protocols::loop_grower::LoopPartialSolutionStore Class Reference

#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

LoopPartialSolutionStore() [1/2]

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

default

LoopPartialSolutionStore() [2/2]

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

clear()

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().

cluster_check()

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().

diversityfilter()

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::TR().

filter()

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::TR(), and protocols::loop_grower::transform_to_closest_symmunit().

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

filterprevious()

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().

get_cutpoint()

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

inline

References cutpoint_.

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

get_filteronly_solutions()

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

inline

References filteronly_solutions_.

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

get_lower_fasta()

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

inline

References lower_fasta_.

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

get_lower_pose()

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

inline

References lower_pose_.

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

get_solutions()

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

inline

References solutions_.

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

get_upper_fasta()

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().

get_upper_pose()

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

inline

References upper_pose_.

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

is_empty()

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

inline

References solutions_.

operator[]()

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

inline

References solutions_.

parametercheck_filter()

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::TR().

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

push()

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::TR().

report_rms_and_scores()

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

set_cutpoint()

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().

set_fastas()

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().

set_filterprevious()

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

inline

References filterprevious(), and filterprevious_.

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

set_poses()

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().

setfilterparams()

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().

size()

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

inline

References solutions_.

Referenced by protocols::loop_grower::LoopGrower::apply(), protocols::loop_grower::LoopGrower::coordinate_filter(), diversityfilter(), protocols::loop_grower::LoopGrower::fafilter(), protocols::loop_grower::LoopGrower::full_atom_beam(), parametercheck_filter(), protocols::loop_grower::LoopGrower::rescoresolutionset(), protocols::loop_grower::LoopComparator::set_scores(), protocols::loop_grower::LoopGrower::single_grow(), protocols::loop_grower::LoopGrower::update_and_writelps(), and protocols::loop_grower::LoopGrower::write_to_disk().

skeleton_filter()

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
	)

References protocols::loop_grower::LoopPartialSolution::apply(), core::conformation::Residue::atom(), core::pose::Pose::residue(), protocols::loop_grower::DensSkeleton::shortest_path_bfs(), core::id::to_string(), protocols::loop_grower::TR(), and core::conformation::Atom::xyz().

sort()

void protocols::loop_grower::LoopPartialSolutionStore::sort ( )

inline

References solutions_.

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

sortrms()

void protocols::loop_grower::LoopPartialSolutionStore::sortrms ( )

inline

References solutions_.

store()

void protocols::loop_grower::LoopPartialSolutionStore::store ( LoopPartialSolution const &  new_entry )

inline

References solutions_.

Referenced by protocols::loop_grower::LoopGrower::addnativesolution(), protocols::loop_grower::LoopGrower::apply(), protocols::loop_grower::LoopGrower::coordinate_filter(), diversityfilter(), protocols::loop_grower::LoopGrower::fafilter(), protocols::loop_grower::LoopGrower::full_atom_beam(), parametercheck_filter(), protocols::loop_grower::LoopGrower::read_from_disk(), protocols::loop_grower::LoopComparator::read_from_file(), protocols::loop_grower::LoopGrower::rescoresolutionset(), protocols::loop_grower::LoopGrower::single_grow(), and protocols::loop_grower::LoopGrower::update_and_writelps().

store_filteronly_solutions()

void protocols::loop_grower::LoopPartialSolutionStore::store_filteronly_solutions ( utility::vector1< LoopPartialSolution >  filteronly )

inline

References filteronly_solutions_.

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

writelpsstore()

void protocols::loop_grower::LoopPartialSolutionStore::writelpsstore	(	core::Size	loopid,
		core::Size	jobid
	)

References protocols::abinitio::filename(), core::id::to_string(), and protocols::loop_grower::LoopPartialSolution::write_beam_lps().

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

zscoretransform()

void protocols::loop_grower::LoopPartialSolutionStore::zscoretransform

(

)

References core::simple_metrics::metrics::mean, core::chemical::element::N, protocols::hybridization::score, core::simple_metrics::metrics::sum, and protocols::loop_grower::TR().

Member Data Documentation

asymmdump_

bool protocols::loop_grower::LoopPartialSolutionStore::asymmdump_ = true

private

Referenced by setfilterparams().

beamscorecutoff_

core::Real protocols::loop_grower::LoopPartialSolutionStore::beamscorecutoff_ = 0.85

private

Referenced by setfilterparams().

checksymm_

bool protocols::loop_grower::LoopPartialSolutionStore::checksymm_ = false

private

Referenced by setfilterparams().

clustercheck_

bool protocols::loop_grower::LoopPartialSolutionStore::clustercheck_ = false

private

Referenced by setfilterparams().

cutpoint_

core::Size protocols::loop_grower::LoopPartialSolutionStore::cutpoint_ = 0

private

Referenced by get_cutpoint(), and set_cutpoint().

dump_beam_

bool protocols::loop_grower::LoopPartialSolutionStore::dump_beam_ = false

private

Referenced by setfilterparams().

dump_errors_

bool protocols::loop_grower::LoopPartialSolutionStore::dump_errors_ = false

private

Referenced by setfilterparams().

dumpfinalbeam_

bool protocols::loop_grower::LoopPartialSolutionStore::dumpfinalbeam_ = false

private

Referenced by setfilterparams().

fafilter_

bool protocols::loop_grower::LoopPartialSolutionStore::fafilter_ = true

private

Referenced by setfilterparams().

filteronly_solutions_

utility::vector1<LoopPartialSolution> protocols::loop_grower::LoopPartialSolutionStore::filteronly_solutions_

private

Referenced by get_filteronly_solutions(), and store_filteronly_solutions().

filterprevious_

bool protocols::loop_grower::LoopPartialSolutionStore::filterprevious_ = false

private

Referenced by set_filterprevious(), and setfilterparams().

fragmelt_

core::Size protocols::loop_grower::LoopPartialSolutionStore::fragmelt_ = 1

private

Referenced by setfilterparams().

lower_fasta_

core::Size protocols::loop_grower::LoopPartialSolutionStore::lower_fasta_ = 0

private

Referenced by get_lower_fasta(), and set_fastas().

lower_pose_

core::Size protocols::loop_grower::LoopPartialSolutionStore::lower_pose_ = 0

private

Referenced by get_lower_pose(), and set_poses().

master_beam_cutoff_

core::Real protocols::loop_grower::LoopPartialSolutionStore::master_beam_cutoff_ = 3.0

private

Referenced by LoopPartialSolutionStore().

master_beam_width_

core::Size protocols::loop_grower::LoopPartialSolutionStore::master_beam_width_ = 1

private

Referenced by LoopPartialSolutionStore().

maxelts_

core::Size protocols::loop_grower::LoopPartialSolutionStore::maxelts_ = 1

private

Referenced by LoopPartialSolutionStore().

old_solutions_

utility::vector1<LoopPartialSolution> protocols::loop_grower::LoopPartialSolutionStore::old_solutions_

private

parallelcount_

core::Size protocols::loop_grower::LoopPartialSolutionStore::parallelcount_ = 0

private

Referenced by setfilterparams().

rank_

core::Size protocols::loop_grower::LoopPartialSolutionStore::rank_ = 0

private

rmscutoff_

core::Real protocols::loop_grower::LoopPartialSolutionStore::rmscutoff_ = 0.0

private

Referenced by LoopPartialSolutionStore().

rmswindow_

core::Size protocols::loop_grower::LoopPartialSolutionStore::rmswindow_ = 1

private

Referenced by setfilterparams().

samplesheets_

bool protocols::loop_grower::LoopPartialSolutionStore::samplesheets_ = true

private

Referenced by setfilterparams().

solutions_

utility::vector1<LoopPartialSolution> protocols::loop_grower::LoopPartialSolutionStore::solutions_

private

Referenced by clear(), get_solutions(), is_empty(), operator[](), size(), sort(), sortrms(), and store().

upper_fasta_

core::Size protocols::loop_grower::LoopPartialSolutionStore::upper_fasta_ = 0

private

Referenced by get_upper_fasta(), and set_fastas().

upper_pose_

core::Size protocols::loop_grower::LoopPartialSolutionStore::upper_pose_ = 0

private

Referenced by get_upper_pose(), and set_poses().

writebeams_

bool protocols::loop_grower::LoopPartialSolutionStore::writebeams_ = false

private

Referenced by setfilterparams().

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

• src/protocols/loop_grower/LoopGrower.hh
• src/protocols/loop_grower/LoopGrower.cc