#include <LoopGrower.hh>

Public Member Functions
	LoopPartialSolutionStore ()=default

	LoopPartialSolutionStore (core::Size N, core::Real rmscutoff, core::Size master_beam_width, core::Real master_beam_cutoff)

void	setfilterparams (core::Size fragmelt, core::Size rmswindow, core::Size parallelcount, core::Real beamscorecutoff, bool dump_errors, bool dump_beam, bool writebeams, bool clustercheck, bool fafilter, bool samplesheets, bool filterprevious, bool checksymm, bool asymmdump, bool dumpfinalbeam)

void	store (LoopPartialSolution const &new_entry)

void	set_filterprevious (bool filterprevious)

void	filter (core::pose::Pose &pose, core::Size maxbeam, core::Size total_lower, core::Size lower_res, core::Size upper_res, core::Size cycle)

void	diversityfilter (core::Size maxbeamsize, core::Size total_lower)

void	parametercheck_filter (core::pose::Pose &pose, core::Size fragmelt, core::Size total_lower, core::Size lower_res, core::Size upper_res, core::Size rmswindow, bool dump_beam, core::Size &totalreqbeam, core::Size &totalreqmaxbeam, core::Real &totalreqscorecut, bool writebeams, core::Size cycle, core::Size parallelcount)

void	zscoretransform ()

void	cluster_check (LoopPartialSolution nearnativelps, core::pose::Pose &pose, core::Size total_lower, core::Size lower_res, core::Size upper_res)

void	push (core::pose::Pose &pose, LoopPartialSolution const &new_entry, core::Size fragmelt, core::Real beamscorecutoff, core::Size total_lower, bool lower, bool dump_errors, core::Real RMS, core::Size lower_res, core::Size upper_res)

void	report_rms_and_scores (core::Size rangelo, core::Size rangehi)

void	sort ()

void	sortrms ()

bool	filterprevious (LoopPartialSolution lps, core::Size total_lower, core::Size fragmelt, core::Real rmscutoff, core::Size masterbeamwidth)

void	skeleton_filter (core::pose::Pose &pose, DensSkeleton &skeleton, core::Size start_res, core::Size stop_res, core::Size lower_term, core::Size res_gap)

LoopPartialSolution	operator[] (core::Size solutions_index)

void	clear ()

void	set_fastas (core::Size lower, core::Size upper)

void	set_poses (core::Size lower, core::Size upper)

void	set_cutpoint (core::Size cutpoint)

core::Size	get_lower_fasta ()

core::Size	get_upper_fasta ()

core::Size	get_lower_pose ()

core::Size	get_upper_pose ()

core::Size	get_cutpoint ()

utility::vector1 < LoopPartialSolution >	get_solutions ()

utility::vector1 < LoopPartialSolution >	get_filteronly_solutions ()

void	store_filteronly_solutions (utility::vector1< LoopPartialSolution > filteronly)

bool	is_empty ()

core::Size	size ()

void	writelpsstore (core::Size loopid, core::Size jobid)

Private Attributes
core::Real	rmscutoff_ = 0.0

core::Real	master_beam_cutoff_ = 3.0

core::Real	beamscorecutoff_ = 0.85

core::Size	maxelts_ = 1

core::Size	master_beam_width_ = 1

core::Size	upper_fasta_ = 0

core::Size	lower_fasta_ = 0

core::Size	lower_pose_ = 0

core::Size	upper_pose_ = 0

core::Size	cutpoint_ = 0

core::Size	fragmelt_ = 1

core::Size	rmswindow_ = 1

core::Size	parallelcount_ = 0

core::Size	rank_ = 0

utility::vector1 < LoopPartialSolution >	solutions_

utility::vector1 < LoopPartialSolution >	old_solutions_

utility::vector1 < LoopPartialSolution >	filteronly_solutions_

bool	dump_errors_ = false

bool	dump_beam_ = false

bool	writebeams_ = false

bool	clustercheck_ = false

bool	fafilter_ = true

bool	samplesheets_ = true

bool	filterprevious_ = false

bool	checksymm_ = false

bool	asymmdump_ = true

bool	dumpfinalbeam_ = false

Constructor & Destructor Documentation

protocols::loop_grower::LoopPartialSolutionStore::LoopPartialSolutionStore ( )

default

protocols::loop_grower::LoopPartialSolutionStore::LoopPartialSolutionStore	(	core::Size	N,
		core::Real	rmscutoff,
		core::Size	master_beam_width,
		core::Real	master_beam_cutoff
	)

inline

References master_beam_cutoff_, master_beam_width_, maxelts_, core::chemical::element::N, and rmscutoff_.

Member Function Documentation

void protocols::loop_grower::LoopPartialSolutionStore::clear ( )

inline

References solutions_.

Referenced by protocols::loop_grower::LoopGrower::coordinate_filter(), protocols::loop_grower::LoopGrower::fafilter(), protocols::loop_grower::LoopGrower::full_atom_beam(), and protocols::loop_grower::LoopGrower::rescoresolutionset().

void protocols::loop_grower::LoopPartialSolutionStore::cluster_check	(	LoopPartialSolution	nearnativelps,
		core::pose::Pose &	pose,
		core::Size	total_lower,
		core::Size	lower_res,
		core::Size	upper_res
	)

References protocols::loop_grower::LoopPartialSolution::apply(), core::pose::PDBInfo::attach_to(), core::conformation::Conformation::chains_from_termini(), core::pose::Pose::conformation(), core::pose::Pose::dump_pdb(), protocols::loop_grower::LoopPartialSolution::get_rms(), protocols::loop_grower::LoopPartialSolution::get_score(), protocols::loop_grower::LoopPartialSolution::partialrms(), protocols::hybridization::score, and core::id::to_string().

void protocols::loop_grower::LoopPartialSolutionStore::diversityfilter	(	core::Size	maxbeamsize,
		core::Size	total_lower
	)

References protocols::loop_grower::LoopPartialSolution::get_rms(), protocols::loop_grower::LoopPartialSolution::get_score(), get_solutions(), protocols::loop_grower::LoopPartialSolution::partialrms(), size(), store(), and protocols::loop_grower::TRACER().

void protocols::loop_grower::LoopPartialSolutionStore::filter	(	core::pose::Pose &	pose,
		core::Size	maxbeam,
		core::Size	total_lower,
		core::Size	lower_res,
		core::Size	upper_res,
		core::Size	cycle
	)

References protocols::loop_grower::LoopPartialSolution::apply(), protocols::loop_grower::LoopPartialSolution::apply_sheets(), core::pose::PDBInfo::attach_to(), core::conformation::Conformation::chains_from_termini(), core::pose::Pose::conformation(), core::pose::Pose::dump_pdb(), core::pose::symmetry::extract_asymmetric_unit(), protocols::loop_grower::LoopPartialSolution::get_id(), protocols::loop_grower::LoopPartialSolution::get_rms(), protocols::loop_grower::LoopPartialSolution::get_score(), core::pose::symmetry::is_symmetric(), core::id::to_string(), protocols::loop_grower::TRACER(), and protocols::loop_grower::transform_to_closest_symmunit().

Referenced by protocols::loop_grower::LoopGrower::fafilter(), and protocols::loop_grower::LoopGrower::single_grow().

bool protocols::loop_grower::LoopPartialSolutionStore::filterprevious	(	LoopPartialSolution	lps,
		core::Size	total_lower,
		core::Size	fragmelt,
		core::Real	rmscutoff,
		core::Size	masterbeamwidth
	)

References protocols::loop_grower::LoopPartialSolution::get_score(), protocols::loop_grower::LoopPartialSolution::partialrms(), and protocols::hybridization::score.

Referenced by set_filterprevious(), and setfilterparams().

core::Size protocols::loop_grower::LoopPartialSolutionStore::get_cutpoint ( )

inline

References cutpoint_.

Referenced by protocols::loop_grower::LoopComparator::fill_pose().

utility::vector1<LoopPartialSolution> protocols::loop_grower::LoopPartialSolutionStore::get_filteronly_solutions ( )

inline

References filteronly_solutions_.

Referenced by protocols::loop_grower::LoopGrower::single_grow().

core::Size protocols::loop_grower::LoopPartialSolutionStore::get_lower_fasta ( )

inline

References lower_fasta_.

Referenced by protocols::loop_grower::LoopComparator::set_scores().

core::Size protocols::loop_grower::LoopPartialSolutionStore::get_lower_pose ( )

inline

References lower_pose_.

Referenced by protocols::loop_grower::LoopComparator::fill_pose().

utility::vector1<LoopPartialSolution> protocols::loop_grower::LoopPartialSolutionStore::get_solutions ( )

inline

References solutions_.

Referenced by protocols::loop_grower::LoopGrower::apply(), diversityfilter(), and parametercheck_filter().

core::Size protocols::loop_grower::LoopPartialSolutionStore::get_upper_fasta ( )

inline

References upper_fasta_.

Referenced by protocols::loop_grower::LoopComparator::fill_pose(), and protocols::loop_grower::LoopComparator::set_scores().

core::Size protocols::loop_grower::LoopPartialSolutionStore::get_upper_pose ( )

inline

References upper_pose_.

Referenced by protocols::loop_grower::LoopComparator::fill_pose().

bool protocols::loop_grower::LoopPartialSolutionStore::is_empty ( )

inline

References solutions_.

LoopPartialSolution protocols::loop_grower::LoopPartialSolutionStore::operator[] ( core::Size solutions_index )

inline

References solutions_.

void protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter	(	core::pose::Pose &	pose,
		core::Size	fragmelt,
		core::Size	total_lower,
		core::Size	lower_res,
		core::Size	upper_res,
		core::Size	rmswindow,
		bool	dump_beam,
		core::Size &	totalreqbeam,
		core::Size &	totalreqmaxbeam,
		core::Real &	totalreqscorecut,
		bool	writebeams,
		core::Size	cycle,
		core::Size	parallelcount
	)

References protocols::loop_grower::LoopPartialSolution::apply(), core::pose::Pose::dump_pdb(), protocols::loop_grower::LoopPartialSolution::get_id(), protocols::loop_grower::LoopPartialSolution::get_rms(), protocols::loop_grower::LoopPartialSolution::get_score(), get_solutions(), protocols::loop_grower::LoopPartialSolution::partialrms(), size(), store(), core::id::to_string(), and protocols::loop_grower::TRACER().

Referenced by protocols::loop_grower::LoopGrower::fafilter(), and protocols::loop_grower::LoopGrower::single_grow().

void protocols::loop_grower::LoopPartialSolutionStore::push	(	core::pose::Pose &	pose,
		LoopPartialSolution const &	new_entry,
		core::Size	fragmelt,
		core::Real	beamscorecutoff,
		core::Size	total_lower,
		bool	lower,
		bool	dump_errors,
		core::Real	RMS,
		core::Size	lower_res,
		core::Size	upper_res
	)

References protocols::loop_grower::LoopPartialSolution::apply(), core::pose::PDBInfo::attach_to(), core::conformation::Conformation::chains_from_termini(), core::pose::Pose::conformation(), core::pose::Pose::dump_pdb(), protocols::loop_grower::LoopPartialSolution::get_score(), protocols::loop_grower::LoopPartialSolution::max_calpha_distance(), protocols::loop_grower::LoopPartialSolution::set_rms(), core::id::to_string(), and protocols::loop_grower::TRACER().

Referenced by protocols::loop_grower::FragmentExtension::apply().

void protocols::loop_grower::LoopPartialSolutionStore::report_rms_and_scores	(	core::Size	rangelo,
		core::Size	rangehi
	)

void protocols::loop_grower::LoopPartialSolutionStore::set_cutpoint ( core::Size cutpoint )

inline

References cutpoint_.

Referenced by protocols::loop_grower::LoopComparator::read_from_file(), and protocols::loop_grower::LoopGrower::update_and_writelps().

void protocols::loop_grower::LoopPartialSolutionStore::set_fastas	(	core::Size	lower,
		core::Size	upper
	)

inline

References lower_fasta_, and upper_fasta_.

Referenced by protocols::loop_grower::LoopGrower::apply(), protocols::loop_grower::LoopComparator::read_from_file(), and protocols::loop_grower::LoopGrower::update_and_writelps().

void protocols::loop_grower::LoopPartialSolutionStore::set_filterprevious ( bool filterprevious )

inline

References filterprevious(), and filterprevious_.

Referenced by protocols::loop_grower::LoopGrower::fafilter().

void protocols::loop_grower::LoopPartialSolutionStore::set_poses	(	core::Size	lower,
		core::Size	upper
	)

inline

References lower_pose_, and upper_pose_.

Referenced by protocols::loop_grower::LoopComparator::read_from_file(), and protocols::loop_grower::LoopGrower::update_and_writelps().

void protocols::loop_grower::LoopPartialSolutionStore::setfilterparams	(	core::Size	fragmelt,
		core::Size	rmswindow,
		core::Size	parallelcount,
		core::Real	beamscorecutoff,
		bool	dump_errors,
		bool	dump_beam,
		bool	writebeams,
		bool	clustercheck,
		bool	fafilter,
		bool	samplesheets,
		bool	filterprevious,
		bool	checksymm,
		bool	asymmdump,
		bool	dumpfinalbeam
	)

inline

References asymmdump_, beamscorecutoff_, checksymm_, clustercheck_, dump_beam_, dump_errors_, dumpfinalbeam_, fafilter_, filterprevious(), filterprevious_, fragmelt_, parallelcount_, rmswindow_, samplesheets_, and writebeams_.

Referenced by protocols::loop_grower::LoopGrower::apply(), and protocols::loop_grower::LoopGrower::single_grow().

core::Size protocols::loop_grower::LoopPartialSolutionStore::size ( )

inline

References solutions_.

void protocols::loop_grower::LoopPartialSolutionStore::skeleton_filter	(	core::pose::Pose &	pose,
		DensSkeleton &	skeleton,
		core::Size	start_res,
		core::Size	stop_res,
		core::Size	lower_term,
		core::Size	res_gap
	)