#include <LoopGrower.hh>

Inheritance diagram for protocols::loop_grower::LoopGrower:

[legend]

Public Member Functions
	LoopGrower ()=default

	LoopGrower (core::sequence::SequenceOP seq, protocols::loops::Loop loop, int resstart, int resstop, utility::vector1< core::fragment::FragSetOP > const &fragments)

void	apply (core::pose::Pose &pose) override
	Main Method. More...

core::Real	single_grow (core::pose::Pose &pose, core::pose::Pose &pose_cen, LoopPartialSolutionStore &solutionset, const core::chemical::ResidueTypeCOPs &restypes_pose, const core::chemical::ResidueTypeCOPs &restypes_pos_cen, core::Size lower_pose, core::Size upper_pose, core::Size upper_term, int lower_fasta, int upper_fasta, core::Size torsionrangelo, core::Size torsionrangehi, bool insert_lower, core::Size initial_melt_left, bool is_cterm, bool is_nterm, core::Size cycle, int n_to_insert)

void	update_to_stored (core::pose::Pose &growpose, core::pose::Pose &growpose_cen, const core::chemical::ResidueTypeCOPs &restypes_pose, const core::chemical::ResidueTypeCOPs &restypes_pose_cen, int &lower_pose, int &upper_pose, int &lower_fasta, int &upper_fasta, core::Size newreslow, core::Size newreshi, bool is_cterm, bool is_nterm)

void	update_and_writelps (LoopPartialSolutionStore &solutionset, core::pose::Pose &fa_pose, core::pose::Pose &pose_cen, core::chemical::ResidueTypeCOPs &restypes_pose, core::chemical::ResidueTypeCOPs &restypes_pose_cen, int lower_pose, int upper_pose, bool is_nterm, bool is_cterm, core::Size fasta_range_low, core::Size fasta_range_hi, core::Size pose_range_low, core::Size pose_range_hi, int torsionrangelo, int torsionrangehi, int tgt_jump, bool update_pose)

core::Real	nton3_hbond_score (core::pose::Pose &pose)

core::Real	get_resrange_hbond_energy (core::pose::Pose &pose, core::Size lower, core::Size upper)

core::Real	modifiedscore (core::pose::Pose &fapose, core::pose::Pose &cen_pose, core::Size rangelo, core::Size rangehi)

core::Real	modifieddensity (core::pose::Pose &pose, core::Size rangelo, core::Size rangehi, core::Real density_weight, core::Size &includesheets)

core::Real	sheetscore (core::pose::Pose &fapose, core::pose::Pose &cen_pose, core::Size rangelo, core::Size rangehi)

bool	is_beta (core::Real phi, core::Real psi)

void	rescoresolutionset (LoopPartialSolutionStore &solutionset, core::pose::Pose &fa_pose, core::pose::Pose &cen_pose, core::Size torsionrangelo, core::Size torsionrangehi)

void	coordinate_filter (LoopPartialSolutionStore &solutionset, core::pose::Pose pose, bool lower, core::Size lower_fasta, core::Size upper_fasta, core::Size lower_pose, core::Size rangehi)

void	addnativesolution (LoopPartialSolutionStore &solutionset, core::pose::Pose &fa_pose, core::pose::Pose &cen_pose, int natlowerstart, int natlowerstop, int natupperstart, int natupperstop, int lower_pose, core::Size torsionrangelo, core::Size torsionrangehi)

void	store_sheets (core::pose::Pose &pose, LoopPartialSolution &lps)

void	refine_cycle (core::pose::Pose &pose, core::pose::Pose &cen_pose, int loop_start, int loop_end, bool finalrefinement, int cycle, int beam, int fragment, core::Size is_lower)

void	full_atom_beam (LoopPartialSolutionStore &solutionset, core::pose::Pose &fa_pose, core::pose::Pose &cen_pose, core::Size lower_pos, core::Size upper_pos)

void	set_scorefunction (core::scoring::ScoreFunctionOP sf)

void	set_cen_scorefunction (core::scoring::ScoreFunctionOP sf)

void	set_cenrot_scorefunction (core::scoring::ScoreFunctionOP sf)

void	set_beamwidth (core::Size beamwidth)

void	set_fragtrials (core::Size fragtrials)

void	set_chainbreak (core::Real chainbreak)

void	set_continuous_weight (core::Real continuous_weight)

void	set_rmscutoff (core::Real rmscutoff)

void	set_master_beam_cutoff (core::Real master_beam_cutoff)

void	set_sheetbonus (core::Real sheetbonus)

void	set_sheet_tolerance (core::Real sheet_tolerance)

void	set_sc_scale (core::Real sc_scale)

void	set_windowdensweight (core::Real windowdensweight)

void	set_master_beam_width (core::Size master_beam_width)

void	set_rmswindow (core::Size rmswindow)

void	set_steps (core::Size steps)

void	set_pcount (core::Size parallelcount)

void	set_sheetcriteria (core::Size sheetcriteria)

void	set_loopnumber (core::Size loopnumber)

void	set_beamscorecutoff (core::Real beamscorecutoff)

void	set_debug (bool debug)

void	set_fragmelt (core::Size fragmelt)

void	set_minmelt (core::Size minmelt)

void	set_pack_min_cycles (core::Size pack_min_cycles)

void	set_dumpbeam (bool dumpbeam)

void	set_dumpfinalbeam (bool dumpfinalbeam)

void	set_dumprms (bool dumprms)

void	set_dumperrors (bool dumperrors)

void	set_direction (core::Size direction)

void	set_minimize (bool minimize)

void	set_native (core::pose::PoseOP native)

void	set_nativegrow (bool nativegrow)

void	set_greedy (bool greedy)

void	set_parametercheck (bool parametercheck)

void	set_cenrot (bool cenrot)

void	set_writebeams (bool writebeams)

void	set_readbeams (bool readbeams)

void	set_clustercheck (bool clustercheck)

void	set_rescorebeams (bool rescorebeams)

void	set_writelps (bool writelps)

void	set_fafilter (bool fafilter)

void	set_famin (bool famin)

void	set_samplesheets (bool samplesheets)

void	set_trackfragments (bool trackfragments)

void	set_filterprevious (bool filterprevious)

void	set_rephasemap (bool rephasemap)

void	set_checksymm (bool checksymm)

void	set_asymmdump (bool asymmdump)

void	set_continuous_sheets (bool continuous_sheets)

void	set_auto_stop (bool auto_stop)

void	set_storedbeams (std::string storedbeams)

void	set_filterbeams (std::string filterbeams)

void	set_coordfile (std::string coordfile)

void	set_skeletonfile (std::string skeletonfile)

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

void	update_fragment_library_pointers ()

void	add_fragment_csts (core::pose::Pose &pose, core::Size startfasta, core::Size endfasta, core::Size natstoplow, core::Size natstarthi, core::Size startlower)

void	add_user_csts (core::pose::Pose &pose)

void	write_to_disk (LoopPartialSolutionStore solutionset, core::Size step, core::Size added_lower, core::Size added_upper, bool filteronly, bool lower)

void	read_from_disk (LoopPartialSolutionStore &solutionset, int &cycle, bool &lower, bool filterbeams)

void	read_coordfile ()

void	fafilter (LoopPartialSolutionStore &solutionset, core::pose::Pose &fapose, core::pose::Pose &cenpose, core::Size total_lower, core::Size torsionrangelo, core::Size torsionrangehi, core::Size cycle, core::Size lower_fasta, core::Size upper_fasta, core::Size lower_pose)

core::Real	GDThatonative (core::pose::Pose const &pose, int natlow, int nathi, int natstoplow, int natstarthi, int startlow, int stoplow, int starthi, int stophi)

core::Real	RMStonative (core::pose::Pose const &pose, int natlow, int nathi, int natstoplow, int natstarthi, int startlow, int stoplow, int starthi, int stophi)

void	atomGDTha (core::Vector atom1, core::Vector atom2, core::Size &GDTha)

core::Size	check_coordinates (core::pose::Pose &pose, core::Size lower_pose, core::Size upper_pose, core::Size lower_fasta, core::Real radius)

bool	check_auto_stop (core::pose::Pose &pose, core::Size lower_res, core::Size upper_res)

LoopPartialSolutionStore	getSolutionSet ()

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

Private Attributes
core::Size	beamwidth_ = 1

core::Size	fragtrials_ = 10

core::Size	fragmelt_ = 1

core::Size	minmelt_ = 1

core::Size	lowest_ranked_native_ = 0

core::Size	storelow_ = 0

core::Size	storehi_ = 0

core::scoring::ScoreFunctionOP	sf_

core::scoring::ScoreFunctionOP	cen_sf_

core::scoring::ScoreFunctionOP	cenrot_sf_

bool	debug_ = false

core::sequence::SequenceOP	seq_

protocols::loops::Loop	loop_

int	resstart_ = 0

int	resstop_ = 0

int	upper_fasta_ = 0

int	lower_fasta_ = 0

int	rmsrangelo_ = 0

int	rmsrangehi_ = 0

core::Real	chainbreak_ = 1.5

core::Real	continuous_weight_ = 0.3

core::Real	rmscutoff_ = 0.0

core::Real	beamscorecutoff_ = 0.85

core::Real	master_beam_cutoff_ = 3.0

core::Real	windowdensweight_ = 30

core::Real	startingscore_ = 0.0

core::Real	censtartingscore_ = 0.0

core::Real	sheetbonus_ = 0.5

core::Real	sheet_tolerance_ = 0.7

core::Real	sc_scale_ = 1

utility::vector1< core::fragment::FragSetOP >	fragments_

utility::vector1< boost::unordered_map< core::Size, core::fragment::Frame > >	library_

core::Size	pack_min_cycles_ = 1

core::Size	fafilter_pmcycles_ = 1

core::Size	direction_ = 0

core::Size	master_beam_width_ = 1

core::Size	rmswindow_ = 1

core::Size	steps_ = 1e4

core::Size	parallelcount_ = 0

core::Size	sheetcriteria_ = 2

core::Size	loopnumber_ = 0

core::Size	sheetsize_ = 4

core::Size	total_residues_ = 0

core::Size	insert_pose_ = 0

core::Size	maxfrag_ = 0

core::Size	numjumps_ = 0

bool	dumpbeam_ = false

bool	dumpfinalbeam_ = false

bool	dumprms_ = false

bool	dumperrors_ = false

bool	minimize_ = true

bool	nativegrow_ = false

bool	greedy_ = true

bool	parametercheck_ = false

bool	cenrot_ = false

bool	writebeams_ = false

bool	readbeams_ = false

bool	clustercheck_ = false

bool	rescorebeams_ = false

bool	writelps_ = false

bool	fafilter_ = true

bool	famin_ = false

bool	samplesheets_ = true

bool	trackfragments_ = false

bool	cenrotfilter_ = false

bool	filterprevious_ = false

bool	rephasemap_ = false

bool	checksymm_ = false

bool	continuous_sheets_ = true

bool	auto_stop_ = false

bool	asymmdump_ = true

std::string	storedbeams_

std::string	filterbeams_

std::string	coordfile_

std::string	skeleton_file_

std::map< std::pair< core::Size, core::Size >, utility::vector1< numeric::xyzVector< core::Real > > >	scoringcoords_

core::pose::PoseOP	native_

core::pose::Pose	fa_seqpose_

core::pose::Pose	cen_seqpose_

DensSkeleton	skeleton_

LoopPartialSolutionStore	solutionset_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Constructor & Destructor Documentation

◆ LoopGrower() [1/2]

protocols::loop_grower::LoopGrower::LoopGrower ( )

default

◆ LoopGrower() [2/2]

protocols::loop_grower::LoopGrower::LoopGrower	(	core::sequence::SequenceOP	seq,
		protocols::loops::Loop	loop,
		int	resstart,
		int	resstop,
		utility::vector1< core::fragment::FragSetOP > const &	fragments
	)

inline

References cen_sf_, cenrot_sf_, core::scoring::ScoreFunctionFactory::create_score_function(), fafilter_pmcycles_, core::scoring::get_score_function(), native_, pack_min_cycles_, rmscutoff_, sf_, and update_fragment_library_pointers().

Member Function Documentation

◆ add_fragment_csts()

void protocols::loop_grower::LoopGrower::add_fragment_csts	(	core::pose::Pose &	pose,
		core::Size	startfasta,
		core::Size	endfasta,
		core::Size	natstoplow,
		core::Size	natstarthi,
		core::Size	startlower
	)

References core::pose::Pose::add_constraint(), core::conformation::Residue::is_protein(), core::chemical::element::N, core::conformation::Residue::name1(), core::pose::Pose::residue(), and protocols::loop_grower::TR().

◆ add_user_csts()

void protocols::loop_grower::LoopGrower::add_user_csts ( core::pose::Pose & pose )

References core::scoring::constraints::add_constraints_from_cmdline_to_pose(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), core::sequence::SWAligner::align(), core::pose::Pose::constraint_set(), core::pose::Pose::is_centroid(), core::pose::Pose::sequence(), core::sequence::SequenceAlignment::sequence_mapping(), and protocols::loop_grower::TR().

◆ addnativesolution()

void protocols::loop_grower::LoopGrower::addnativesolution	(	LoopPartialSolutionStore &	solutionset,
		core::pose::Pose &	fa_pose,
		core::pose::Pose &	cen_pose,
		int	natlowerstart,
		int	natlowerstop,
		int	natupperstart,
		int	natupperstop,
		int	lower_pose,
		core::Size	torsionrangelo,
		core::Size	torsionrangehi
	)

References core::pose::PDBInfo::attach_to(), core::pose::Pose::batch_set_xyz(), core::conformation::Conformation::chains_from_termini(), core::pose::Pose::conformation(), core::pose::Pose::dump_pdb(), core::pose::Pose::residue_type(), protocols::loop_grower::LoopPartialSolution::set_gdt(), protocols::loop_grower::LoopPartialSolution::set_rms(), protocols::loop_grower::LoopPartialSolutionStore::store(), protocols::loop_grower::TR(), and core::pose::Pose::xyz().

◆ apply()

void protocols::loop_grower::LoopGrower::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

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

◆ atomGDTha()

void protocols::loop_grower::LoopGrower::atomGDTha	(	core::Vector	atom1,
		core::Vector	atom2,
		core::Size &	GDTha
	)

References core::kinematics::distance().

◆ check_auto_stop()

bool protocols::loop_grower::LoopGrower::check_auto_stop	(	core::pose::Pose &	pose,
		core::Size	lower_res,
		core::Size	upper_res
	)

References core::scoring::elec_dens_fast, core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::matchResFast(), core::simple_metrics::metrics::mean, core::pose::Pose::residue(), protocols::hybridization::score, core::simple_metrics::metrics::sum, and protocols::loop_grower::TR().

◆ check_coordinates()

Size protocols::loop_grower::LoopGrower::check_coordinates	(	core::pose::Pose &	pose,
		core::Size	lower_pose,
		core::Size	upper_pose,
		core::Size	lower_fasta,
		core::Real	radius
	)

References core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::kinematics::distance(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

◆ clone()

protocols::moves::MoverOP protocols::loop_grower::LoopGrower::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ coordinate_filter()

void protocols::loop_grower::LoopGrower::coordinate_filter	(	LoopPartialSolutionStore &	solutionset,
		core::pose::Pose	pose,
		bool	lower,
		core::Size	lower_fasta,
		core::Size	upper_fasta,
		core::Size	lower_pose,
		core::Size	rangehi
	)

References protocols::loop_grower::LoopPartialSolution::apply(), protocols::loop_grower::LoopPartialSolutionStore::clear(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::name3(), core::pose::Pose::residue(), protocols::loop_grower::LoopPartialSolutionStore::size(), protocols::loop_grower::LoopPartialSolutionStore::store(), and protocols::loop_grower::TR().

◆ fafilter()

void protocols::loop_grower::LoopGrower::fafilter	(	LoopPartialSolutionStore &	solutionset,
		core::pose::Pose &	fapose,
		core::pose::Pose &	cenpose,
		core::Size	total_lower,
		core::Size	torsionrangelo,
		core::Size	torsionrangehi,
		core::Size	cycle,
		core::Size	lower_fasta,
		core::Size	upper_fasta,
		core::Size	lower_pose
	)

References protocols::loop_grower::LoopPartialSolution::apply(), protocols::loop_grower::LoopPartialSolutionStore::clear(), protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter(), protocols::loop_grower::LoopPartialSolutionStore::set_filterprevious(), protocols::loop_grower::LoopPartialSolution::set_gdt(), protocols::loop_grower::LoopPartialSolution::set_rms(), protocols::loop_grower::LoopPartialSolutionStore::size(), and protocols::loop_grower::LoopPartialSolutionStore::store().

Referenced by set_fafilter().

◆ fresh_instance()

protocols::moves::MoverOP protocols::loop_grower::LoopGrower::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ full_atom_beam()

void protocols::loop_grower::LoopGrower::full_atom_beam	(	LoopPartialSolutionStore &	solutionset,
		core::pose::Pose &	fa_pose,
		core::pose::Pose &	cen_pose,
		core::Size	lower_pos,
		core::Size	upper_pos
	)

References protocols::loop_grower::LoopPartialSolution::apply(), protocols::loop_grower::LoopPartialSolutionStore::clear(), core::scoring::elec_dens_fast, core::pose::Pose::energies(), protocols::loop_grower::LoopPartialSolution::get_score(), core::scoring::Energies::residue_total_energies(), core::scoring::score_type_from_name(), protocols::loop_grower::LoopPartialSolution::set_bonus_score(), protocols::loop_grower::LoopPartialSolution::set_score(), protocols::loop_grower::LoopPartialSolutionStore::size(), and protocols::loop_grower::LoopPartialSolutionStore::store().

◆ GDThatonative()

Real protocols::loop_grower::LoopGrower::GDThatonative	(	core::pose::Pose const &	pose,
		int	natlow,
		int	nathi,
		int	natstoplow,
		int	natstarthi,
		int	startlow,
		int	stoplow,
		int	starthi,
		int	stophi
	)

References core::conformation::Residue::atom(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::name3(), core::pose::Pose::residue(), protocols::loop_grower::TR(), and core::conformation::Atom::xyz().

◆ get_name()

std::string protocols::loop_grower::LoopGrower::get_name ( ) const

inlineoverridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

◆ get_resrange_hbond_energy()

Real protocols::loop_grower::LoopGrower::get_resrange_hbond_energy	(	core::pose::Pose &	pose,
		core::Size	lower,
		core::Size	upper
	)

References core::scoring::hbonds::HBond::acc_res(), core::chemical::CENTROID_ROT_t, core::pose::Pose::conformation(), core::scoring::hbonds::HBond::don_res(), core::scoring::hbonds::HBond::energy(), protocols::buns::energy, core::scoring::hbonds::HBondSet::hbond(), core::conformation::Conformation::is_centroid(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), core::conformation::Conformation::residue_typeset_mode(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), core::pose::Pose::update_residue_neighbors(), and core::scoring::hbonds::HBond::weight().

◆ getSolutionSet()

LoopPartialSolutionStore protocols::loop_grower::LoopGrower::getSolutionSet ( )

inline

References solutionset_.

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

◆ is_beta()

bool protocols::loop_grower::LoopGrower::is_beta	(	core::Real	phi,
		core::Real	psi
	)

◆ modifieddensity()

Real protocols::loop_grower::LoopGrower::modifieddensity	(	core::pose::Pose &	pose,
		core::Size	rangelo,
		core::Size	rangehi,
		core::Real	density_weight,
		core::Size &	includesheets
	)

References core::conformation::Residue::atom_name(), core::scoring::electron_density::getDensityMap(), core::scoring::hbond, core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::mean_field::min(), core::conformation::Residue::name3(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::scoring::electron_density::ElectronDensity::setSCscaling(), core::pose::Pose::total_residue(), and protocols::loop_grower::TR().

◆ modifiedscore()

Real protocols::loop_grower::LoopGrower::modifiedscore	(	core::pose::Pose &	fapose,
		core::pose::Pose &	cen_pose,
		core::Size	rangelo,
		core::Size	rangehi
	)

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_range_slow(), core::scoring::elec_dens_fast, core::scoring::hbond_sr_bb, protocols::hybridization::score, core::pose::Pose::total_residue(), and protocols::loop_grower::TR().

◆ nton3_hbond_score()

Real protocols::loop_grower::LoopGrower::nton3_hbond_score ( core::pose::Pose & pose )

References core::scoring::hbonds::HBond::acc_res(), core::chemical::CENTROID_ROT_t, core::pose::Pose::conformation(), core::scoring::hbonds::HBond::don_res(), core::scoring::hbonds::HBond::energy(), protocols::buns::energy, core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), core::conformation::Conformation::residue_typeset_mode(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), core::pose::Pose::update_residue_neighbors(), and core::scoring::hbonds::HBond::weight().

◆ provide_citation_info()

void protocols::loop_grower::LoopGrower::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References core::chemical::rdkit::get_name().

◆ read_coordfile()

void protocols::loop_grower::LoopGrower::read_coordfile ( )

References protocols::loop_grower::TR().

◆ read_from_disk()

void protocols::loop_grower::LoopGrower::read_from_disk	(	LoopPartialSolutionStore &	solutionset,
		int &	cycle,
		bool &	lower,
		bool	filterbeams
	)

◆ refine_cycle()

void protocols::loop_grower::LoopGrower::refine_cycle	(	core::pose::Pose &	pose,
		core::pose::Pose &	cen_pose,
		int	loop_start,
		int	loop_end,
		bool	finalrefinement,
		int	cycle,
		int	beam,
		int	fragment,
		core::Size	is_lower
	)

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, protocols::loop_grower::LoopPartialSolution::apply(), protocols::loop_grower::LoopPartialSolution::apply_sheets(), core::conformation::Residue::atom_index(), core::pose::PDBInfo::attach_to(), core::conformation::Conformation::chains_from_termini(), core::pose::Pose::conformation(), core::id::D, core::pose::Pose::dump_pdb(), core::scoring::fa_rep, core::pose::Pose::fold_tree(), core::chemical::ResidueType::has(), core::kinematics::FoldTree::is_cutpoint(), core::pose::symmetry::is_symmetric(), core::pack::make_new_symmetric_PackerTask_by_requested_method(), core::pose::symmetry::make_symmetric_movemap(), core::optimization::MinimizerOptions::max_iter(), core::pack::pack_rotamers(), core::pack::task::ResidueLevelTask::prevent_repacking(), core::pose::Pose::residue(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::id::THETA, core::id::to_string(), core::pose::Pose::total_residue(), and core::conformation::Residue::type().

◆ rescoresolutionset()

void protocols::loop_grower::LoopGrower::rescoresolutionset	(	LoopPartialSolutionStore &	solutionset,
		core::pose::Pose &	fa_pose,
		core::pose::Pose &	cen_pose,
		core::Size	torsionrangelo,
		core::Size	torsionrangehi
	)

◆ RMStonative()

Real protocols::loop_grower::LoopGrower::RMStonative	(	core::pose::Pose const &	pose,
		int	natlow,
		int	nathi,
		int	natstoplow,
		int	natstarthi,
		int	startlow,
		int	stoplow,
		int	starthi,
		int	stophi
	)

References core::conformation::Residue::atom(), core::kinematics::distance(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::name3(), core::pose::Pose::residue(), protocols::loop_grower::TR(), and core::conformation::Atom::xyz().

◆ set_asymmdump()

void protocols::loop_grower::LoopGrower::set_asymmdump ( bool asymmdump )

inline

References asymmdump_.

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

◆ set_auto_stop()

void protocols::loop_grower::LoopGrower::set_auto_stop ( bool auto_stop )

inline

References auto_stop_.

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

◆ set_beamscorecutoff()

void protocols::loop_grower::LoopGrower::set_beamscorecutoff ( core::Real beamscorecutoff )

inline

References beamscorecutoff_.

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

◆ set_beamwidth()

void protocols::loop_grower::LoopGrower::set_beamwidth ( core::Size beamwidth )

inline

References beamwidth_.

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

◆ set_cen_scorefunction()

void protocols::loop_grower::LoopGrower::set_cen_scorefunction ( core::scoring::ScoreFunctionOP sf )

inline

References cen_sf_.

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

◆ set_cenrot()

void protocols::loop_grower::LoopGrower::set_cenrot ( bool cenrot )

inline

References cenrot_.

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

◆ set_cenrot_scorefunction()

void protocols::loop_grower::LoopGrower::set_cenrot_scorefunction ( core::scoring::ScoreFunctionOP sf )

inline

References cenrot_sf_.

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

◆ set_chainbreak()

void protocols::loop_grower::LoopGrower::set_chainbreak ( core::Real chainbreak )

inline

References core::scoring::chainbreak, and chainbreak_.

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

◆ set_checksymm()

void protocols::loop_grower::LoopGrower::set_checksymm ( bool checksymm )

inline

References checksymm_.

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

◆ set_clustercheck()

void protocols::loop_grower::LoopGrower::set_clustercheck ( bool clustercheck )

inline

References clustercheck_.

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

◆ set_continuous_sheets()

void protocols::loop_grower::LoopGrower::set_continuous_sheets ( bool continuous_sheets )

inline

References continuous_sheets_.

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

◆ set_continuous_weight()

void protocols::loop_grower::LoopGrower::set_continuous_weight ( core::Real continuous_weight )

inline

References continuous_weight_.

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

◆ set_coordfile()

void protocols::loop_grower::LoopGrower::set_coordfile ( std::string coordfile )

inline

References coordfile_.

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

◆ set_debug()

void protocols::loop_grower::LoopGrower::set_debug ( bool debug )

inline

References core::pack::interaction_graph::debug, and debug_.

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

◆ set_direction()

void protocols::loop_grower::LoopGrower::set_direction ( core::Size direction )

inline

References direction_.

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

◆ set_dumpbeam()

void protocols::loop_grower::LoopGrower::set_dumpbeam ( bool dumpbeam )

inline

References dumpbeam_.

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

◆ set_dumperrors()

void protocols::loop_grower::LoopGrower::set_dumperrors ( bool dumperrors )

inline

References dumperrors_.

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

◆ set_dumpfinalbeam()

void protocols::loop_grower::LoopGrower::set_dumpfinalbeam ( bool dumpfinalbeam )

inline

References dumpfinalbeam_.

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

◆ set_dumprms()

void protocols::loop_grower::LoopGrower::set_dumprms ( bool dumprms )

inline

References dumprms_.

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

◆ set_fafilter()

void protocols::loop_grower::LoopGrower::set_fafilter ( bool fafilter )

inline

References fafilter(), and fafilter_.

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

◆ set_famin()

void protocols::loop_grower::LoopGrower::set_famin ( bool famin )

inline

References famin_.

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

◆ set_filterbeams()

void protocols::loop_grower::LoopGrower::set_filterbeams ( std::string filterbeams )

inline

References filterbeams_.

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

◆ set_filterprevious()

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

inline

References filterprevious_.

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

◆ set_fragmelt()

void protocols::loop_grower::LoopGrower::set_fragmelt ( core::Size fragmelt )

inline

References fragmelt_.

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

◆ set_fragtrials()

void protocols::loop_grower::LoopGrower::set_fragtrials ( core::Size fragtrials )

inline

References fragtrials_.

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

◆ set_greedy()

void protocols::loop_grower::LoopGrower::set_greedy ( bool greedy )

inline

References greedy_.

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

◆ set_loopnumber()

void protocols::loop_grower::LoopGrower::set_loopnumber ( core::Size loopnumber )

inline

References loopnumber_.

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

◆ set_master_beam_cutoff()

void protocols::loop_grower::LoopGrower::set_master_beam_cutoff ( core::Real master_beam_cutoff )

inline

References master_beam_cutoff_.

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

◆ set_master_beam_width()

void protocols::loop_grower::LoopGrower::set_master_beam_width ( core::Size master_beam_width )

inline

References master_beam_width_.

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

◆ set_minimize()

void protocols::loop_grower::LoopGrower::set_minimize ( bool minimize )

inline

References protocols::antibody::design::minimize, and minimize_.

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

◆ set_minmelt()

void protocols::loop_grower::LoopGrower::set_minmelt ( core::Size minmelt )

inline

References minmelt_.

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

◆ set_native()

void protocols::loop_grower::LoopGrower::set_native ( core::pose::PoseOP native )

inline

References native_.

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

◆ set_nativegrow()

void protocols::loop_grower::LoopGrower::set_nativegrow ( bool nativegrow )

inline

References nativegrow_.

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

◆ set_pack_min_cycles()

void protocols::loop_grower::LoopGrower::set_pack_min_cycles ( core::Size pack_min_cycles )

inline

References pack_min_cycles_.

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

◆ set_parametercheck()

void protocols::loop_grower::LoopGrower::set_parametercheck ( bool parametercheck )

inline

References parametercheck_.

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

◆ set_pcount()

void protocols::loop_grower::LoopGrower::set_pcount ( core::Size parallelcount )

inline

References parallelcount_.

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

◆ set_readbeams()

void protocols::loop_grower::LoopGrower::set_readbeams ( bool readbeams )

inline

References readbeams_.

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

◆ set_rephasemap()

void protocols::loop_grower::LoopGrower::set_rephasemap ( bool rephasemap )

inline

References rephasemap_.

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

◆ set_rescorebeams()

void protocols::loop_grower::LoopGrower::set_rescorebeams ( bool rescorebeams )

inline

References rescorebeams_.

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

◆ set_rmscutoff()

void protocols::loop_grower::LoopGrower::set_rmscutoff ( core::Real rmscutoff )

inline

References rmscutoff_.

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

◆ set_rmswindow()

void protocols::loop_grower::LoopGrower::set_rmswindow ( core::Size rmswindow )

inline

References rmswindow_.

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

◆ set_samplesheets()

void protocols::loop_grower::LoopGrower::set_samplesheets ( bool samplesheets )

inline

References samplesheets_.

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

◆ set_sc_scale()

void protocols::loop_grower::LoopGrower::set_sc_scale ( core::Real sc_scale )

inline

References sc_scale_.

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

◆ set_scorefunction()

void protocols::loop_grower::LoopGrower::set_scorefunction ( core::scoring::ScoreFunctionOP sf )

inline

References sf_.

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

◆ set_sheet_tolerance()

void protocols::loop_grower::LoopGrower::set_sheet_tolerance ( core::Real sheet_tolerance )

inline

References sheet_tolerance_.

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

◆ set_sheetbonus()

void protocols::loop_grower::LoopGrower::set_sheetbonus ( core::Real sheetbonus )

inline

References sheetbonus_.

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

◆ set_sheetcriteria()

void protocols::loop_grower::LoopGrower::set_sheetcriteria ( core::Size sheetcriteria )

inline

References sheetcriteria_.

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

◆ set_skeletonfile()

void protocols::loop_grower::LoopGrower::set_skeletonfile ( std::string skeletonfile )

inline

References skeleton_file_.

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

◆ set_steps()

void protocols::loop_grower::LoopGrower::set_steps ( core::Size steps )

inline

References steps_.

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

◆ set_storedbeams()

void protocols::loop_grower::LoopGrower::set_storedbeams ( std::string storedbeams )

inline

References storedbeams_.

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

◆ set_trackfragments()

void protocols::loop_grower::LoopGrower::set_trackfragments ( bool trackfragments )

inline

References trackfragments_.

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

◆ set_windowdensweight()

void protocols::loop_grower::LoopGrower::set_windowdensweight ( core::Real windowdensweight )

inline

References windowdensweight_.

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

◆ set_writebeams()

void protocols::loop_grower::LoopGrower::set_writebeams ( bool writebeams )

inline

References writebeams_.

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

◆ set_writelps()

void protocols::loop_grower::LoopGrower::set_writelps ( bool writelps )

inline

References writelps_.

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

◆ sheetscore()

Real protocols::loop_grower::LoopGrower::sheetscore	(	core::pose::Pose &	fapose,
		core::pose::Pose &	cen_pose,
		core::Size	rangelo,
		core::Size	rangehi
	)

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_range_slow(), core::scoring::elec_dens_fast, and core::pose::Pose::total_residue().

◆ single_grow()

Real protocols::loop_grower::LoopGrower::single_grow	(	core::pose::Pose &	pose,
		core::pose::Pose &	pose_cen,
		LoopPartialSolutionStore &	solutionset,
		const core::chemical::ResidueTypeCOPs &	restypes_pose,
		const core::chemical::ResidueTypeCOPs &	restypes_pos_cen,
		core::Size	lower_pose,
		core::Size	upper_pose,
		core::Size	upper_term,
		int	lower_fasta,
		int	upper_fasta,
		core::Size	torsionrangelo,
		core::Size	torsionrangehi,
		bool	insert_lower,
		core::Size	initial_melt_left,
		bool	is_cterm,
		bool	is_nterm,
		core::Size	cycle,
		int	n_to_insert
	)

◆ store_sheets()

void protocols::loop_grower::LoopGrower::store_sheets	(	core::pose::Pose &	pose,
		LoopPartialSolution &	lps
	)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), core::kinematics::FoldTree::is_jump_point(), protocols::loop_grower::LoopPartialSolution::store_sheetpositions(), core::pose::Pose::total_residue(), and protocols::loop_grower::TR().

◆ update_and_writelps()

void protocols::loop_grower::LoopGrower::update_and_writelps	(	LoopPartialSolutionStore &	solutionset,
		core::pose::Pose &	fa_pose,
		core::pose::Pose &	pose_cen,
		core::chemical::ResidueTypeCOPs &	restypes_pose,
		core::chemical::ResidueTypeCOPs &	restypes_pose_cen,
		int	lower_pose,
		int	upper_pose,
		bool	is_nterm,
		bool	is_cterm,
		core::Size	fasta_range_low,
		core::Size	fasta_range_hi,
		core::Size	pose_range_low,
		core::Size	pose_range_hi,
		int	torsionrangelo,
		int	torsionrangehi,
		int	tgt_jump,
		bool	update_pose
	)

◆ update_fragment_library_pointers()

void protocols::loop_grower::LoopGrower::update_fragment_library_pointers ( )

Referenced by LoopGrower().

◆ update_to_stored()

void protocols::loop_grower::LoopGrower::update_to_stored	(	core::pose::Pose &	growpose,
		core::pose::Pose &	growpose_cen,
		const core::chemical::ResidueTypeCOPs &	restypes_pose,
		const core::chemical::ResidueTypeCOPs &	restypes_pose_cen,
		int &	lower_pose,
		int &	upper_pose,
		int &	lower_fasta,
		int &	upper_fasta,
		core::Size	newreslow,
		core::Size	newreshi,
		bool	is_cterm,
		bool	is_nterm
	)

References core::pose::PDBInfo::attach_to(), core::conformation::Conformation::chains_from_termini(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::declare_chemical_bond(), core::conformation::remove_lower_terminus_type_from_conformation_residue(), core::conformation::remove_upper_terminus_type_from_conformation_residue(), core::pose::remove_variant_type_from_pose_residue(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), and core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos().

◆ write_to_disk()

void protocols::loop_grower::LoopGrower::write_to_disk	(	LoopPartialSolutionStore	solutionset,
		core::Size	step,
		core::Size	added_lower,
		core::Size	added_upper,
		bool	filteronly,
		bool	lower
	)

References protocols::abinitio::filename(), protocols::loop_grower::LoopPartialSolution::size(), protocols::loop_grower::LoopPartialSolutionStore::size(), core::id::to_string(), and protocols::loop_grower::LoopPartialSolution::write_beam().

Member Data Documentation

◆ asymmdump_

bool protocols::loop_grower::LoopGrower::asymmdump_ = true

private

Referenced by set_asymmdump().

◆ auto_stop_

bool protocols::loop_grower::LoopGrower::auto_stop_ = false

private

Referenced by set_auto_stop().

◆ beamscorecutoff_

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

private

Referenced by set_beamscorecutoff().

◆ beamwidth_

core::Size protocols::loop_grower::LoopGrower::beamwidth_ = 1

private

Referenced by set_beamwidth().

◆ cen_seqpose_

core::pose::Pose protocols::loop_grower::LoopGrower::cen_seqpose_

private

◆ cen_sf_

core::scoring::ScoreFunctionOP protocols::loop_grower::LoopGrower::cen_sf_

private

Referenced by LoopGrower(), and set_cen_scorefunction().

◆ cenrot_

bool protocols::loop_grower::LoopGrower::cenrot_ = false

private

Referenced by set_cenrot().

◆ cenrot_sf_

core::scoring::ScoreFunctionOP protocols::loop_grower::LoopGrower::cenrot_sf_

private

Referenced by LoopGrower(), and set_cenrot_scorefunction().

◆ cenrotfilter_

bool protocols::loop_grower::LoopGrower::cenrotfilter_ = false

private

◆ censtartingscore_

core::Real protocols::loop_grower::LoopGrower::censtartingscore_ = 0.0

private

◆ chainbreak_

core::Real protocols::loop_grower::LoopGrower::chainbreak_ = 1.5

private

Referenced by set_chainbreak().

◆ checksymm_

bool protocols::loop_grower::LoopGrower::checksymm_ = false

private

Referenced by set_checksymm().

◆ clustercheck_

bool protocols::loop_grower::LoopGrower::clustercheck_ = false

private

Referenced by set_clustercheck().

◆ continuous_sheets_

bool protocols::loop_grower::LoopGrower::continuous_sheets_ = true

private

Referenced by set_continuous_sheets().

◆ continuous_weight_

core::Real protocols::loop_grower::LoopGrower::continuous_weight_ = 0.3

private

Referenced by set_continuous_weight().

◆ coordfile_

std::string protocols::loop_grower::LoopGrower::coordfile_

private

Referenced by set_coordfile().

◆ debug_

bool protocols::loop_grower::LoopGrower::debug_ = false

private

Referenced by set_debug().

◆ direction_

core::Size protocols::loop_grower::LoopGrower::direction_ = 0

private

Referenced by set_direction().

◆ dumpbeam_

bool protocols::loop_grower::LoopGrower::dumpbeam_ = false

private

Referenced by set_dumpbeam().

◆ dumperrors_

bool protocols::loop_grower::LoopGrower::dumperrors_ = false

private

Referenced by set_dumperrors().

◆ dumpfinalbeam_

bool protocols::loop_grower::LoopGrower::dumpfinalbeam_ = false

private

Referenced by set_dumpfinalbeam().

◆ dumprms_

bool protocols::loop_grower::LoopGrower::dumprms_ = false

private

Referenced by set_dumprms().

◆ fa_seqpose_

core::pose::Pose protocols::loop_grower::LoopGrower::fa_seqpose_

private

◆ fafilter_

bool protocols::loop_grower::LoopGrower::fafilter_ = true

private

Referenced by set_fafilter().

◆ fafilter_pmcycles_

core::Size protocols::loop_grower::LoopGrower::fafilter_pmcycles_ = 1

private

Referenced by LoopGrower().

◆ famin_

bool protocols::loop_grower::LoopGrower::famin_ = false

private

Referenced by set_famin().

◆ filterbeams_

std::string protocols::loop_grower::LoopGrower::filterbeams_

private

Referenced by set_filterbeams().

◆ filterprevious_

bool protocols::loop_grower::LoopGrower::filterprevious_ = false

private

Referenced by set_filterprevious().

◆ fragmelt_

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

private

Referenced by set_fragmelt().

◆ fragments_

utility::vector1<core::fragment::FragSetOP> protocols::loop_grower::LoopGrower::fragments_

private

◆ fragtrials_

core::Size protocols::loop_grower::LoopGrower::fragtrials_ = 10

private

Referenced by set_fragtrials().

◆ greedy_

bool protocols::loop_grower::LoopGrower::greedy_ = true

private

Referenced by set_greedy().

◆ insert_pose_

core::Size protocols::loop_grower::LoopGrower::insert_pose_ = 0

private

◆ library_

utility::vector1<boost::unordered_map<core::Size, core::fragment::Frame> > protocols::loop_grower::LoopGrower::library_

private

◆ loop_

protocols::loops::Loop protocols::loop_grower::LoopGrower::loop_

private

◆ loopnumber_

core::Size protocols::loop_grower::LoopGrower::loopnumber_ = 0

private

Referenced by set_loopnumber().

◆ lower_fasta_

int protocols::loop_grower::LoopGrower::lower_fasta_ = 0

private

◆ lowest_ranked_native_

core::Size protocols::loop_grower::LoopGrower::lowest_ranked_native_ = 0

private

◆ master_beam_cutoff_

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

private

Referenced by set_master_beam_cutoff().

◆ master_beam_width_

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

private

Referenced by set_master_beam_width().

◆ maxfrag_

core::Size protocols::loop_grower::LoopGrower::maxfrag_ = 0

private

◆ minimize_

bool protocols::loop_grower::LoopGrower::minimize_ = true

private

Referenced by set_minimize().

◆ minmelt_

core::Size protocols::loop_grower::LoopGrower::minmelt_ = 1

private

Referenced by set_minmelt().

◆ native_

core::pose::PoseOP protocols::loop_grower::LoopGrower::native_

private

Referenced by LoopGrower(), and set_native().

◆ nativegrow_

bool protocols::loop_grower::LoopGrower::nativegrow_ = false

private

Referenced by set_nativegrow().

◆ numjumps_

core::Size protocols::loop_grower::LoopGrower::numjumps_ = 0

private

◆ pack_min_cycles_

core::Size protocols::loop_grower::LoopGrower::pack_min_cycles_ = 1

private

Referenced by LoopGrower(), and set_pack_min_cycles().

◆ parallelcount_

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

private

Referenced by set_pcount().

◆ parametercheck_

bool protocols::loop_grower::LoopGrower::parametercheck_ = false

private

Referenced by set_parametercheck().

◆ readbeams_

bool protocols::loop_grower::LoopGrower::readbeams_ = false

private

Referenced by set_readbeams().

◆ rephasemap_

bool protocols::loop_grower::LoopGrower::rephasemap_ = false

private

Referenced by set_rephasemap().

◆ rescorebeams_

bool protocols::loop_grower::LoopGrower::rescorebeams_ = false

private

Referenced by set_rescorebeams().

◆ resstart_

int protocols::loop_grower::LoopGrower::resstart_ = 0

private

◆ resstop_

int protocols::loop_grower::LoopGrower::resstop_ = 0

private

◆ rmscutoff_

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

private

Referenced by LoopGrower(), and set_rmscutoff().

◆ rmsrangehi_

int protocols::loop_grower::LoopGrower::rmsrangehi_ = 0

private

◆ rmsrangelo_

int protocols::loop_grower::LoopGrower::rmsrangelo_ = 0

private

◆ rmswindow_

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

private

Referenced by set_rmswindow().

◆ samplesheets_

bool protocols::loop_grower::LoopGrower::samplesheets_ = true

private

Referenced by set_samplesheets().

◆ sc_scale_

core::Real protocols::loop_grower::LoopGrower::sc_scale_ = 1

private

Referenced by set_sc_scale().

◆ scoringcoords_

std::map< std::pair< core::Size, core::Size >, utility::vector1< numeric::xyzVector< core::Real > > > protocols::loop_grower::LoopGrower::scoringcoords_

private

◆ seq_

core::sequence::SequenceOP protocols::loop_grower::LoopGrower::seq_

private

◆ sf_

core::scoring::ScoreFunctionOP protocols::loop_grower::LoopGrower::sf_

private

Referenced by LoopGrower(), and set_scorefunction().

◆ sheet_tolerance_

core::Real protocols::loop_grower::LoopGrower::sheet_tolerance_ = 0.7

private

Referenced by set_sheet_tolerance().

◆ sheetbonus_

core::Real protocols::loop_grower::LoopGrower::sheetbonus_ = 0.5

private

Referenced by set_sheetbonus().

◆ sheetcriteria_

core::Size protocols::loop_grower::LoopGrower::sheetcriteria_ = 2

private

Referenced by set_sheetcriteria().

◆ sheetsize_

core::Size protocols::loop_grower::LoopGrower::sheetsize_ = 4

private

◆ skeleton_

DensSkeleton protocols::loop_grower::LoopGrower::skeleton_

private

◆ skeleton_file_

std::string protocols::loop_grower::LoopGrower::skeleton_file_

private

Referenced by set_skeletonfile().

◆ solutionset_

LoopPartialSolutionStore protocols::loop_grower::LoopGrower::solutionset_

private

Referenced by getSolutionSet().

◆ startingscore_

core::Real protocols::loop_grower::LoopGrower::startingscore_ = 0.0

private

◆ steps_

core::Size protocols::loop_grower::LoopGrower::steps_ = 1e4

private

Referenced by set_steps().

◆ storedbeams_

std::string protocols::loop_grower::LoopGrower::storedbeams_

private

Referenced by set_storedbeams().

◆ storehi_

core::Size protocols::loop_grower::LoopGrower::storehi_ = 0

private

◆ storelow_

core::Size protocols::loop_grower::LoopGrower::storelow_ = 0

private

◆ total_residues_

core::Size protocols::loop_grower::LoopGrower::total_residues_ = 0

private

◆ trackfragments_

bool protocols::loop_grower::LoopGrower::trackfragments_ = false

private

Referenced by set_trackfragments().

◆ upper_fasta_

int protocols::loop_grower::LoopGrower::upper_fasta_ = 0

private

◆ windowdensweight_

core::Real protocols::loop_grower::LoopGrower::windowdensweight_ = 30

private

Referenced by set_windowdensweight().

◆ writebeams_

bool protocols::loop_grower::LoopGrower::writebeams_ = false

private

Referenced by set_writebeams().

◆ writelps_

bool protocols::loop_grower::LoopGrower::writelps_ = false

private

Referenced by set_writelps().

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

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

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ LoopGrower() [1/2]

◆ LoopGrower() [2/2]

Member Function Documentation

◆ add_fragment_csts()

◆ add_user_csts()

◆ addnativesolution()

◆ apply()

◆ atomGDTha()

◆ check_auto_stop()

◆ check_coordinates()

◆ clone()

◆ coordinate_filter()

◆ fafilter()

◆ fresh_instance()

◆ full_atom_beam()

◆ GDThatonative()

◆ get_name()

◆ get_resrange_hbond_energy()

◆ getSolutionSet()

◆ is_beta()

◆ modifieddensity()

◆ modifiedscore()

◆ nton3_hbond_score()

◆ provide_citation_info()

◆ read_coordfile()

◆ read_from_disk()

◆ refine_cycle()

◆ rescoresolutionset()

◆ RMStonative()

◆ set_asymmdump()

◆ set_auto_stop()

◆ set_beamscorecutoff()

◆ set_beamwidth()

◆ set_cen_scorefunction()

◆ set_cenrot()

◆ set_cenrot_scorefunction()

◆ set_chainbreak()

◆ set_checksymm()

◆ set_clustercheck()

◆ set_continuous_sheets()

◆ set_continuous_weight()

◆ set_coordfile()

◆ set_debug()

◆ set_direction()

◆ set_dumpbeam()

◆ set_dumperrors()

◆ set_dumpfinalbeam()

◆ set_dumprms()

◆ set_fafilter()

◆ set_famin()

◆ set_filterbeams()

◆ set_filterprevious()

◆ set_fragmelt()

◆ set_fragtrials()

◆ set_greedy()

◆ set_loopnumber()

◆ set_master_beam_cutoff()

◆ set_master_beam_width()

◆ set_minimize()

◆ set_minmelt()

◆ set_native()

◆ set_nativegrow()

◆ set_pack_min_cycles()

◆ set_parametercheck()

◆ set_pcount()

◆ set_readbeams()

◆ set_rephasemap()

◆ set_rescorebeams()

◆ set_rmscutoff()

◆ set_rmswindow()

◆ set_samplesheets()

◆ set_sc_scale()

◆ set_scorefunction()

◆ set_sheet_tolerance()

◆ set_sheetbonus()

◆ set_sheetcriteria()