protocols::loophash Namespace Reference

Classes
struct	BBExtraData
struct	BBData
class	BackboneSegment
class	BackboneDB
class	EXCN_DB_IO_Failed
class	EXCN_Invalid_Hashmap
class	EXCN_No_Extra_Data_To_Write
class	EXCN_Wrong_DB_Format
class	EXCN_bbdb_Merge_Failed
class	FastGapMover
	Mover class for closing gaps. This Mover checks for any gaps using residue residue distances Then eats back at the chain surrounding it until loophash finds a fragment that fits in the space without changing the rest of pose too much. More...
class	LocalInserter
class	LocalInserter_SimpleMin
class	LoopHashDiversifier
class	LoopHashDiversifierCreator
class	LoopHashLibrary
struct	LeapIndex
	The LeapIndex stores information about a particular Leap. It hold the oroiginal high precision rigid body transform and an Index to a Backbone Database (BackboneDB) that has the actual phi psi angles. THe storage of the precise RT takes a lot of space and may be deprecated at some point, since once it is hashed, it is rarely needed and can be recomputed if it is. Note that the length of the loop is not stored either, this is again done for saving memory, as huge lists of Leaps are typically created all with the same length. THe length is stored and handled by the owner of LeapIndex list. The LeapIndex does not store the actual backbone coordinates of the Leap. It merely contains an index (the BackboneIndex) which refers to a serial store of backbone triples (phi,psi, omega) which are stored somewhere else in a BackboneDB. THis is improtant to save memory storage since multiple Leaps cna share the same backbone triple and redundant storage would be hugely wasteful. More...
struct	LegacyLeapIndex
class	LoopHashMap
	the loop hash map stores LeapIndexes and a hashmap to access those LeapIndexes quickly by their 6D coordinates. More...
class	LoopHashMoverWrapper
class	LoopHashMoverWrapperCreator
class	LoopHashRelaxProtocol
struct	FilterBucket
class	LoopHashSampler
class	Mover_LoopHashRefine
class	MPI_LoopHashRefine
class	MPI_LoopHashRefine_Emperor
class	MPI_LoopHashRefine_Master
class	WorkUnit_LoopHash

Typedefs
typedef boost::unordered_multimap < boost::uint64_t, core::Size, numeric::geometry::hashing::bin_index_hasher >	BackboneIndexMap
typedef numeric::geometry::BoundingBox < core::Vector >	BoundingBox
typedef utility::pointer::owning_ptr < FastGapMover >	FastGapMoverOP
typedef utility::pointer::owning_ptr < FastGapMover const >	FastGapMoverCOP
typedef utility::pointer::owning_ptr < LocalInserter >	LocalInserterOP
typedef utility::pointer::owning_ptr < LocalInserter const >	LocalInserterCOP
typedef utility::pointer::owning_ptr < LocalInserter_SimpleMin >	LocalInserter_SimpleMinOP
typedef utility::pointer::owning_ptr < LocalInserter_SimpleMin const >	LocalInserter_SimpleMinCOP
typedef utility::pointer::owning_ptr < LoopHashInserter >	LoopHashInserterOP
typedef utility::pointer::owning_ptr < LoopHashInserter const >	LoopHashInserterCOP
typedef utility::pointer::owning_ptr < LoopHashLibrary >	LoopHashLibraryOP
typedef utility::pointer::owning_ptr < LoopHashLibrary const >	LoopHashLibraryCOP
typedef utility::pointer::owning_ptr < LoopHashRelaxProtocol >	LoopHashRelaxProtocolOP
typedef utility::pointer::owning_ptr < LoopHashRelaxProtocol const >	LoopHashRelaxProtocolCOP
typedef utility::pointer::owning_ptr < LoopHashSampler >	LoopHashSamplerOP
typedef utility::pointer::owning_ptr < LoopHashSampler const >	LoopHashSamplerCOP
typedef utility::pointer::owning_ptr < Mover_LoopHashRefine >	Mover_LoopHashRefineOP
typedef utility::pointer::owning_ptr < Mover_LoopHashRefine const >	Mover_LoopHashRefineCOP
typedef utility::pointer::owning_ptr < WorkUnit_LoopHash >	WorkUnit_LoopHashOP
typedef utility::pointer::owning_ptr < WorkUnit_LoopHash const >	WorkUnit_LoopHashCOP

Functions
static basic::Tracer	TR ("BackboneDB")
short	RealAngleToShort (core::Real angle)
core::Real	ShortToRealAngle (short angle)
core::Real	get_rmsd (const BackboneSegment &bs1, const BackboneSegment &bs2)
template<class T >
T	sqr (T a)
static basic::Tracer	TR ("protocols.loophash.FastGapMover")
static basic::Tracer	TR ("LocalInserter")
static basic::Tracer	TR ("protocols.loophash.LoopHashDiversifier")
static basic::Tracer	TR ("LoopHashLibrary")
static basic::Tracer	TR ("LoopHashMap")
bool	get_rt_over_leap (const core::pose::Pose &orig_pose, core::Size ir, core::Size jr, numeric::geometry::hashing::Real6 &rt_6)
	This takes a pose and two residue positions and determines the rigid body transform of the Leap described by those two residues. Returns true is successful or false if something went haywire and one should just ignore this loop (this can happen at the ends) More...
bool	get_rt_over_leap_fast (core::pose::Pose &pose, core::Size ir, core::Size jr, numeric::geometry::hashing::Real6 &rt_6)
	This takes a pose and two residue positions and determines the rigid body transform of the Leap described by those two residues THe difference between this and the get_rt_over_leap function is that this version doesnt make a copy of the pose which makes it faster. However this means that the pose passed cannot be a const pose, even though the function restores the fold tree afterwards.. More...
bool	get_rt_over_leap_without_foldtree_bs (core::pose::Pose const &pose, core::Size ir, core::Size jr, numeric::geometry::hashing::Real6 &rt_6)
	This takes a pose and two residue positions and determines the rigid body transform of the Leap described by those two residues. More...
static basic::Tracer	TR ("protocols.loophash.LoopHashMoverWrapper")
static basic::Tracer	TR ("LocalHashSampler")
bool	cmp (core::pose::Pose a, core::pose::Pose b)
utility::vector1< core::Real >	extract_sample_weights (const core::pose::Pose &pose)
bool	is_valid_backbone (const std::string &sequence, const core::Size &ir, const std::vector< core::Real > &phi, const std::vector< core::Real > &psi, bool &filter_pro, bool &filter_beta, bool &filter_gly)
static numeric::random::RandomGenerator	RG (9479)
int	loophash_main ()
static basic::Tracer	TR ("MPI.LHR")
static numeric::random::RandomGenerator	RG (9788321)
static basic::Tracer	TR ("MPI.LHR.Emperor")
static numeric::random::RandomGenerator	RG (1248321)
static basic::Tracer	TR ("MPI.LHR.Master")
static numeric::random::RandomGenerator	RG (3893251)
static basic::Tracer	TR ("WorkUnit_LoopHash")

Variables
const core::Real	MAXIMAL_FLOAT = 100000000.0
const int	HASH_POSITION_GRID_BASE = 5

Typedef Documentation

typedef boost::unordered_multimap< boost::uint64_t, core::Size , numeric::geometry::hashing::bin_index_hasher > protocols::loophash::BackboneIndexMap

Definition at line 49 of file BackboneDB.hh.

typedef numeric::geometry::BoundingBox< core::Vector > protocols::loophash::BoundingBox

Definition at line 50 of file BackboneDB.hh.

typedef utility::pointer::owning_ptr< FastGapMover const > protocols::loophash::FastGapMoverCOP

Definition at line 28 of file FastGapMover.fwd.hh.

typedef utility::pointer::owning_ptr< FastGapMover > protocols::loophash::FastGapMoverOP

Definition at line 24 of file FastGapMover.fwd.hh.

typedef utility::pointer::owning_ptr< LocalInserter_SimpleMin const > protocols::loophash::LocalInserter_SimpleMinCOP

Definition at line 29 of file LocalInserter.fwd.hh.

typedef utility::pointer::owning_ptr< LocalInserter_SimpleMin > protocols::loophash::LocalInserter_SimpleMinOP

Definition at line 27 of file LocalInserter.fwd.hh.

typedef utility::pointer::owning_ptr< LocalInserter const > protocols::loophash::LocalInserterCOP

Definition at line 25 of file LocalInserter.fwd.hh.

typedef utility::pointer::owning_ptr< LocalInserter > protocols::loophash::LocalInserterOP

Definition at line 23 of file LocalInserter.fwd.hh.

typedef utility::pointer::owning_ptr< LoopHashInserter const > protocols::loophash::LoopHashInserterCOP

Definition at line 26 of file LoopHashInserter.fwd.hh.

typedef utility::pointer::owning_ptr< LoopHashInserter > protocols::loophash::LoopHashInserterOP

Definition at line 24 of file LoopHashInserter.fwd.hh.

typedef utility::pointer::owning_ptr< LoopHashLibrary const > protocols::loophash::LoopHashLibraryCOP

Definition at line 25 of file LoopHashLibrary.fwd.hh.

typedef utility::pointer::owning_ptr< LoopHashLibrary > protocols::loophash::LoopHashLibraryOP

Definition at line 23 of file LoopHashLibrary.fwd.hh.

typedef utility::pointer::owning_ptr< LoopHashRelaxProtocol const > protocols::loophash::LoopHashRelaxProtocolCOP

Definition at line 41 of file LoopHashRelaxProtocol.hh.

typedef utility::pointer::owning_ptr< LoopHashRelaxProtocol > protocols::loophash::LoopHashRelaxProtocolOP

Definition at line 39 of file LoopHashRelaxProtocol.hh.

typedef utility::pointer::owning_ptr< LoopHashSampler const > protocols::loophash::LoopHashSamplerCOP

Definition at line 26 of file LoopHashSampler.fwd.hh.

typedef utility::pointer::owning_ptr< LoopHashSampler > protocols::loophash::LoopHashSamplerOP

Definition at line 24 of file LoopHashSampler.fwd.hh.

typedef utility::pointer::owning_ptr< Mover_LoopHashRefine const > protocols::loophash::Mover_LoopHashRefineCOP

Definition at line 42 of file Mover_LoopHashRefine.hh.

typedef utility::pointer::owning_ptr< Mover_LoopHashRefine > protocols::loophash::Mover_LoopHashRefineOP

Definition at line 40 of file Mover_LoopHashRefine.hh.

typedef utility::pointer::owning_ptr< WorkUnit_LoopHash const > protocols::loophash::WorkUnit_LoopHashCOP

Definition at line 28 of file WorkUnit_LoopHash.hh.

typedef utility::pointer::owning_ptr< WorkUnit_LoopHash > protocols::loophash::WorkUnit_LoopHashOP

Definition at line 26 of file WorkUnit_LoopHash.hh.

Function Documentation

bool protocols::loophash::cmp	(	core::pose::Pose	a,
		core::pose::Pose	b
	)

Definition at line 91 of file LoopHashSampler.cc.

References core::pose::getPoseExtraScores().

utility::vector1< core::Real > protocols::loophash::extract_sample_weights

(

const core::pose::Pose &

pose)

Definition at line 100 of file LoopHashSampler.cc.

References core::pose::get_comment(), core::io::pdb::split(), and core::pose::Pose::total_residue().

core::Real protocols::loophash::get_rmsd	(	const BackboneSegment &	bs1,
		const BackboneSegment &	bs2
	)

Definition at line 194 of file BackboneDB.cc.

References protocols::loophash::BackboneSegment::omega(), protocols::loophash::BackboneSegment::phi(), and protocols::loophash::BackboneSegment::psi().

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().

bool protocols::loophash::get_rt_over_leap	(	const core::pose::Pose &	orig_pose,
		core::Size	ir,
		core::Size	jr,
		numeric::geometry::hashing::Real6 &	rt_6
	)

This takes a pose and two residue positions and determines the rigid body transform of the Leap described by those two residues. Returns true is successful or false if something went haywire and one should just ignore this loop (this can happen at the ends)

Definition at line 99 of file LoopHashMap.cc.

References core::chemical::aa_vrt, core::kinematics::FoldTree::add_edge(), core::pose::Pose::fold_tree(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::pose::Pose::total_residue(), and protocols::moves::TR().

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

bool protocols::loophash::get_rt_over_leap_fast	(	core::pose::Pose &	pose,
		core::Size	ir,
		core::Size	jr,
		numeric::geometry::hashing::Real6 &	rt_6
	)

This takes a pose and two residue positions and determines the rigid body transform of the Leap described by those two residues THe difference between this and the get_rt_over_leap function is that this version doesnt make a copy of the pose which makes it faster. However this means that the pose passed cannot be a const pose, even though the function restores the fold tree afterwards..

This takes a pose and two residue positions and determines the rigid body transform of the Leap described by those two residues Returns true is successful or false if something went haywire and one should just ignore this loop (this can happen at the ends) THe difference between this and the get_rt_over_leap function is that this version doesnt make a copy of the pose which makes it faster. However this means that the pose passed cannot be a const pose, even though the function restores the fold tree afterwards..

Definition at line 214 of file LoopHashMap.cc.

References core::chemical::aa_vrt, core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::cutpoints(), core::pose::Pose::fold_tree(), core::chemical::ResidueType::is_polymer(), core::pose::Pose::jump(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::pose::Pose::total_residue(), and protocols::moves::TR().

Referenced by protocols::loophash::LoopHashLibrary::extract_data_from_pose(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), and protocols::loophash::LoopHashLibrary::test_saving_library().

bool protocols::loophash::get_rt_over_leap_without_foldtree_bs	(	core::pose::Pose const &	pose,
		core::Size	ir,
		core::Size	jr,
		numeric::geometry::hashing::Real6 &	rt_6
	)

This takes a pose and two residue positions and determines the rigid body transform of the Leap described by those two residues.

Definition at line 330 of file LoopHashMap.cc.

References core::conformation::Residue::atom_index(), core::pose::Pose::conformation(), core::kinematics::RT::get_rotation(), core::conformation::Conformation::get_stub_transform(), core::kinematics::RT::get_translation(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

bool protocols::loophash::is_valid_backbone	(	const std::string &	sequence,
		const core::Size &	ir,
		const std::vector< core::Real > &	phi,
		const std::vector< core::Real > &	psi,
		bool &	filter_pro,
		bool &	filter_beta,
		bool &	filter_gly
	)

Definition at line 120 of file LoopHashSampler.cc.

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

int protocols::loophash::loophash_main

(

)

Definition at line 269 of file Mover_LoopHashRefine.cc.

References protocols::jd2::JobDistributor::get_instance(), and protocols::jd2::JobDistributor::go().

short protocols::loophash::RealAngleToShort

(

core::Real

angle)

Definition at line 45 of file BackboneDB.cc.

Referenced by protocols::loophash::BackboneDB::add_pose().

static numeric::random::RandomGenerator protocols::loophash::RG ( 1248321  )

static

static numeric::random::RandomGenerator protocols::loophash::RG ( 9788321  )

static

static numeric::random::RandomGenerator protocols::loophash::RG ( 3893251  )

static

static numeric::random::RandomGenerator protocols::loophash::RG ( 9479  )

static

core::Real protocols::loophash::ShortToRealAngle

(

short

angle)

Definition at line 53 of file BackboneDB.cc.

Referenced by protocols::loophash::BackboneDB::angle(), and protocols::loophash::BackboneDB::get_backbone_segment().

template<class T >

T protocols::loophash::sqr

(

T

a)

Definition at line 45 of file BackboneDB.hh.

static basic::Tracer protocols::loophash::TR ( "BackboneDB"  )

static

Referenced by protocols::loophash::FastGapMover::apply(), protocols::loophash::LoopHashDiversifier::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::loophash::LoopHashLibrary::apply_random(), protocols::loophash::LoopHashSampler::build_structures(), protocols::loophash::LoopHashLibrary::create_db(), protocols::loophash::LoopHashLibrary::delete_db(), protocols::loophash::LoopHashLibrary::extract_data_from_pose(), protocols::loophash::LoopHashLibrary::get_all(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::loophash::LoopHashLibrary::load_db(), protocols::loophash::LoopHashLibrary::load_mergeddb(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), protocols::loophash::LoopHashLibrary::mem_foot_print(), protocols::loophash::LoopHashLibrary::merge(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::loophash::LoopHashLibrary::save_db(), protocols::loophash::WorkUnit_LoopHash::set_defaults(), protocols::loophash::LoopHashLibrary::setup_hash_maps(), protocols::loophash::LoopHashLibrary::test_loop_sample(), and protocols::loophash::LoopHashLibrary::test_saving_library().

static basic::Tracer protocols::loophash::TR ( "LocalInserter"  )

static

static basic::Tracer protocols::loophash::TR ( "LocalHashSampler"  )

static

static basic::Tracer protocols::loophash::TR ( "WorkUnit_LoopHash"  )

static

static basic::Tracer protocols::loophash::TR ( "MPI.LHR.Emperor"  )

static

static basic::Tracer protocols::loophash::TR ( "protocols.loophash.LoopHashDiversifier"  )

static

static basic::Tracer protocols::loophash::TR ( "MPI.LHR"  )

static

static basic::Tracer protocols::loophash::TR ( "protocols.loophash.LoopHashMoverWrapper"  )

static

static basic::Tracer protocols::loophash::TR ( "protocols.loophash.FastGapMover"  )

static

static basic::Tracer protocols::loophash::TR ( "MPI.LHR.Master"  )

static

static basic::Tracer protocols::loophash::TR ( "LoopHashLibrary"  )

static

static basic::Tracer protocols::loophash::TR ( "LoopHashMap"  )

static

Variable Documentation

const int protocols::loophash::HASH_POSITION_GRID_BASE = 5

Definition at line 51 of file BackboneDB.hh.

Referenced by protocols::loophash::LoopHashMap::setup().

const core::Real protocols::loophash::MAXIMAL_FLOAT = 100000000.0

Definition at line 47 of file BackboneDB.hh.

Referenced by protocols::loophash::Mover_LoopHashRefine::apply(), protocols::loophash::LoopHashLibrary::apply(), and protocols::loophash::LoopHashRelaxProtocol::manual_call().