#include <LoopHashLibrary.hh>

Inheritance diagram for protocols::loophash::LoopHashLibrary:

Collaboration diagram for protocols::loophash::LoopHashLibrary:

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
	clone has to be overridden only if clone invocation is expected. 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). 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

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 (TagPtr const tag, 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
	this function informs 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
	this function informs 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

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::ScoreFunction	scorefxn_rama_cst

core::scoring::ScoreFunction	scorefxn_cen_cst

core::optimization::MinimizerOptions	options

core::optimization::MinimizerOptions	options2

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

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...

Detailed Description

Definition at line 45 of file LoopHashLibrary.hh.

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`
	)

Definition at line 92 of file LoopHashLibrary.cc.

References assigned_num_, assigned_string_, db_path_, do_sanity_check_, extra_, hash_sizes_, loopdb_range_, num_partitions_, set_default_score_functions(), and setup_hash_maps().

Referenced by clone(), and fresh_instance().

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

Definition at line 471 of file LoopHashLibrary.cc.

References core::scoring::CA_rmsd(), core::chemical::CENTROID, get_all(), core::scoring::getScoreFunction(), protocols::loophash::MAXIMAL_FLOAT, core::import_pose::pose_from_pdb(), RG(), core::scoring::rms, protocols::noesy_assign::round(), core::pose::set_ss_from_phipsi(), core::util::switch_to_residue_type_set(), protocols::loophash::TR(), and core::io::silent::SilentFileData::write_silent_struct().

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

Definition at line 586 of file LoopHashLibrary.cc.

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

inline

Definition at line 104 of file LoopHashLibrary.hh.

References bbdb_.

Referenced by test_saving_library().

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

inlinevirtual

clone has to be overridden only if clone invocation is expected.

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.

Definition at line 82 of file LoopHashLibrary.hh.

References LoopHashLibrary().

void protocols::loophash::LoopHashLibrary::create_db ( )

Definition at line 350 of file LoopHashLibrary.cc.

References assigned_num_, assigned_string_, extra_, extract_data_from_pose(), core::chemical::ChemicalManager::get_instance(), num_partitions_, core::chemical::ChemicalManager::residue_type_set(), core::import_pose::pose_stream::streams_from_cmd_line(), and protocols::loophash::TR().

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

Definition at line 167 of file LoopHashLibrary.cc.

References assigned_string_, db_path_, hash_sizes_, 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`
	)

Definition at line 890 of file LoopHashLibrary.cc.

References core::kinematics::FoldTree::add_edge(), 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::loophash::BackboneSegment::read_from_pose(), core::scoring::hbonds::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)

Definition at line 885 of file LoopHashLibrary.cc.

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

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

inlinevirtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

Definition at line 91 of file LoopHashLibrary.hh.

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`
	)