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
	Not implemented! Mover class for closing gaps. More...
class	LocalInserter
	Manages the insertion of an arbitrary length of backbone in a local manner. More...
class	LocalInserter_SimpleMin
	Insert a backbone segment and use minimization with coordinate constraints to keep the insertion local. More...
class	LoopHashDiversifier
	Use LoopHash to generate low-resolution alternate conformations for the given pose. More...
class	LoopHashDiversifierCreator
class	LoopHashLibrary
class	LoopHashLibraryLoader
	LoopHashLibraryLoader constructs a LoopHashLibrary instance from data provided by the ResourceManager. More...
class	LoopHashLibraryLoaderCreator
	LoopHashLibraryLoaderCreator allows the ResourceLoaderFactory to create a LoopHashLibraryLoader instance. More...
struct	LeapIndex
	Store information about a particular Leap. 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
	Use LoopHash to sample new high-resolution conformations for the given pose. More...
class	LoopHashMoverWrapperCreator
class	LoopHashRelaxProtocol
	Not implemented! More...
struct	FilterBucket
class	LoopHashSampler
	Create candidate structures where some residues have been sampled by loophash. More...
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::shared_ptr< FastGapMover >	FastGapMoverOP
typedef utility::pointer::shared_ptr< FastGapMover const >	FastGapMoverCOP
typedef utility::pointer::shared_ptr< LocalInserter >	LocalInserterOP
typedef utility::pointer::shared_ptr< LocalInserter const >	LocalInserterCOP
typedef utility::pointer::shared_ptr< LocalInserter_SimpleMin >	LocalInserter_SimpleMinOP
typedef utility::pointer::shared_ptr< LocalInserter_SimpleMin const >	LocalInserter_SimpleMinCOP
typedef utility::pointer::shared_ptr< LoopHashLibrary >	LoopHashLibraryOP
typedef utility::pointer::shared_ptr< LoopHashLibrary const >	LoopHashLibraryCOP
typedef utility::pointer::shared_ptr< LoopHashLibraryLoader >	LoopHashLibraryLoaderOP
typedef utility::pointer::shared_ptr< LoopHashLibraryLoader const >	LoopHashLibraryLoaderCOP
typedef utility::pointer::shared_ptr< LoopHashRelaxProtocol >	LoopHashRelaxProtocolOP
typedef utility::pointer::shared_ptr< LoopHashRelaxProtocol const >	LoopHashRelaxProtocolCOP
typedef utility::pointer::shared_ptr< LoopHashSampler >	LoopHashSamplerOP
typedef utility::pointer::shared_ptr< LoopHashSampler const >	LoopHashSamplerCOP
typedef utility::pointer::shared_ptr< Mover_LoopHashRefine >	Mover_LoopHashRefineOP
typedef utility::pointer::shared_ptr< Mover_LoopHashRefine const >	Mover_LoopHashRefineCOP
typedef utility::pointer::shared_ptr< WorkUnit_LoopHash >	WorkUnit_LoopHashOP
typedef utility::pointer::shared_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)
int	loophash_main ()
static basic::Tracer	TR ("MPI.LHR")
static basic::Tracer	TR ("MPI.LHR.Emperor")
static basic::Tracer	TR ("MPI.LHR.Master")
static basic::Tracer	TR ("WorkUnit_LoopHash")

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

Typedef Documentation

BackboneIndexMap

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

BoundingBox

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

FastGapMoverCOP

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

FastGapMoverOP

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

LocalInserter_SimpleMinCOP

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

LocalInserter_SimpleMinOP

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

LocalInserterCOP

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

LocalInserterOP

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

LoopHashLibraryCOP

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

LoopHashLibraryLoaderCOP

typedef utility::pointer::shared_ptr< LoopHashLibraryLoader const > protocols::loophash::LoopHashLibraryLoaderCOP

LoopHashLibraryLoaderOP

typedef utility::pointer::shared_ptr< LoopHashLibraryLoader > protocols::loophash::LoopHashLibraryLoaderOP

LoopHashLibraryOP

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

LoopHashRelaxProtocolCOP

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

LoopHashRelaxProtocolOP

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

LoopHashSamplerCOP

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

LoopHashSamplerOP

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

Mover_LoopHashRefineCOP

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

Mover_LoopHashRefineOP

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

WorkUnit_LoopHashCOP

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

WorkUnit_LoopHashOP

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

Function Documentation

cmp()

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

References core::pose::motif::a(), protocols::match::upstream::b, and core::pose::getPoseExtraScore().

Referenced by core::environment::LocalPosition::operator<().

extract_sample_weights()

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

(

const core::pose::Pose &

pose

)

References core::pose::get_comment(), core::pose::Pose::size(), and protocols::sparta::split().

get_rmsd()

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

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().

get_rt_over_leap()

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)

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::cutpoints(), core::pose::Pose::fold_tree(), core::kinematics::RT::get_rotation(), core::kinematics::RT::get_translation(), core::chemical::ResidueTypeBase::is_polymer(), core::pose::Pose::jump(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::kinematics::Jump::rt(), core::pose::Pose::size(), 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().

get_rt_over_leap_fast()

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..

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::cutpoints(), core::pose::Pose::fold_tree(), core::kinematics::RT::get_rotation(), core::kinematics::RT::get_translation(), core::chemical::ResidueTypeBase::is_polymer(), core::pose::Pose::jump(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::kinematics::Jump::rt(), core::pose::Pose::size(), and protocols::moves::TR().

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

get_rt_over_leap_without_foldtree_bs()

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.

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(), core::chemical::ResidueTypeBase::name1(), core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by protocols::loop_modeler::perturbers::LoopHashPerturber::get_backbone_segments().

is_valid_backbone()

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
	)

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

loophash_main()

int protocols::loophash::loophash_main

(

)

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

RealAngleToShort()

short protocols::loophash::RealAngleToShort

(

core::Real

angle

)

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

ShortToRealAngle()

core::Real protocols::loophash::ShortToRealAngle

(

short

angle

)

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

sqr()

template<class T >

T protocols::loophash::sqr

(

T

a

)

References core::pose::motif::a().

TR() [1/12]

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

static

Referenced by protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_add_n_replace(), protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_single_replace(), protocols::loophash::MPI_LoopHashRefine::add_structures_to_library(), protocols::loophash::LoopHashDiversifier::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::loophash::FastGapMover::apply(), protocols::loophash::LoopHashLibrary::apply_random(), protocols::loophash::LoopHashSampler::build_structures(), protocols::loophash::LoopHashLibrary::create_db(), protocols::loophash::LoopHashLibrary::delete_db(), protocols::loophash::MPI_LoopHashRefine::dump_structures(), protocols::loophash::LoopHashLibrary::extract_data_from_pose(), protocols::loophash::LoopHashMoverWrapper::get_additional_output(), protocols::loophash::LoopHashLibrary::get_all(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::loophash::LoopHashLibrary::load_db(), protocols::loophash::LoopHashLibrary::load_mergeddb(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), protocols::loophash::LoopHashLibrary::mem_foot_print(), protocols::loophash::LoopHashLibrary::merge(), protocols::loophash::LoopHashMoverWrapper::parse_my_tag(), protocols::loophash::MPI_LoopHashRefine::print_library(), protocols::loophash::MPI_LoopHashRefine::print_stats(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::loophash::LoopHashLibrary::save_db(), protocols::loophash::MPI_LoopHashRefine::save_state(), protocols::loophash::MPI_LoopHashRefine::save_state_auto(), protocols::loophash::MPI_LoopHashRefine::send_random_library_struct(), protocols::loophash::MPI_LoopHashRefine::set_defaults(), 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().

TR() [2/12]

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

static

TR() [3/12]

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

static

TR() [4/12]

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

static

TR() [5/12]

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

static

TR() [6/12]

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

static

TR() [7/12]

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

static

Referenced by protocols::loophash::MPI_LoopHashRefine_Emperor::go(), protocols::loophash::MPI_LoopHashRefine_Emperor::init(), and protocols::loophash::MPI_LoopHashRefine_Emperor::process_inbound_wus().

TR() [8/12]

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

static

Referenced by protocols::loophash::MPI_LoopHashRefine_Master::add_relax_batch(), protocols::loophash::MPI_LoopHashRefine_Master::add_structure_to_library(), protocols::loophash::MPI_LoopHashRefine_Master::check_library_expiry_dates(), protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs(), protocols::loophash::MPI_LoopHashRefine_Master::go(), protocols::loophash::MPI_LoopHashRefine_Master::init(), protocols::loophash::MPI_LoopHashRefine_Master::load_sample_weight(), protocols::loophash::MPI_LoopHashRefine_Master::process_inbound_wus(), protocols::loophash::MPI_LoopHashRefine_Master::process_outbound_wus(), and protocols::loophash::MPI_LoopHashRefine_Master::report_structure_to_emperor().

TR() [9/12]

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

static

TR() [10/12]

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

static

TR() [11/12]

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

static

TR() [12/12]

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

static

Variable Documentation

HASH_POSITION_GRID_BASE

const int protocols::loophash::HASH_POSITION_GRID_BASE = 5

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

MAXIMAL_FLOAT

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

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