protocols::toolbox Namespace Reference

Namespaces
	match_enzdes_util
	pose_manipulation
	py_inheritance_test
	rigid_body
	rotamer_set_operations
	sample_around

Classes
class	CalcInterNeighborGroup
class	ClusterBase
class	ClusterPhilStyle
class	ClusterOptions
class	OP_const_iterator
	const_iterator class for SilentFileData container. More...
class	DecoySetEvaluation
class	ScoreRmsPoint
class	ScoreRmsPoints
class	EnergyLandscapeEvaluator
	Evaluates a set of score/rms points. More...
class	RotamerBoltzmannWeightEvaluator
	Evaluates a set of score/rms points using the RotamerBoltzmann original method. More...
class	MulliganPNearEvaluator
	Evaluates a set of score/rms points using Vikram's pnear method. More...
class	IGLigandDesignEdgeUpweighter
class	ResidueGroupIGEdgeUpweighter
class	IGInterfaceEdgeUpweighter
class	InteratomicVarianceMatrix
class	KClusterElement
class	KClusterData
	database of a K-style Clustering algorithm More...
class	KCluster
	basic class for performing a K-style Clustering algorithm More...
class	KMedoid
	Typical K-Medoids Clustering Algorithm. More...
class	GreedyKCenter
	Greedy K-Center Clustering Algorithm. More...
class	ResidueNetwork
	residuenetwork base class More...
class	DistanceResidueNetwork
	Creates networks based on residue proximity in space. More...
class	CovalentResidueNetwork
	Creates networks based on covalent connections between residues. More...
struct	Node
class	DummyClass
class	SF_Replica
class	SamplerPlusPlus

Typedefs
typedef utility::pointer::shared_ptr< CalcInterNeighborGroup >	CalcInterNeighborGroupOP
typedef utility::pointer::shared_ptr< CalcInterNeighborGroup const >	CalcInterNeighborGroupCOP
typedef core::Real	matrix[3][3]
typedef core::Real	rvec[3]
typedef utility::pointer::shared_ptr< DecoySetEvaluation >	DecoySetEvaluationOP
typedef utility::pointer::shared_ptr< DecoySetEvaluation const >	DecoySetEvaluationCOP
typedef utility::pointer::shared_ptr< ScoreRmsPoint >	ScoreRmsPointOP
typedef utility::pointer::shared_ptr< ScoreRmsPoint const >	ScoreRmsPointCOP
typedef utility::pointer::shared_ptr< ScoreRmsPoints >	ScoreRmsPointsOP
typedef utility::pointer::shared_ptr< ScoreRmsPoints const >	ScoreRmsPointsCOP
typedef utility::pointer::shared_ptr< EnergyLandscapeEvaluator >	EnergyLandscapeEvaluatorOP
typedef utility::pointer::shared_ptr< EnergyLandscapeEvaluator const >	EnergyLandscapeEvaluatorCOP
typedef utility::pointer::shared_ptr< KClusterElement >	KClusterElementOP
typedef utility::pointer::shared_ptr< KClusterElement const >	KClusterElementCOP
typedef utility::pointer::shared_ptr< KClusterData >	KClusterDataOP
typedef utility::pointer::shared_ptr< KClusterData const >	KClusterDataCOP
typedef utility::pointer::shared_ptr< KCluster >	KClusterOP
typedef utility::pointer::shared_ptr< KCluster const >	KClusterCOP
typedef utility::pointer::shared_ptr< KMedoid >	KMedoidOP
typedef utility::pointer::shared_ptr< KMedoid const >	KMedoidCOP
typedef utility::pointer::shared_ptr< GreedyKCenter >	GreedyKCenterOP
typedef utility::pointer::shared_ptr< GreedyKCenter const >	GreedyKCenterCOP
typedef utility::pointer::shared_ptr< Node >	NodeOP
typedef utility::pointer::shared_ptr< Node const >	NodeCOP
typedef utility::pointer::shared_ptr< ResidueNetwork >	ResidueNetworkOP
typedef utility::pointer::shared_ptr< ResidueNetwork const >	ResidueNetworkCOP
typedef utility::pointer::shared_ptr< DistanceResidueNetwork >	DistanceResidueNetworkOP
typedef utility::pointer::shared_ptr< DistanceResidueNetwork const >	DistanceResidueNetworkCOP
typedef utility::pointer::shared_ptr< CovalentResidueNetwork >	CovalentResidueNetworkOP
typedef utility::pointer::shared_ptr< CovalentResidueNetwork const >	CovalentResidueNetworkCOP
typedef utility::pointer::shared_ptr< DummyClass >	DummyClassOP
typedef utility::pointer::shared_ptr< DummyClass const >	DummyClassCOP
typedef utility::pointer::shared_ptr< SF_Replica >	SF_ReplicaOP
typedef utility::pointer::shared_ptr< SF_Replica const >	SF_ReplicaCOP
typedef utility::pointer::shared_ptr< SamplerPlusPlus >	SamplerPlusPlusOP
typedef numeric::xyzMatrix< core::Real >	Matrix
typedef numeric::xyzVector< core::Real >	Vector

Enumerations
enum	SamplerPlusPlusType {   NO_ROTAMER_TYPE , ANY , COMB , COPY_DOF ,   INPUT_STREAM , JUMP , ONE_TORSION , ONE_DOF ,   ONE_VALUE , ONE_VALUE_COMB , PROTEIN_FRAGMENT , PROTEIN_MAIN_CHAIN ,   PROTEIN_BETA_ANTIPARALLEL , RESIDUE_LIST , RESIDUE_ALTERNATIVE , RESIDUE_ALTERNATIVE_COMB ,   RING_CONFORMERS , RIGID_BODY , RIGID_BODY_WITH_RESIDUE_LIST , RIGID_BODY_WITH_RESIDUE_ALTERNATIVES ,   RNA_CHI , RNA_KIC , RNA_KINEMATIC_CLOSER , MC_ANY ,   MC_COMB , MC_ONE_TORSION , MC_LOOP , MC_RNA_KIC ,   MC_RNA_MULTI_SUITE , MC_RNA_ONE_JUMP , MC_RNA_SUGAR , MC_RNA_SUITE ,   RNA_NUCLEOSIDE , RNA_SUGAR , RNA_SUITE , SIZED ,   SIZED_ANY , SIZED_COMB }

Functions
static basic::Tracer	tr ("protocols.cluster", basic::t_info)
std::ostream &	operator<< (std::ostream &out, ClusterBase const &cl)
std::ostream &	operator<< (std::ostream &out, ClusterBase::ClusterList const &cl)
std::istream &	operator>> (std::istream &in, ClusterBase &cl)
std::istream &	operator>> (std::istream &in, ClusterBase::ClusterList &cl)
bool	compareIndexEnergyPair (const std::pair< int, float > &p1, const std::pair< int, float > &p2)
template<typename SilentStructIterator , typename StructureContainer >
void	cluster_silent_structs (core::Size n_decoys, SilentStructIterator input_decoys_begin, SilentStructIterator input_decoys_end, StructureContainer &new_structs, ClusterOptions opts)
template<typename SilentStructIterator , typename StructureContainer >
void	cluster_silent_structs (DecoySetEvaluation const &CA_set, SilentStructIterator input_decoys_begin, SilentStructIterator input_decoys_end, StructureContainer &new_structs, ClusterOptions opts)
static basic::Tracer	_impl_tr ("protocols.toolbox.cluster")
static basic::Tracer	tr ("protocols.toolbox.DecoySetEvaluation", basic::t_info)
std::ostream &	operator<< (std::ostream &os, ScoreRmsPoint const &score)
static basic::Tracer	tr ("protocols.evaluation.PCA", basic::t_info)
KClusterOP	get_K_cluster_engine (const string &style)
string	file_full_path (string tag)
string	fix_tag_suffix (string str)
NodeOP	ExtractSmallest (std::list< NodeOP > &nodes)
std::list< NodeOP >	AdjacentRemainingNodes (NodeOP node)
bool	Contains (std::list< NodeOP > const &nodes, NodeCOP node)
void	out_of_bounds_memory_access ()
DummyClassOP	PyReturnValuePolicyTest_DummyClassOP (void)
DummyClassCOP	PyReturnValuePolicyTest_DummyClassCOP (void)
SF_ReplicaOP	PyReturnValuePolicyTest_SF_ReplicaOP (void)
SF_ReplicaCOP	PyReturnValuePolicyTest_SF_ReplicaCOP (void)
core::pose::PoseOP	PyReturnValuePolicyTest_PoseOP (void)
core::pose::PoseCOP	PyReturnValuePolicyTest_PoseCOP (void)
core::scoring::ScoreFunctionOP	PyReturnValuePolicyTest_ScoreFunctionOP (void)
core::scoring::ScoreFunctionCOP	PyReturnValuePolicyTest_ScoreFunctionCOP (void)
core::scoring::ScoreFunctionCOP	PyReturnValuePolicyTest_ScoreFunctionCOP2 (void)
void	take_pose_op (core::pose::PoseOP const &)
static basic::Tracer	tr ("protocols.evaluation.PCA", basic::t_info)
template<typename T >
void	vector_vector_to_FArray2 (utility::vector1< numeric::xyzVector< T > > &from, ObjexxFCL::FArray2D< T > &to)
void	superposition_transform (utility::vector1< numeric::xyzVector< core::Real > > &init_coords, utility::vector1< numeric::xyzVector< core::Real > > &ref_coords, numeric::xyzMatrix< core::Real > &rotation, numeric::xyzVector< core::Real > &to_init_center, numeric::xyzVector< core::Real > &to_fit_center)
void	superposition_transform (utility::vector1< numeric::xyzVector< core::Real > > &init_coords, utility::vector1< numeric::xyzVector< core::Real > > &ref_coords, utility::vector1< core::Real > &coord_weights, numeric::xyzMatrix< core::Real > &rotation, numeric::xyzVector< core::Real > &to_init_center, numeric::xyzVector< core::Real > &to_fit_center)
void	apply_superposition_transform_to_jump (core::pose::Pose &pose, core::Size jump_id, Matrix rotation, Vector to_init_center, Vector to_fit_center)
void	apply_superposition_transform (core::pose::Pose &pose, Matrix rotation, Vector to_init_center, Vector to_fit_center)
void	fill_CA_coords (core::pose::Pose const &pose, FArray2_double &coords)
void	fill_CA_coords (core::pose::Pose const &pose, core::Size n_atoms, FArray2_double &coords)
void	CA_superimpose (FArray1_double const &weights, core::pose::Pose const &ref_pose, core::pose::Pose &fit_pose)
void	superposition_transform (core::Size natoms, ObjexxFCL::FArray1_double const &weights, ObjexxFCL::FArray2_double &ref_coords, ObjexxFCL::FArray2_double &coords, Matrix &R, Vector &toCenter, Vector &toFitCenter)
void	superimpose (core::Size natoms, FArray1_double const &weights, FArray2_double &ref_coords, FArray2_double &coords)
	compute projections for given pose More...
void	superimpose (core::Size natoms, FArray1_double const &weights, FArray2_double &ref_coords, FArray2_double &coords, Matrix &R)
	compute projections for given pose More...
void	CA_superimpose (core::pose::Pose const &ref_pose, core::pose::Pose &fit_pose)
void	calc_fit_R (int natoms, Real const *weights, rvec const *xp, rvec const *x, matrix R)
void	jacobi (core::Real a[6][6], core::Real d[], core::Real v[6][6], int *nrot)
template<class T >
void	dump_matrix (core::Size, T const &, basic::Tracer &)
	A function (not a macro) that will not print a square matrix to tr.Debug. More...
template<class T >
void	dump_matrix_no (core::Size nr, T const &a, basic::Tracer &tracer)
	A function (not a macro) that will print a square matrix to tr.Debug. More...
void	rotate_vec (int natoms, rvec *x, matrix R)
void	add_vec (int natoms, rvec *x, const rvec transvec)
void	reset_x (core::Size n, FArray2_double &x, FArray1_double const &wts, FArray1_double &transvec)
void	dump_as_pdb (std::string filename, core::Size n, FArray2_double &x, FArray1D_double transvec)
void	fit_centered_coords (core::Size natoms, FArray1_double const &weights, FArray2_double const &ref_coords, FArray2_double &coords, Matrix &R)
void	oprod (const rvec a, const rvec b, rvec c)
template<class T >
void	ROTATE (T &a, int i, int j, int k, int l, core::Real s, core::Real tau)
void	CA_superimpose (ObjexxFCL::FArray1_double const &weights, core::pose::Pose const &ref_pose, core::pose::Pose &fit_pose)
void	superposition_transform (utility::vector1< numeric::xyzVector< core::Real > > &init_coords, utility::vector1< numeric::xyzVector< core::Real > > &ref_coords, Matrix &rotation, Vector &to_init_center, Vector &to_fit_center)
void	superposition_transform (utility::vector1< numeric::xyzVector< core::Real > > &init_coords, utility::vector1< numeric::xyzVector< core::Real > > &ref_coords, utility::vector1< core::Real > &coord_weights, Matrix &rotation, Vector &to_init_center, Vector &to_fit_center)
void	fit_centered_coords (core::Size natoms, ObjexxFCL::FArray1_double const &weights, ObjexxFCL::FArray2_double const &ref_coords, ObjexxFCL::FArray2_double &coords, Matrix &R)
void	reset_x (core::Size n, ObjexxFCL::FArray2_double &x, ObjexxFCL::FArray1_double const &wts, ObjexxFCL::FArray1_double &transvec)
void	dump_as_pdb (std::string filename, core::Size n, ObjexxFCL::FArray2_double &coords, ObjexxFCL::FArray1D_double transvec=ObjexxFCL::FArray1D_double(3, 0.0))
	write a CA ALA pdb More...
void	fill_CA_coords (core::pose::Pose const &pose, core::Size natoms, ObjexxFCL::FArray2_double &coords)
void	fill_CA_coords (core::pose::Pose const &pose, ObjexxFCL::FArray2_double &coords)

Variables
constexpr int	DIM6 = 6
constexpr int	XX = 0
constexpr int	YY = 1
constexpr int	ZZ = 2

Typedef Documentation

CalcInterNeighborGroupCOP

typedef utility::pointer::shared_ptr< CalcInterNeighborGroup const > protocols::toolbox::CalcInterNeighborGroupCOP

CalcInterNeighborGroupOP

typedef utility::pointer::shared_ptr< CalcInterNeighborGroup > protocols::toolbox::CalcInterNeighborGroupOP

CovalentResidueNetworkCOP

typedef utility::pointer::shared_ptr< CovalentResidueNetwork const > protocols::toolbox::CovalentResidueNetworkCOP

CovalentResidueNetworkOP

typedef utility::pointer::shared_ptr< CovalentResidueNetwork > protocols::toolbox::CovalentResidueNetworkOP

DecoySetEvaluationCOP

typedef utility::pointer::shared_ptr< DecoySetEvaluation const > protocols::toolbox::DecoySetEvaluationCOP

DecoySetEvaluationOP

typedef utility::pointer::shared_ptr< DecoySetEvaluation > protocols::toolbox::DecoySetEvaluationOP

DistanceResidueNetworkCOP

typedef utility::pointer::shared_ptr< DistanceResidueNetwork const > protocols::toolbox::DistanceResidueNetworkCOP

DistanceResidueNetworkOP

typedef utility::pointer::shared_ptr< DistanceResidueNetwork > protocols::toolbox::DistanceResidueNetworkOP

DummyClassCOP

typedef utility::pointer::shared_ptr< DummyClass const > protocols::toolbox::DummyClassCOP

DummyClassOP

typedef utility::pointer::shared_ptr< DummyClass > protocols::toolbox::DummyClassOP

EnergyLandscapeEvaluatorCOP

typedef utility::pointer::shared_ptr< EnergyLandscapeEvaluator const > protocols::toolbox::EnergyLandscapeEvaluatorCOP

EnergyLandscapeEvaluatorOP

typedef utility::pointer::shared_ptr< EnergyLandscapeEvaluator > protocols::toolbox::EnergyLandscapeEvaluatorOP

GreedyKCenterCOP

typedef utility::pointer::shared_ptr< GreedyKCenter const > protocols::toolbox::GreedyKCenterCOP

GreedyKCenterOP

typedef utility::pointer::shared_ptr< GreedyKCenter > protocols::toolbox::GreedyKCenterOP

KClusterCOP

typedef utility::pointer::shared_ptr< KCluster const > protocols::toolbox::KClusterCOP

KClusterDataCOP

typedef utility::pointer::shared_ptr< KClusterData const > protocols::toolbox::KClusterDataCOP

KClusterDataOP

typedef utility::pointer::shared_ptr< KClusterData > protocols::toolbox::KClusterDataOP

KClusterElementCOP

typedef utility::pointer::shared_ptr< KClusterElement const > protocols::toolbox::KClusterElementCOP

KClusterElementOP

typedef utility::pointer::shared_ptr< KClusterElement > protocols::toolbox::KClusterElementOP

KClusterOP

typedef utility::pointer::shared_ptr< KCluster > protocols::toolbox::KClusterOP

KMedoidCOP

typedef utility::pointer::shared_ptr< KMedoid const > protocols::toolbox::KMedoidCOP

KMedoidOP

typedef utility::pointer::shared_ptr< KMedoid > protocols::toolbox::KMedoidOP

matrix

typedef core::Real protocols::toolbox::matrix

Matrix

typedef numeric::xyzMatrix< core::Real > protocols::toolbox::Matrix

NodeCOP

typedef utility::pointer::shared_ptr< Node const > protocols::toolbox::NodeCOP

NodeOP

typedef utility::pointer::shared_ptr< Node > protocols::toolbox::NodeOP

ResidueNetworkCOP

typedef utility::pointer::shared_ptr< ResidueNetwork const > protocols::toolbox::ResidueNetworkCOP

ResidueNetworkOP

typedef utility::pointer::shared_ptr< ResidueNetwork > protocols::toolbox::ResidueNetworkOP

rvec

typedef core::Real protocols::toolbox::rvec

SamplerPlusPlusOP

typedef utility::pointer::shared_ptr< SamplerPlusPlus > protocols::toolbox::SamplerPlusPlusOP

ScoreRmsPointCOP

typedef utility::pointer::shared_ptr< ScoreRmsPoint const > protocols::toolbox::ScoreRmsPointCOP

ScoreRmsPointOP

typedef utility::pointer::shared_ptr< ScoreRmsPoint > protocols::toolbox::ScoreRmsPointOP

ScoreRmsPointsCOP

typedef utility::pointer::shared_ptr< ScoreRmsPoints const > protocols::toolbox::ScoreRmsPointsCOP

ScoreRmsPointsOP

typedef utility::pointer::shared_ptr< ScoreRmsPoints > protocols::toolbox::ScoreRmsPointsOP

SF_ReplicaCOP

typedef utility::pointer::shared_ptr< SF_Replica const > protocols::toolbox::SF_ReplicaCOP

SF_ReplicaOP

typedef utility::pointer::shared_ptr< SF_Replica > protocols::toolbox::SF_ReplicaOP

Vector

typedef numeric::xyzVector< core::Real > protocols::toolbox::Vector

Enumeration Type Documentation

SamplerPlusPlusType

enum protocols::toolbox::SamplerPlusPlusType

Enumerator
NO_ROTAMER_TYPE
ANY
COMB
COPY_DOF
INPUT_STREAM
JUMP
ONE_TORSION
ONE_DOF
ONE_VALUE
ONE_VALUE_COMB
PROTEIN_FRAGMENT
PROTEIN_MAIN_CHAIN
PROTEIN_BETA_ANTIPARALLEL
RESIDUE_LIST
RESIDUE_ALTERNATIVE
RESIDUE_ALTERNATIVE_COMB
RING_CONFORMERS
RIGID_BODY
RIGID_BODY_WITH_RESIDUE_LIST
RIGID_BODY_WITH_RESIDUE_ALTERNATIVES
RNA_CHI
RNA_KIC
RNA_KINEMATIC_CLOSER
MC_ANY
MC_COMB
MC_ONE_TORSION
MC_LOOP
MC_RNA_KIC
MC_RNA_MULTI_SUITE
MC_RNA_ONE_JUMP
MC_RNA_SUGAR
MC_RNA_SUITE
RNA_NUCLEOSIDE
RNA_SUGAR
RNA_SUITE
SIZED
SIZED_ANY
SIZED_COMB

Function Documentation

_impl_tr()

static basic::Tracer protocols::toolbox::_impl_tr ( "protocols.toolbox.cluster"  )

static

Referenced by cluster_silent_structs(), and protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz_from_silent_file().

add_vec()

void protocols::toolbox::add_vec	(	int	natoms,
		rvec *	x,
		const rvec	transvec
	)

References DIM.

Referenced by protocols::evaluation::PCA::eval(), and core::chemical::parse_adduct_string().

AdjacentRemainingNodes()

std::list< NodeOP > protocols::toolbox::AdjacentRemainingNodes

(

NodeOP

node

)

Referenced by protocols::toolbox::ResidueNetwork::dijkstras().

apply_superposition_transform()

void protocols::toolbox::apply_superposition_transform	(	core::pose::Pose &	pose,
		Matrix	rotation,
		Vector	to_init_center,
		Vector	to_fit_center
	)

References core::pose::motif::a(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), and core::pose::Pose::xyz().

Referenced by protocols::fold_from_loops::movers::AlignByResidueSelectorMover::apply(), protocols::simple_moves::AlignChainMover::apply(), protocols::splice::AlignEndsMover::apply(), protocols::protein_interface_design::filters::RmsdFilter::compute(), protocols::simple_filters::SSMotifFinder::superimpose_pose_on_template(), protocols::splice::Splice::superimpose_source_on_pose(), protocols::splice::SpliceOut::superimpose_source_on_pose(), protocols::splice::SpliceOutTail::superimpose_source_on_pose(), protocols::splice::RBOutMover::superimpose_source_on_pose(), and protocols::simple_moves::AddChainMover::swap_chain().

apply_superposition_transform_to_jump()

void protocols::toolbox::apply_superposition_transform_to_jump	(	core::pose::Pose &	pose,
		core::Size	jump_id,
		Matrix	rotation,
		Vector	to_init_center,
		Vector	to_fit_center
	)

References core::pose::Pose::conformation(), core::pose::Pose::jump(), core::kinematics::Jump::rotation_by_matrix(), core::pose::Pose::set_jump(), core::kinematics::Jump::translation_along_axis(), and core::conformation::Conformation::upstream_jump_stub().

CA_superimpose() [1/3]

void protocols::toolbox::CA_superimpose	(	core::pose::Pose const &	ref_pose,
		core::pose::Pose &	fit_pose
	)

References CA_superimpose(), and core::pose::Pose::size().

CA_superimpose() [2/3]

void protocols::toolbox::CA_superimpose	(	FArray1_double const &	weights,
		core::pose::Pose const &	ref_pose,
		core::pose::Pose &	fit_pose
	)

References protocols::simple_filters::coords(), fill_CA_coords(), fit_centered_coords(), core::chemical::ResidueTypeBase::is_protein(), reset_x(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), tr(), and core::pose::Pose::xyz().

Referenced by protocols::docking::membrane::MPDockingSetupMover::apply(), and CA_superimpose().

CA_superimpose() [3/3]

void protocols::toolbox::CA_superimpose	(	ObjexxFCL::FArray1_double const &	weights,
		core::pose::Pose const &	ref_pose,
		core::pose::Pose &	fit_pose
	)

calc_fit_R()

void protocols::toolbox::calc_fit_R	(	int	natoms,
		Real const *	weights,
		rvec const *	xp,
		rvec const *	x,
		matrix	R
	)

References DIM, DIM6, dump_matrix(), jacobi(), core::scoring::omega, oprod(), tr(), and protocols::hybridization::u.

Referenced by protocols::evaluation::PCA::eval(), and fit_centered_coords().

cluster_silent_structs() [1/2]

template<typename SilentStructIterator , typename StructureContainer >

void protocols::toolbox::cluster_silent_structs	(	core::Size	n_decoys,
		SilentStructIterator	input_decoys_begin,
		SilentStructIterator	input_decoys_end,
		StructureContainer &	new_structs,
		ClusterOptions	opts
	)

References protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz_from_silent_file().

cluster_silent_structs() [2/2]

template<typename SilentStructIterator , typename StructureContainer >

void protocols::toolbox::cluster_silent_structs	(	DecoySetEvaluation const &	CA_set,
		SilentStructIterator	input_decoys_begin,
		SilentStructIterator	input_decoys_end,
		StructureContainer &	new_structs,
		ClusterOptions	opts
	)

References _impl_tr(), protocols::toolbox::DecoySetEvaluation::all_energies(), protocols::toolbox::ClusterOptions::assign_new_cluster_tag, protocols::toolbox::ClusterOptions::cluster_radius, protocols::toolbox::ClusterBase::clusterlist(), protocols::toolbox::DecoySetEvaluation::compute_distance_matrix(), protocols::toolbox::ClusterBase::distance_matrix(), protocols::toolbox::ClusterPhilStyle::do_clustering(), protocols::toolbox::ClusterOptions::keep_center, protocols::toolbox::ClusterOptions::limit_cluster_size, protocols::toolbox::ClusterBase::limit_groupsize(), protocols::toolbox::DecoySetEvaluation::n_decoys(), protocols::toolbox::ClusterBase::print_summary(), protocols::toolbox::ClusterPhilStyle::set_n_max_cluster(), and protocols::toolbox::ClusterBase::sort_each_group_by_energy().

compareIndexEnergyPair()

bool protocols::toolbox::compareIndexEnergyPair	(	const std::pair< int, float > &	p1,
		const std::pair< int, float > &	p2
	)

Referenced by protocols::toolbox::ClusterBase::sort_each_group_by_energy().

Contains()

bool protocols::toolbox::Contains	(	std::list< NodeOP > const &	nodes,
		NodeCOP	node
	)

dump_as_pdb() [1/2]

void protocols::toolbox::dump_as_pdb	(	std::string	filename,
		core::Size	n,
		FArray2_double &	x,
		FArray1D_double	transvec
	)

References protocols::abinitio::filename(), and core::conformation::membrane::out.

dump_as_pdb() [2/2]

void protocols::toolbox::dump_as_pdb	(	std::string	filename,
		core::Size	n,
		ObjexxFCL::FArray2_double &	coords,
		ObjexxFCL::FArray1D_double	transvec = ObjexxFCL::FArray1D_double(3, 0.0)
	)

write a CA ALA pdb

dump_matrix()

template<class T >

void protocols::toolbox::dump_matrix	(	core::Size	,
		T const &	,
		basic::Tracer &
	)

A function (not a macro) that will not print a square matrix to tr.Debug.

Referenced by calc_fit_R().

dump_matrix_no()

template<class T >

void protocols::toolbox::dump_matrix_no	(	core::Size	nr,
		T const &	a,
		basic::Tracer &	tracer
	)

A function (not a macro) that will print a square matrix to tr.Debug.

References core::pose::motif::a(), and protocols::frag_picker::tracer().

ExtractSmallest()

NodeOP protocols::toolbox::ExtractSmallest

(

std::list< NodeOP > &

nodes

)

Referenced by protocols::toolbox::ResidueNetwork::dijkstras().

file_full_path()

std::string protocols::toolbox::file_full_path

(

string

tag

)

Referenced by protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), and protocols::toolbox::KClusterData::save_cluster_tree().

fill_CA_coords() [1/4]

void protocols::toolbox::fill_CA_coords	(	core::pose::Pose const &	pose,
		core::Size	n_atoms,
		FArray2_double &	coords
	)

References protocols::simple_filters::coords(), core::pose::Pose::xyz(), and protocols::kinmatch::xyz().

fill_CA_coords() [2/4]

void protocols::toolbox::fill_CA_coords	(	core::pose::Pose const &	pose,
		core::Size	natoms,
		ObjexxFCL::FArray2_double &	coords
	)

fill_CA_coords() [3/4]

void protocols::toolbox::fill_CA_coords	(	core::pose::Pose const &	pose,
		FArray2_double &	coords
	)

References protocols::simple_filters::coords(), and core::pose::Pose::size().

Referenced by protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add(), CA_superimpose(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate(), and protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate_and_add().

fill_CA_coords() [4/4]

void protocols::toolbox::fill_CA_coords	(	core::pose::Pose const &	pose,
		ObjexxFCL::FArray2_double &	coords
	)

fit_centered_coords() [1/2]

void protocols::toolbox::fit_centered_coords	(	core::Size	natoms,
		FArray1_double const &	weights,
		FArray2_double const &	ref_coords,
		FArray2_double &	coords,
		Matrix &	R
	)

References calc_fit_R(), and protocols::simple_filters::coords().

Referenced by CA_superimpose(), protocols::toolbox::DecoySetEvaluation::compute_distance_matrix(), protocols::toolbox::KClusterData::dist_square(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::dist_square(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate_core(), protocols::toolbox::DecoySetEvaluation::rmsd(), protocols::topology_broker::CoordConstraintClaimer::superimpose(), superimpose(), superposition_transform(), protocols::motif_grafting::movers::MotifGraftMover::superposition_transform(), and protocols::protein_interface_design::filters::RmsdSimpleFilter::superposition_transform().

fit_centered_coords() [2/2]

void protocols::toolbox::fit_centered_coords	(	core::Size	natoms,
		ObjexxFCL::FArray1_double const &	weights,
		ObjexxFCL::FArray2_double const &	ref_coords,
		ObjexxFCL::FArray2_double &	coords,
		Matrix &	R
	)

fix_tag_suffix()

std::string protocols::toolbox::fix_tag_suffix

(

string

str

)

References protocols::kinmatch::str().

Referenced by protocols::toolbox::KClusterData::save_cluster_tree().

get_K_cluster_engine()

KClusterOP protocols::toolbox::get_K_cluster_engine

(

const string &

style

)

jacobi()

void protocols::toolbox::jacobi	(	core::Real	a[6][6],
		core::Real	d[],
		core::Real	v[6][6],
		int *	nrot
	)

References core::pose::motif::a(), protocols::match::upstream::b, DIM6, ROTATE(), and protocols::hybridization::t.

Referenced by calc_fit_R().

operator<<() [1/3]

std::ostream& protocols::toolbox::operator<<	(	std::ostream &	os,
		ScoreRmsPoint const &	score
	)

operator<<() [2/3]

std::ostream & protocols::toolbox::operator<<	(	std::ostream &	out,
		ClusterBase const &	cl
	)

References core::conformation::membrane::out, and protocols::toolbox::ClusterBase::show().

operator<<() [3/3]

std::ostream & protocols::toolbox::operator<<	(	std::ostream &	out,
		ClusterBase::ClusterList const &	cl
	)

References core::conformation::membrane::out.

operator>>() [1/2]

std::istream & protocols::toolbox::operator>>	(	std::istream &	in,
		ClusterBase &	cl
	)

References core::conformation::membrane::in, and protocols::toolbox::ClusterBase::read().

operator>>() [2/2]

std::istream & protocols::toolbox::operator>>	(	std::istream &	in,
		ClusterBase::ClusterList &	cl
	)

References core::conformation::membrane::in.

oprod()

void protocols::toolbox::oprod	(	const rvec	a,
		const rvec	b,
		rvec	c
	)

References core::pose::motif::a(), protocols::match::upstream::b, XX, YY, and ZZ.

Referenced by calc_fit_R(), and protocols::evaluation::PCA::calc_fit_R().

out_of_bounds_memory_access()

void protocols::toolbox::out_of_bounds_memory_access

(

)

PyReturnValuePolicyTest_DummyClassCOP()

DummyClassCOP protocols::toolbox::PyReturnValuePolicyTest_DummyClassCOP ( void  )

inline

References protocols::toolbox::DummyClass::create().

PyReturnValuePolicyTest_DummyClassOP()

DummyClassOP protocols::toolbox::PyReturnValuePolicyTest_DummyClassOP ( void  )

inline

References protocols::toolbox::DummyClass::create().

PyReturnValuePolicyTest_PoseCOP()

core::pose::PoseCOP protocols::toolbox::PyReturnValuePolicyTest_PoseCOP ( void  )

inline

PyReturnValuePolicyTest_PoseOP()

core::pose::PoseOP protocols::toolbox::PyReturnValuePolicyTest_PoseOP ( void  )

inline

PyReturnValuePolicyTest_ScoreFunctionCOP()

core::scoring::ScoreFunctionCOP protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionCOP ( void  )

inline

References core::scoring::get_score_function_legacy(), and core::scoring::PRE_TALARIS_2013_STANDARD_WTS.

PyReturnValuePolicyTest_ScoreFunctionCOP2()

core::scoring::ScoreFunctionCOP protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionCOP2 ( void  )

inline

PyReturnValuePolicyTest_ScoreFunctionOP()

core::scoring::ScoreFunctionOP protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionOP ( void  )

inline

References core::scoring::get_score_function_legacy(), and core::scoring::PRE_TALARIS_2013_STANDARD_WTS.

PyReturnValuePolicyTest_SF_ReplicaCOP()

SF_ReplicaCOP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaCOP ( void  )

inline

PyReturnValuePolicyTest_SF_ReplicaOP()

SF_ReplicaOP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaOP ( void  )

inline

reset_x() [1/2]

void protocols::toolbox::reset_x	(	core::Size	n,
		FArray2_double &	x,
		FArray1_double const &	wts,
		FArray1_double &	transvec
	)

References core::pose::mass().

Referenced by CA_superimpose(), protocols::toolbox::DecoySetEvaluation::compute_distance_matrix(), protocols::evaluation::PCA::eval(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate_core(), protocols::toolbox::KClusterData::load_silent_files(), protocols::toolbox::DecoySetEvaluation::rmsd(), protocols::topology_broker::CoordConstraintClaimer::superimpose(), superimpose(), superposition_transform(), protocols::motif_grafting::movers::MotifGraftMover::superposition_transform(), and protocols::protein_interface_design::filters::RmsdSimpleFilter::superposition_transform().

reset_x() [2/2]

void protocols::toolbox::reset_x	(	core::Size	n,
		ObjexxFCL::FArray2_double &	x,
		ObjexxFCL::FArray1_double const &	wts,
		ObjexxFCL::FArray1_double &	transvec
	)

ROTATE()

template<class T >

void protocols::toolbox::ROTATE	(	T &	a,
		int	i,
		int	j,
		int	k,
		int	l,
		core::Real	s,
		core::Real	tau
	)

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

Referenced by jacobi().

rotate_vec()

void protocols::toolbox::rotate_vec	(	int	natoms,
		rvec *	x,
		matrix	R
	)

References DIM.

Referenced by protocols::evaluation::PCA::eval().

superimpose() [1/2]

void protocols::toolbox::superimpose	(	core::Size	natoms,
		FArray1_double const &	weights,
		FArray2_double &	ref_coords,
		FArray2_double &	coords
	)

compute projections for given pose

References protocols::simple_filters::coords(), fit_centered_coords(), and reset_x().

Referenced by core::scoring::automorphic_rmsd(), protocols::mpi_refinement::CA_Sscore(), and protocols::mpi_refinement::distance().

superimpose() [2/2]

void protocols::toolbox::superimpose	(	core::Size	natoms,
		FArray1_double const &	weights,
		FArray2_double &	ref_coords,
		FArray2_double &	coords,
		Matrix &	R
	)

compute projections for given pose

References protocols::simple_filters::coords(), fit_centered_coords(), and reset_x().

superposition_transform() [1/5]

void protocols::toolbox::superposition_transform	(	core::Size	natoms,
		ObjexxFCL::FArray1_double const &	weights,
		ObjexxFCL::FArray2_double &	ref_coords,
		ObjexxFCL::FArray2_double &	coords,
		Matrix &	R,
		Vector &	toCenter,
		Vector &	toFitCenter
	)

References protocols::simple_filters::coords(), fit_centered_coords(), and reset_x().

superposition_transform() [2/5]

void protocols::toolbox::superposition_transform	(	utility::vector1< numeric::xyzVector< core::Real > > &	init_coords,
		utility::vector1< numeric::xyzVector< core::Real > > &	ref_coords,
		Matrix &	rotation,
		Vector &	to_init_center,
		Vector &	to_fit_center
	)

superposition_transform() [3/5]

void protocols::toolbox::superposition_transform	(	utility::vector1< numeric::xyzVector< core::Real > > &	init_coords,
		utility::vector1< numeric::xyzVector< core::Real > > &	ref_coords,
		numeric::xyzMatrix< core::Real > &	rotation,
		numeric::xyzVector< core::Real > &	to_init_center,
		numeric::xyzVector< core::Real > &	to_fit_center
	)

Referenced by superposition_transform(), and protocols::seeded_abinitio::superposition_transform().

superposition_transform() [4/5]

void protocols::toolbox::superposition_transform	(	utility::vector1< numeric::xyzVector< core::Real > > &	init_coords,
		utility::vector1< numeric::xyzVector< core::Real > > &	ref_coords,
		utility::vector1< core::Real > &	coord_weights,
		Matrix &	rotation,
		Vector &	to_init_center,
		Vector &	to_fit_center
	)

superposition_transform() [5/5]

void protocols::toolbox::superposition_transform	(	utility::vector1< numeric::xyzVector< core::Real > > &	init_coords,
		utility::vector1< numeric::xyzVector< core::Real > > &	ref_coords,
		utility::vector1< core::Real > &	coord_weights,
		numeric::xyzMatrix< core::Real > &	rotation,
		numeric::xyzVector< core::Real > &	to_init_center,
		numeric::xyzVector< core::Real > &	to_fit_center
	)

References superposition_transform(), and vector_vector_to_FArray2().

take_pose_op()

void protocols::toolbox::take_pose_op ( core::pose::PoseOP const &  )

inline

tr() [1/4]

static basic::Tracer protocols::toolbox::tr ( "protocols.cluster"  , basic::t_info    )

static

Referenced by CA_superimpose(), calc_fit_R(), protocols::toolbox::DecoySetEvaluation::compute_distance_matrix(), protocols::toolbox::DecoySetEvaluation::create_dist_constraints(), protocols::toolbox::DecoySetEvaluation::create_dist_constraints_median(), protocols::toolbox::DecoySetEvaluation::create_xyz_constraints_median(), protocols::toolbox::DecoySetEvaluation::find_closest_to_average(), protocols::toolbox::InteratomicVarianceMatrix::init(), protocols::toolbox::InteratomicVarianceMatrix::optimize_kurtosis(), protocols::toolbox::InteratomicVarianceMatrix::order_parameter(), protocols::toolbox::ClusterBase::print_summary(), protocols::toolbox::DecoySetEvaluation::set_n_atom(), and protocols::toolbox::DecoySetEvaluation::wRMSD().

tr() [2/4]

static basic::Tracer protocols::toolbox::tr ( "protocols.evaluation.PCA"  , basic::t_info    )

static

tr() [3/4]

static basic::Tracer protocols::toolbox::tr ( "protocols.evaluation.PCA"  , basic::t_info    )

static

tr() [4/4]

static basic::Tracer protocols::toolbox::tr ( "protocols.toolbox.DecoySetEvaluation"  , basic::t_info    )

static

vector_vector_to_FArray2()

template<typename T >

void protocols::toolbox::vector_vector_to_FArray2	(	utility::vector1< numeric::xyzVector< T > > &	from,
		ObjexxFCL::FArray2D< T > &	to
	)

Referenced by superposition_transform().

Variable Documentation

DIM6

constexpr int protocols::toolbox::DIM6 = 6

constexpr

Referenced by calc_fit_R(), and jacobi().

XX

constexpr int protocols::toolbox::XX = 0

constexpr

Referenced by oprod().

YY

constexpr int protocols::toolbox::YY = 1

constexpr

Referenced by oprod().

ZZ

constexpr int protocols::toolbox::ZZ = 2

constexpr

Referenced by oprod().