the loop hash map stores LeapIndexes and a hashmap to access those LeapIndexes quickly by their 6D coordinates. More...

#include <LoopHashMap.hh>

Collaboration diagram for protocols::loophash::LoopHashMap:

Classes
struct	by_index
	A functor for sort() More...

Public Member Functions
	LoopHashMap (core::Size loop_size=10)
	Constructor - must give loop_size. More...

void	add_leap (const LeapIndex &leap_index, numeric::geometry::hashing::Real6 &transform)
	Add a leap/loop to the HashMap. More...

void	add_leap (const LeapIndex &leap_index, boost::uint64_t key)
	Add a leap/loop to the HashMap with a key, skipping hashing. More...

void	add_legacyleap (const LegacyLeapIndex &legacyleap_index)
	Add an legacy leap/loop to the HashMap. More...

const LeapIndex &	get_peptide (core::Size index)
	Obtain an index to a given peptide saved. More...

core::Size	n_loops () const

void	radial_lookup_withkey (boost::uint64_t key, core::Size radius, std::vector< core::Size > &result)
	Return a vector of loops with equal keys given a key. More...

void	lookup_withkey (boost::uint64_t key, std::vector< core::Size > &result)
	Return a vector of loops with equal keys given a key. More...

void	lookup (numeric::geometry::hashing::Real6 transform, std::vector< core::Size > &result)
	Append to a bucket of vectors in the appropriate bin, lookup by transform. More...

void	radial_lookup (core::Size radius, numeric::geometry::hashing::Real6 transform, std::vector< core::Size > &result)
	Append to a bucket of vectors in the appropriate bin, radial lookup by transform. More...

core::Size	radial_count (core::Size radius, numeric::geometry::hashing::Real6 center) const
	count hits in the appropriate bin, radial lookup by transform More...

void	lookup (core::Size index, std::vector< core::Size > &result)
	Append to a bucket of vectors in the appropriate bin, lookup by bin index. More...

void	bbdb_range (std::pair< BackboneIndexMap::iterator, BackboneIndexMap::iterator > &range)
	Returns begin() and end() of backbone_index_map_. More...

boost::uint64_t	return_key (core::Size bb_index)
	Returns a hashmap key given a member of a bucket Don't think boost implements this, have to manually look it up. More...

core::Size	get_loop_size () const
	Query the loopsize of this LoopHashMap. More...

void	read_legacydb (std::string filename)
	Reads legacy binary dbs. More...

void	write_db (std::string filename)
	Basic IO functionality - allows reading and writing text states to/from disk. More...

void	read_db (std::string filename, std::pair< core::Size, core::Size > loopdb_range, std::map< core::Size, bool > &homolog_index)
	Basic IO functionality - allows reading and writing text states to/from disk. More...

void	read_db (std::string filename)

void	mem_foot_print ()
	Return the memory usage of this class. More...

void	sort ()
	Sorts the loopdb_ by leap_index.index. More...

Private Member Functions
void	setup (core::Size loop_size)
	Setup this class give a loop_size. More...

void	hash_index (numeric::geometry::hashing::Real6 transform, core::Size data)
	Add a given piece of data to the hash. More...

Private Attributes
numeric::geometry::hashing::SixDCoordinateBinnerOP	hash_
	A class that will take a 6D rigid body transform and turn it into a serial hashbin number for hashing. THis is the actual hash so to speak. More...

BackboneIndexMap	backbone_index_map_
	The actual Boost-based hashmap. More...

std::vector< LeapIndex >	loopdb_
	List of LeadIndexes. More...

core::Size	loop_size_
	The length of the the loops in number of residues. More...

Detailed Description

the loop hash map stores LeapIndexes and a hashmap to access those LeapIndexes quickly by their 6D coordinates.

Definition at line 89 of file LoopHashMap.hh.

Constructor & Destructor Documentation

protocols::loophash::LoopHashMap::LoopHashMap ( core::Size loop_size = 10)

Constructor - must give loop_size.

Definition at line 361 of file LoopHashMap.cc.

Member Function Documentation

void protocols::loophash::LoopHashMap::add_leap	(	const LeapIndex &	leap_index,
		numeric::geometry::hashing::Real6 &	transform
	)

Add a leap/loop to the HashMap.

Definition at line 451 of file LoopHashMap.cc.

Referenced by protocols::loophash::LoopHashLibrary::extract_data_from_pose(), protocols::loophash::LoopHashLibrary::merge(), and protocols::loophash::LoopHashLibrary::test_loop_sample().

void protocols::loophash::LoopHashMap::add_leap	(	const LeapIndex &	leap_index,
		boost::uint64_t	key
	)

Add a leap/loop to the HashMap with a key, skipping hashing.

Definition at line 444 of file LoopHashMap.cc.

void protocols::loophash::LoopHashMap::add_legacyleap ( const LegacyLeapIndex & legacyleap_index)

Add an legacy leap/loop to the HashMap.

Definition at line 429 of file LoopHashMap.cc.

References protocols::loophash::LegacyLeapIndex::ba, protocols::loophash::LeapIndex::index, protocols::loophash::LeapIndex::offset, protocols::loophash::LegacyLeapIndex::rotx, protocols::loophash::LegacyLeapIndex::roty, protocols::loophash::LegacyLeapIndex::rotz, protocols::loophash::LegacyLeapIndex::vecx, protocols::loophash::LegacyLeapIndex::vecy, and protocols::loophash::LegacyLeapIndex::vecz.

void protocols::loophash::LoopHashMap::bbdb_range ( std::pair< BackboneIndexMap::iterator, BackboneIndexMap::iterator > & range)

Returns begin() and end() of backbone_index_map_.

Definition at line 488 of file LoopHashMap.cc.

Referenced by protocols::loophash::LoopHashLibrary::merge().

core::Size protocols::loophash::LoopHashMap::get_loop_size ( ) const

inline

Query the loopsize of this LoopHashMap.

Definition at line 150 of file LoopHashMap.hh.

References loop_size_.

Referenced by protocols::loophash::LoopHashLibrary::apply_random(), protocols::loophash::LoopHashSampler::build_structures(), protocols::loophash::LoopHashLibrary::get_all(), and protocols::loophash::LoopHashLibrary::test_loop_sample().

const LeapIndex& protocols::loophash::LoopHashMap::get_peptide ( core::Size index)

inline

Obtain an index to a given peptide saved.

Definition at line 112 of file LoopHashMap.hh.

References loopdb_.

Referenced by protocols::loophash::LoopHashLibrary::apply_random(), protocols::loophash::LoopHashSampler::build_structures(), protocols::loophash::LoopHashLibrary::get_all(), protocols::loophash::LoopHashLibrary::merge(), and protocols::loophash::LoopHashLibrary::test_loop_sample().

void protocols::loophash::LoopHashMap::hash_index	(	numeric::geometry::hashing::Real6	transform,
		core::Size	data
	)

private

Add a given piece of data to the hash.

Definition at line 473 of file LoopHashMap.cc.

void protocols::loophash::LoopHashMap::lookup	(	numeric::geometry::hashing::Real6	transform,
		std::vector< core::Size > &	result
	)

Append to a bucket of vectors in the appropriate bin, lookup by transform.

Definition at line 495 of file LoopHashMap.cc.

References core::scoring::pair, and protocols::sic_dock::range().

Referenced by protocols::loophash::LoopHashLibrary::apply_random(), and protocols::loophash::LoopHashLibrary::get_all().

void protocols::loophash::LoopHashMap::lookup	(	core::Size	index,
		std::vector< core::Size > &	result
	)

Append to a bucket of vectors in the appropriate bin, lookup by bin index.

Using core::Size instead of boost::uinst64_t

Definition at line 554 of file LoopHashMap.cc.

References core::sequence::end.

void protocols::loophash::LoopHashMap::lookup_withkey	(	boost::uint64_t	key,
		std::vector< core::Size > &	result
	)

Return a vector of loops with equal keys given a key.

Definition at line 588 of file LoopHashMap.cc.

References core::scoring::pair, and protocols::sic_dock::range().

Referenced by protocols::loophash::LoopHashLibrary::test_loop_sample().

void protocols::loophash::LoopHashMap::mem_foot_print ( )

Return the memory usage of this class.

Definition at line 366 of file LoopHashMap.cc.

References protocols::moves::TR().

core::Size protocols::loophash::LoopHashMap::n_loops ( ) const

inline

Definition at line 117 of file LoopHashMap.hh.

References loopdb_.

Size protocols::loophash::LoopHashMap::radial_count	(	core::Size	radius,
		numeric::geometry::hashing::Real6	center
	)		const

count hits in the appropriate bin, radial lookup by transform

Definition at line 541 of file LoopHashMap.cc.

void protocols::loophash::LoopHashMap::radial_lookup	(	core::Size	radius,
		numeric::geometry::hashing::Real6	transform,
		std::vector< core::Size > &	result
	)

Append to a bucket of vectors in the appropriate bin, radial lookup by transform.

Definition at line 521 of file LoopHashMap.cc.

References core::scoring::pair, and protocols::sic_dock::range().

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

void protocols::loophash::LoopHashMap::radial_lookup_withkey	(	boost::uint64_t	key,
		core::Size	radius,
		std::vector< core::Size > &	result
	)

Return a vector of loops with equal keys given a key.

Definition at line 580 of file LoopHashMap.cc.

Referenced by protocols::loophash::LoopHashLibrary::merge().

void protocols::loophash::LoopHashMap::read_db	(	std::string	filename,
		std::pair< core::Size, core::Size >	loopdb_range,
		std::map< core::Size, bool > &	homolog_index
	)

Basic IO functionality - allows reading and writing text states to/from disk.

Definition at line 631 of file LoopHashMap.cc.

References protocols::loophash::LeapIndex::index, protocols::loophash::LeapIndex::key, protocols::loophash::LeapIndex::offset, core::scoring::hbonds::t(), and protocols::moves::TR().

Referenced by read_db().

void protocols::loophash::LoopHashMap::read_db ( std::string filename)

inline

Definition at line 162 of file LoopHashMap.hh.

References protocols::sic_dock::range(), and read_db().

void protocols::loophash::LoopHashMap::read_legacydb ( std::string filename)

Reads legacy binary dbs.

Definition at line 599 of file LoopHashMap.cc.

References protocols::moves::TR().

boost::uint64_t protocols::loophash::LoopHashMap::return_key ( core::Size bb_index)

Returns a hashmap key given a member of a bucket Don't think boost implements this, have to manually look it up.

Definition at line 573 of file LoopHashMap.cc.

References protocols::loophash::LeapIndex::key.

void protocols::loophash::LoopHashMap::setup ( core::Size loop_size)

private

Setup this class give a loop_size.

Definition at line 376 of file LoopHashMap.cc.

References protocols::loophash::HASH_POSITION_GRID_BASE, and protocols::moves::TR().

void protocols::loophash::LoopHashMap::sort ( )

Sorts the loopdb_ by leap_index.index.

Definition at line 371 of file LoopHashMap.cc.

void protocols::loophash::LoopHashMap::write_db ( std::string filename)

Basic IO functionality - allows reading and writing text states to/from disk.

Definition at line 621 of file LoopHashMap.cc.

Member Data Documentation

BackboneIndexMap protocols::loophash::LoopHashMap::backbone_index_map_

private

The actual Boost-based hashmap.

Definition at line 181 of file LoopHashMap.hh.

numeric::geometry::hashing::SixDCoordinateBinnerOP protocols::loophash::LoopHashMap::hash_

private

A class that will take a 6D rigid body transform and turn it into a serial hashbin number for hashing. THis is the actual hash so to speak.

Definition at line 178 of file LoopHashMap.hh.

core::Size protocols::loophash::LoopHashMap::loop_size_

private

The length of the the loops in number of residues.

Definition at line 187 of file LoopHashMap.hh.

Referenced by get_loop_size().

std::vector< LeapIndex> protocols::loophash::LoopHashMap::loopdb_

private

List of LeadIndexes.

Definition at line 184 of file LoopHashMap.hh.

Referenced by get_peptide(), and n_loops().

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

src/protocols/loophash/LoopHashMap.hh
src/protocols/loophash/LoopHashMap.cc

Classes

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation