#include <LoopHashLibrary.hh>

Inheritance 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=nullptr)

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)

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

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

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

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

void	setup_hash_maps ()

LoopHashMap const &	gethash (core::Size size) const

LoopHashMap &	gethash (core::Size size)

std::vector< core::Size > const &	hash_sizes () const
	Return a list of the loop lengths present in the library. More...

BackboneDB const &	backbone_database () const

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

void	save_db () const

void	load_db ()

void	load_mergeddb ()

void	delete_db ()

void	merge (LoopHashLibraryOP second_lib, utility::vector1< core::Real > rms_cutoffs)
	Take two LoopHash libraries and merge them. More...

bool	merge_bbdb (const BackboneDB &second_bbdb, core::Size &index_offset)
	Take two backbone databases and merge them. More...

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 () const

bool	get_extra () const

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...

virtual bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Private Attributes
BackboneDB	bbdb_
	The backbone library for this HashLibrary (the actual data) More...

std::map< core::Size, LoopHashMap >	hash_
	A map of Hashmaps, each for a different loop size. More...

std::vector< core::Size >	hash_sizes_
	Kind-of a redundant store of sizes (remove this?) More...

std::string	db_path_
	Path to database. More...

core::Size	num_partitions_
	The number of partitions the database is split into. More...

core::Size	assigned_num_
	Which partition slice is assigned to this library. More...

std::string	assigned_string_
	Need so we can set the database string once. More...

bool	extra_
	Whether this database holds extra data in the backbone database or not. More...

std::pair< core::Size, core::Size >	loopdb_range_
	The proteins of the backbone database that are loaded (when loading a merged database, otherwise (0,0)) More...

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_

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

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_, db_path_, do_sanity_check_, extra_, hash_sizes_, loopdb_range_, num_partitions_, set_default_score_functions(), setup_hash_maps(), and core::id::to_string().

Member Function Documentation

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::scoring::CA_rmsd(), core::chemical::CENTROID_t, get_all(), core::scoring::get_score_function(), protocols::loophash::MAXIMAL_FLOAT, core::import_pose::PDB_file, core::import_pose::pose_from_file(), protocols::antibody::design::relax, core::scoring::rg, core::scoring::rms, protocols::noesy_assign::round(), protocols::hybridization::score, 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
	)

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

inline

References bbdb_.

Referenced by test_saving_library().

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

inlineoverridevirtual

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.

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

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

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

References assigned_string_, db_path_, hash_sizes_, core::id::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 = `nullptr`
	)

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::make_rot_lib::PEPTIDE, protocols::loophash::BackboneSegment::read_from_pose(), core::pose::Pose::size(), protocols::hybridization::t, 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::size().

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

inlineoverridevirtual

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.

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_.

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

inlineoverridevirtual

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

Implements protocols::moves::Mover.

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

References hash_.

Referenced by apply_random(), extract_data_from_pose(), get_all(), merge(), test_loop_sample(), and test_saving_library().

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

References hash_.

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(), 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(), and core::pose::transfer_phi_psi().

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

inline

Return a list of the loop lengths present in the library.

References hash_sizes_.

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

Only support reading from text, extra data is mandatory. Used when created merged text db.

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

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

Only support reading from merged text. Extra data is optional and handled by extra_.

References assigned_num_, assigned_string_, bbdb_, db_path_, extra_, hash_, hash_sizes_, loopdb_range_, num_partitions_, protocols::loophash::BackboneDB::read_db(), core::id::to_string(), and protocols::loophash::TR().

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

inline

References loopdb_range_.

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

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

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

Take two LoopHash libraries and merge them.

Throws out non-unique fragments defined as follows: if a new fragment is in a bucket with a key also in the master library, and if the RMS between the new fragment and the members of the master bucket is lower than the rms_cutoff, it is non-unique. Thus, an rms_cutoff of zero will not throw away any fragments.

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

Take two backbone databases and merge them.

Just takes Data structs from one and copies to the other

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 ( ) const

Only support writing to text, always include extra data

References assigned_string_, bbdb_, db_path_, hash_, hash_sizes_, core::id::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_.

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

References core::scoring::cbeta, core::scoring::cenpack, core::scoring::coordinate_constraint, core::scoring::env, core::scoring::hs_pair, core::scoring::pair, core::scoring::rama, core::scoring::rg, core::scoring::rsigma, scorefxn_cen_cst_, scorefxn_rama_cst_, core::scoring::sheet, core::scoring::ss_pair, and core::scoring::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 ( )

This function destroys the backbone_index_map reference, so sorting is only done when the hash will not longer be used. Required after merging, before saving so that merged db can be loaded as slices.

References hash_, and hash_sizes_.