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

#include <Pool_ConvergenceCheck.hh>

Public Member Functions
	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	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::Size >	excluded_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

Referenced by protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::add_elem_to_cache(), protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::HierarchicalLevel(), and protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::load_pool().

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

virtual

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"
	)

References add(), and core::io::silent::SilentStruct::get_CA_xyz().

Referenced by protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::add().

void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add	(	core::pose::Pose const &	pose,
		std::string	new_tag
	)

References add(), protocols::simple_filters::coords(), protocols::toolbox::fill_CA_coords(), runtime_assert, and core::pose::Pose::total_residue().

void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add	(	ObjexxFCL::FArray2D_double const &	xyz,
		core::Size	nres,
		std::string	new_tag
	)

References basic::POOL_RMSD_ADD_STRUCTURE, PROF_START, PROF_STOP, and runtime_assert.

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

References protocols::toolbox::DecoySetEvaluation::coords(), and pool_.

Referenced by protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::dist_square(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate_core(), and protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::sort_pool().

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(), evaluate, protocols::toolbox::fill_CA_coords(), runtime_assert, and core::pose::Pose::total_residue().

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

References protocols::simple_filters::coords(), evaluate, core::io::silent::SilentStruct::get_CA_xyz(), and runtime_assert.

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

Reimplemented in protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD, and protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD.

References protocols::simple_filters::coords(), protocols::toolbox::fill_CA_coords(), core::pose::Pose::total_residue(), and protocols::canonical_sampling::tr.

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
	)

References add(), protocols::jd2::current_output_name(), evaluate, jobname, size(), and protocols::canonical_sampling::tr.

void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::fill_pool ( std::string const &  silentfile )

private

References core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), core::io::silent::SilentFileData::read_file(), utility::excn::EXCN_BadInput::show(), core::io::silent::SilentFileData::size(), and protocols::canonical_sampling::tr.

Referenced by Pool_RMSD().

virtual void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::finalize ( )

inlinevirtual

Reimplemented in protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD, protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD, and protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD.

void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::get	(	core::Size	index,
		ObjexxFCL::FArray2D_double &	result
	)

References protocols::canonical_sampling::tr.

std::string & protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::get_tag

(

core::Size

index

)

References protocols::canonical_sampling::tr.

core::Size protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::natom ( ) const

inlineprotected

References protocols::toolbox::DecoySetEvaluation::n_atoms(), and pool_.

Referenced by protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::add(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::dist_square(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), and protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate_core().

void protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::pop_back

(

)

References runtime_assert, and protocols::canonical_sampling::tr.

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

References protocols::toolbox::DecoySetEvaluation::n_decoys(), and pool_.

Referenced by protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::add(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::build_pair_dis_matrix(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::debug(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate_core(), and protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::HPool_RMSD().

std::string const& protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::tag ( core::Size  index ) const

inlineprotected

References tags_.

Referenced by protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::add_elem_to_cache(), protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::add_new(), protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::add_to_top_level(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate_core(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::HPool_RMSD(), and protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::load_lib().

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

Referenced by protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::add_new(), protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::add_to_top_level(), coords(), protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::evaluate(), protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::fill_top_level(), natom(), size(), and protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::top_level_pool_size().

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

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

• src/protocols/canonical_sampling/mc_convergence_checks/Pool_ConvergenceCheck.hh
• src/protocols/canonical_sampling/mc_convergence_checks/Pool_ConvergenceCheck.cc