#include <LoopHashLibrary.hh>

Public Member Functions
	LoopHashLibrary (const utility::vector1< core::Size > &init_sizes=utility::vector1< core::Size >(), const core::Size num_partitions=1, const core::Size assigned_num=0)

void	extract_data_from_pose (core::pose::Pose &pose, core::Size nres, protocols::frag_picker::VallChunkOP chunk=NULL)

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

bool	test_saving_library (core::pose::Pose, core::Size ir, bool deposit)

void	test_loop_sample (core::pose::Pose &pose, core::Size nres)

void	apply_random (core::pose::Pose &pose, core::Size &fir, core::Size &fjr, core::Real min_rms, core::Real max_rms)

void	get_all (core::pose::Pose &pose, std::vector< core::io::silent::SilentStructOP > &lib_structs, core::Size start_res=1, core::Size stop_res=0, core::Real min_bbrms=0.0, core::Real max_bbrms=100000.0, core::Real min_rms=0.0, core::Real max_rms=100.0)

virtual void	apply (core::pose::Pose &pose)

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

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

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

void	setup_hash_maps ()

LoopHashMap &	gethash (core::Size size)

const std::vector< core::Size > &	hash_sizes () const

const BackboneDB &	backbone_database () const

const std::pair< core::Size, core::Size >	loopdb_range ()

void	save_db ()

void	load_db ()

void	load_mergeddb ()

void	delete_db ()

void	merge (LoopHashLibraryOP second_lib, utility::vector1< core::Real > rms_cutoffs)

bool	merge_bbdb (const BackboneDB &second_bbdb, core::Size &index_offset)

void	sort ()

void	create_db ()

void	set_create_db (bool setting=true)

void	set_db_path (std::string setting)

void	graft_loop (const core::pose::Pose &src_pose, core::pose::Pose &tgt_pose, protocols::loops::Loop myloop)

void	set_default_score_functions ()

void	mem_foot_print ()

bool	get_extra () const

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

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

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

std::string	get_type () const

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...

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...

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...

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

jobdist::BasicJobCOP	get_current_job () const

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

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 protocols::filters::Filters_map	Filters_map

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

protocols::loophash::LoopHashLibrary::LoopHashLibrary	(	const utility::vector1< core::Size > &	init_sizes = `utility::vector1< core::Size >()`,
		const core::Size	num_partitions = `1`,
		const core::Size	assigned_num = `0`
	)

References assigned_num_, assigned_string_, basic::options::OptionKeys::lh::db_path, db_path_, do_sanity_check_, extra_, hash_sizes_, loopdb_range_, num_partitions_, basic::options::option, options, scoring, set_default_score_functions(), setup_hash_maps(), and utility::to_string().

Referenced by clone(), and fresh_instance().

Member Function Documentation

void protocols::loophash::LoopHashLibrary::apply ( core::pose::Pose & pose )

virtual

void protocols::loophash::LoopHashLibrary::apply_random	(	core::pose::Pose &	pose,
		core::Size &	fir,
		core::Size &	fjr,
		core::Real	min_rms,
		core::Real	max_rms
	)

const BackboneDB& protocols::loophash::LoopHashLibrary::backbone_database ( ) const

inline

References bbdb_.

Referenced by protocols::loophash::LoopHashSampler::build_structures(), protocols::sic_dock::dump_loophash_linkers(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), merge(), and test_saving_library().

virtual protocols::moves::MoverOP protocols::loophash::LoopHashLibrary::clone ( ) const

inlinevirtual

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.

References LoopHashLibrary().

void protocols::loophash::LoopHashLibrary::delete_db ( )

References assigned_string_, db_path_, hash_sizes_, utility::to_string(), and protocols::loophash::TR.

void protocols::loophash::LoopHashLibrary::extract_data_from_pose	(	core::pose::Pose &	pose,
		core::Size	nres,
		protocols::frag_picker::VallChunkOP	chunk = `NULL`
	)

References protocols::loophash::LoopHashMap::add_leap(), protocols::loophash::BackboneDB::add_pose(), bbdb_, core::pose::Pose::fold_tree(), protocols::loophash::get_rt_over_leap_fast(), gethash(), hash_sizes_, protocols::loophash::LeapIndex::index, protocols::loophash::LeapIndex::offset, protocols::make_rot_lib::PEPTIDE, protocols::loophash::BackboneSegment::read_from_pose(), t, core::pose::Pose::total_residue(), and protocols::loophash::TR.

Referenced by create_db(), and extract_data_from_pose().

void protocols::loophash::LoopHashLibrary::extract_data_from_pose ( core::pose::Pose & pose )

References extract_data_from_pose(), and core::pose::Pose::total_residue().

virtual protocols::moves::MoverOP protocols::loophash::LoopHashLibrary::fresh_instance ( ) const

inlinevirtual

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.

References LoopHashLibrary().

void protocols::loophash::LoopHashLibrary::get_all	(	core::pose::Pose &	pose,
		std::vector< core::io::silent::SilentStructOP > &	lib_structs,
		core::Size	start_res = `1`,
		core::Size	stop_res = `0`,
		core::Real	min_bbrms = `0.0`,
		core::Real	max_bbrms = `100000.0`,
		core::Real	min_rms = `0.0`,
		core::Real	max_rms = `100.0`
	)

Referenced by apply().

bool protocols::loophash::LoopHashLibrary::get_extra ( ) const

inline

References extra_.

Referenced by merge().

virtual std::string protocols::loophash::LoopHashLibrary::get_name ( ) const

inlinevirtual

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

Implements protocols::moves::Mover.

LoopHashMap & protocols::loophash::LoopHashLibrary::gethash ( core::Size size )

References hash_.

Referenced by apply_random(), protocols::loophash::LoopHashSampler::build_structures(), protocols::sic_dock::count_linkers(), protocols::sic_dock::dump_loophash_linkers(), extract_data_from_pose(), get_all(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), merge(), test_loop_sample(), and test_saving_library().

void protocols::loophash::LoopHashLibrary::graft_loop	(	const core::pose::Pose &	src_pose,
		core::pose::Pose &	tgt_pose,
		protocols::loops::Loop	myloop
	)

References protocols::loops::add_coordinate_constraints_to_pose(), protocols::loops::Loops::add_loop(), core::scoring::CA_rmsd(), options, options2, core::optimization::AtomTreeMinimizer::run(), scorefxn_cen_cst, scorefxn_rama_cst, core::kinematics::MoveMap::set_bb(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::loophash::TR, core::pose::transfer_phi_psi(), and transfer_phi_psi().

const std::vector< core::Size >& protocols::loophash::LoopHashLibrary::hash_sizes ( ) const

inline

References hash_sizes_.

Referenced by protocols::loophash::LoopHashSampler::build_structures().

void protocols::loophash::LoopHashLibrary::load_db ( )

References assigned_string_, bbdb_, db_path_, extra_, hash_, hash_sizes_, protocols::loophash::BackboneDB::read_db(), utility::to_string(), and protocols::loophash::TR.

void protocols::loophash::LoopHashLibrary::load_mergeddb ( )

const std::pair< core::Size, core::Size > protocols::loophash::LoopHashLibrary::loopdb_range ( )

inline

References loopdb_range_.

Referenced by protocols::loophash::LoopHashSampler::build_structures().

void protocols::loophash::LoopHashLibrary::mem_foot_print ( )

References bbdb_, protocols::loophash::BackboneDB::get_mem_foot_print(), hash_, hash_sizes_, and protocols::loophash::TR.

Referenced by protocols::loophash::WorkUnit_LoopHash::init_from_cmd(), protocols::loophash::LoopHashDiversifier::LoopHashDiversifier(), protocols::loophash::LoopHashMoverWrapper::parse_my_tag(), and protocols::loophash::LoopHashDiversifier::parse_my_tag().

void protocols::loophash::LoopHashLibrary::merge	(	LoopHashLibraryOP	second_lib,
		utility::vector1< core::Real >	rms_cutoffs
	)

bool protocols::loophash::LoopHashLibrary::merge_bbdb	(	const BackboneDB &	second_bbdb,
		core::Size &	index_offset
	)

References protocols::loophash::BackboneDB::add_extra_data(), protocols::loophash::BackboneDB::add_protein(), bbdb_, extra_, protocols::loophash::BBData::extra_key, protocols::loophash::BackboneDB::extra_size(), protocols::loophash::BackboneDB::get_extra_data(), protocols::loophash::BackboneDB::get_protein(), and protocols::loophash::BackboneDB::size().

Referenced by merge().

void protocols::loophash::LoopHashLibrary::save_db ( )

References assigned_string_, bbdb_, db_path_, hash_, hash_sizes_, utility::to_string(), protocols::loophash::TR, and protocols::loophash::BackboneDB::write_db().

void protocols::loophash::LoopHashLibrary::set_create_db ( bool setting = true )

inline

References create_db_.

void protocols::loophash::LoopHashLibrary::set_db_path ( std::string setting )

inline

References db_path_.

Referenced by protocols::loophash::LoopHashMoverWrapper::parse_my_tag(), and protocols::loophash::LoopHashDiversifier::parse_my_tag().

void protocols::loophash::LoopHashLibrary::set_default_score_functions ( )

References cbeta, cenpack, coordinate_constraint, env, hs_pair, pair, rama, protocols::simple_moves::rg, rsigma, scorefxn_cen_cst, scorefxn_rama_cst, sheet, ss_pair, and vdw.

Referenced by LoopHashLibrary().

void protocols::loophash::LoopHashLibrary::setup_hash_maps ( )

References hash_, hash_sizes_, and protocols::loophash::TR.

Referenced by LoopHashLibrary().

void protocols::loophash::LoopHashLibrary::sort ( )

References hash_, and hash_sizes_.

void protocols::loophash::LoopHashLibrary::test_loop_sample	(	core::pose::Pose &	pose,
		core::Size	nres
	)

bool protocols::loophash::LoopHashLibrary::test_saving_library	(	core::pose::Pose	pose,
		core::Size	ir,
		bool	deposit
	)

References protocols::loophash::BackboneDB::add_pose(), backbone_database(), bbdb_, cp, protocols::loophash::BackboneDB::get_backbone_segment(), protocols::loophash::get_rt_over_leap_fast(), gethash(), hash_sizes_, protocols::loophash::LeapIndex::index, protocols::loophash::BackboneSegment::read_from_pose(), t, core::pose::Pose::total_residue(), and protocols::loophash::TR.

Member Data Documentation

core::Size protocols::loophash::LoopHashLibrary::assigned_num_

private

Referenced by create_db(), load_mergeddb(), and LoopHashLibrary().

std::string protocols::loophash::LoopHashLibrary::assigned_string_

private

Referenced by create_db(), delete_db(), load_db(), load_mergeddb(), LoopHashLibrary(), and save_db().

BackboneDB protocols::loophash::LoopHashLibrary::bbdb_

private

Referenced by apply_random(), backbone_database(), extract_data_from_pose(), get_all(), load_db(), load_mergeddb(), mem_foot_print(), merge(), merge_bbdb(), save_db(), test_loop_sample(), and test_saving_library().

bool protocols::loophash::LoopHashLibrary::create_db_

private

Referenced by set_create_db().

std::string protocols::loophash::LoopHashLibrary::db_path_

private

Referenced by delete_db(), load_db(), load_mergeddb(), LoopHashLibrary(), save_db(), and set_db_path().

bool protocols::loophash::LoopHashLibrary::do_sanity_check_

private

Referenced by LoopHashLibrary(), and test_loop_sample().

bool protocols::loophash::LoopHashLibrary::extra_

private

Referenced by create_db(), get_extra(), load_db(), load_mergeddb(), LoopHashLibrary(), merge(), and merge_bbdb().

std::map< core::Size, LoopHashMap > protocols::loophash::LoopHashLibrary::hash_

private

Referenced by gethash(), load_db(), load_mergeddb(), mem_foot_print(), save_db(), setup_hash_maps(), and sort().

std::vector< core::Size > protocols::loophash::LoopHashLibrary::hash_sizes_

private

Referenced by apply_random(), delete_db(), extract_data_from_pose(), get_all(), hash_sizes(), load_db(), load_mergeddb(), LoopHashLibrary(), mem_foot_print(), merge(), save_db(), setup_hash_maps(), sort(), test_loop_sample(), and test_saving_library().

std::pair< core::Size, core::Size > protocols::loophash::LoopHashLibrary::loopdb_range_

private

Referenced by load_mergeddb(), loopdb_range(), and LoopHashLibrary().

core::Size protocols::loophash::LoopHashLibrary::num_partitions_

private

Referenced by create_db(), load_mergeddb(), and LoopHashLibrary().

core::optimization::MinimizerOptions protocols::loophash::LoopHashLibrary::options

private

Referenced by get_all(), and graft_loop().

core::optimization::MinimizerOptions protocols::loophash::LoopHashLibrary::options2

private

Referenced by get_all(), and graft_loop().

core::scoring::ScoreFunctionOP protocols::loophash::LoopHashLibrary::scorefxn_cen_cst

private

Referenced by get_all(), graft_loop(), and set_default_score_functions().

core::scoring::ScoreFunctionOP protocols::loophash::LoopHashLibrary::scorefxn_rama_cst

private

Referenced by get_all(), graft_loop(), and set_default_score_functions().

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

src/protocols/loophash/LoopHashLibrary.hh
src/protocols/loophash/LoopHashLibrary.cc

Private Attributes
BackboneDB	bbdb_

std::map< core::Size, LoopHashMap >	hash_

std::vector< core::Size >	hash_sizes_

std::string	db_path_

core::Size	num_partitions_

core::Size	assigned_num_

std::string	assigned_string_

bool	extra_

std::pair< core::Size, core::Size >	loopdb_range_

bool	do_sanity_check_

bool	create_db_

core::scoring::ScoreFunctionOP	scorefxn_rama_cst

core::scoring::ScoreFunctionOP	scorefxn_cen_cst

core::optimization::MinimizerOptions	options

core::optimization::MinimizerOptions	options2

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation