

Referenced by evaluate(), and HPool_RMSD().

std::string protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::silent_file_
private
std::deque< core::Size > protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::sub_ndx_deque_
private

Referenced by load_lib().

utility::vector1< HPool_RMSD_OP > protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::subpools_
private
std::string protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::tag_prefix_
private

Referenced by evaluate(), and HPool_RMSD().


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