#include <HPool.hh>

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 ()

virtual	~Pool_RMSD ()

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_OP >	subpools_

utility::vector1< core::Real >	pair_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::Size >	sub_ndx_deque_

Constructor & Destructor Documentation

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

References build_pair_dis_matrix(), has_child_, cluster::K_level, cluster::K_radius, level_, old_size_, option, radius_, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::size(), subpools_, t, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::tag(), tag_prefix_, and protocols::canonical_sampling::mc_convergence_checks::TR.

Referenced by load_lib().

Member Function Documentation

void protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::add	(	ObjexxFCL::FArray2D_double &	coord,
		std::string &	tag
	)

protected

References protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add(), dist_square(), has_child_, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::natom(), pair_dis_, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::size(), and subpools_.

Referenced by evaluate().

void protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::build_pair_dis_matrix ( )

private

References dist_square(), pair_dis_, and protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::size().

Referenced by HPool_RMSD().

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 ( )

References get_pair_dist(), and protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::size().

core::Real protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::dist_square	(	ObjexxFCL::FArray2_double &	conf1,
		ObjexxFCL::FArray2_double &	conf2
	)

private

References protocols::toolbox::fit_centered_coords(), cluster::K_not_fit_xyz, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::natom(), option, sum(), and weights.

Referenced by add(), build_pair_dis_matrix(), and dist_square().

core::Real protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::dist_square	(	core::Size	ndx1,
		core::Size	ndx2
	)

private

References protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::coords(), dist_square(), and protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::natom().

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
	)

References protocols::toolbox::fill_CA_coords(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::natom(), runtime_assert, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::size(), and core::pose::Pose::total_residue().

Referenced by evaluate().

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
	)

References utility::file::create_directory_recursive(), evaluate(), protocols::toolbox::file_full_path(), filename(), core::io::silent::SilentStruct::get_CA_xyz(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::natom(), path, runtime_assert, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::size(), protocols::canonical_sampling::mc_convergence_checks::TR, and core::io::silent::SilentFileData::write_silent_struct().

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

References add(), evaluate_core(), has_child_, load_lib(), n_extra_, old_size_, radius_, subpools_, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::tag(), tag_prefix_, and protocols::canonical_sampling::mc_convergence_checks::TR.

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

References protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::coords(), protocols::toolbox::fit_centered_coords(), get_pair_dist(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::natom(), protocols::toolbox::reset_x(), rmsd, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::size(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::tag(), and weights.

Referenced by evaluate().

core::Real protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::get_pair_dist	(	core::Size	i,
		core::Size	j
	)		const

private

References pair_dis_.

Referenced by debug(), and evaluate_core().

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 )

References clear_lib(), utility::file::file_exists(), filename(), has_child_, HPool_RMSD(), cluster::K_deque_level, cluster::K_deque_size, level_, protocols::canonical_sampling::mc_convergence_checks::lib_full_path(), option, sub_ndx_deque_, subpools_, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::tag(), and protocols::canonical_sampling::mc_convergence_checks::TR.

Referenced by evaluate().

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

Referenced by add(), build_pair_dis_matrix(), and get_pair_dist().

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

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

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:

src/protocols/canonical_sampling/mc_convergence_checks/HPool.hh
src/protocols/canonical_sampling/mc_convergence_checks/HPool.cc

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation