Namespaces
	match_enzdes_util

	pose_manipulation

	pose_metric_calculators

	rotamer_set_operations

	task_operations

Classes
class	AllowInsert

class	ClusterBase

class	ClusterOptions

class	ClusterPhilStyle

class	CovalentResidueNetwork
	Creates networks based on covalent connections between residues. More...

class	DecoySetEvaluation

class	DistanceResidueNetwork
	Creates networks based on residue proximity in space. More...

class	DummyClass

class	GreedyKCenter
	Greedy K-Center Clustering Algorithm. More...

class	IGLigandDesignEdgeUpweighter

class	InteratomicVarianceMatrix

class	KCluster
	basic class for performing a K-style Clustering algorithm More...

class	KClusterData
	database of a K-style Clustering algorithm More...

class	KClusterElement

class	KMedoid
	Typical K-Medoids Clustering Algorithm. More...

class	Node

class	OP_const_iterator
	const_iterator class for SilentFileData container. More...

class	ResidueGroupIGEdgeUpweighter

class	ResidueNetwork
	residuenetwork base class More...

class	SelectResiduesByLayer

class	SF_Replica

Typedefs
typedef utility::pointer::owning_ptr < AllowInsert >	AllowInsertOP

typedef core::Real	matrix [3][3]

typedef core::Real	rvec [3]

typedef utility::pointer::owning_ptr < DecoySetEvaluation >	DecoySetEvaluationOP

typedef utility::pointer::owning_ptr < DecoySetEvaluation const >	DecoySetEvaluationCOP

typedef utility::pointer::owning_ptr < KClusterElement >	KClusterElementOP

typedef utility::pointer::owning_ptr < KClusterElement const >	KClusterElementCOP

typedef utility::pointer::owning_ptr < KClusterData >	KClusterDataOP

typedef utility::pointer::owning_ptr < KClusterData const >	KClusterDataCOP

typedef utility::pointer::owning_ptr < KCluster >	KClusterOP

typedef utility::pointer::owning_ptr < KCluster const >	KClusterCOP

typedef utility::pointer::owning_ptr < KMedoid >	KMedoidOP

typedef utility::pointer::owning_ptr < KMedoid const >	KMedoidCOP

typedef utility::pointer::owning_ptr < GreedyKCenter >	GreedyKCenterOP

typedef utility::pointer::owning_ptr < GreedyKCenter const >	GreedyKCenterCOP

typedef utility::pointer::owning_ptr < Node >	NodeOP

typedef utility::pointer::owning_ptr < Node const >	NodeCOP

typedef utility::pointer::owning_ptr < ResidueNetwork >	ResidueNetworkOP

typedef utility::pointer::owning_ptr < ResidueNetwork const >	ResidueNetworkCOP

typedef utility::pointer::owning_ptr < DistanceResidueNetwork >	DistanceResidueNetworkOP

typedef utility::pointer::owning_ptr < DistanceResidueNetwork const >	DistanceResidueNetworkCOP

typedef utility::pointer::owning_ptr < CovalentResidueNetwork >	CovalentResidueNetworkOP

typedef utility::pointer::owning_ptr < CovalentResidueNetwork const >	CovalentResidueNetworkCOP

typedef utility::pointer::owning_ptr < DummyClass >	DummyClassOP

typedef utility::pointer::owning_ptr < DummyClass const >	DummyClassCOP

typedef utility::pointer::access_ptr < DummyClass >	DummyClassAP

typedef utility::pointer::access_ptr < DummyClass const >	DummyClassCAP

typedef utility::pointer::owning_ptr < SF_Replica >	SF_ReplicaOP

typedef utility::pointer::owning_ptr < SF_Replica const >	SF_ReplicaCOP

typedef utility::pointer::access_ptr < SF_Replica >	SF_ReplicaAP

typedef utility::pointer::access_ptr < SF_Replica const >	SF_ReplicaCAP

typedef utility::pointer::owning_ptr < SelectResiduesByLayer >	SelectResiduesByLayerOP

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

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

Functions
Size const	FIXED_DOMAIN (999)

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)

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)

DummyClassOP	PyReturnValuePolicyTest_DummyClassOP (void)

DummyClassCOP	PyReturnValuePolicyTest_DummyClassCOP (void)

DummyClassAP	PyReturnValuePolicyTest_DummyClassAP (void)

DummyClassCAP	PyReturnValuePolicyTest_DummyClassCAP (void)

SF_ReplicaOP	PyReturnValuePolicyTest_SF_ReplicaOP (void)

SF_ReplicaCOP	PyReturnValuePolicyTest_SF_ReplicaCOP (void)

SF_ReplicaAP	PyReturnValuePolicyTest_SF_ReplicaAP (void)

SF_ReplicaCAP	PyReturnValuePolicyTest_SF_ReplicaCAP (void)

core::pose::PoseOP	PyReturnValuePolicyTest_PoseOP (void)

core::pose::PoseCOP	PyReturnValuePolicyTest_PoseCOP (void)

core::pose::PoseAP	PyReturnValuePolicyTest_PoseAP (void)

core::pose::PoseCAP	PyReturnValuePolicyTest_PoseCAP (void)

core::scoring::ScoreFunctionOP	PyReturnValuePolicyTest_ScoreFunctionOP (void)

core::scoring::ScoreFunctionCOP	PyReturnValuePolicyTest_ScoreFunctionCOP (void)

core::scoring::ScoreFunctionCOP	PyReturnValuePolicyTest_ScoreFunctionCOP2 (void)

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, 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 (Size natoms, FArray1_double const &weights, FArray2_double &ref_coords, FArray2_double &coords)
	compute projections for given pose More...

void	superimpose (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 (double a[6][6], double d[], double v[6][6], int *nrot)

template<class T >
void	dump_matrix (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 (Size nr, T const &a, basic::Tracer &tr)
	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, rvec transvec)

void	reset_x (Size n, FArray2_double &x, FArray1_double const &wts, FArray1_double &transvec)

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

void	fit_centered_coords (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)

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
core::Size const	FIXED_DOMAIN

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

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

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

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

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

Typedef Documentation

typedef utility::pointer::owning_ptr< AllowInsert > protocols::toolbox::AllowInsertOP

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

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

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

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

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

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

typedef utility::pointer::access_ptr< DummyClass > protocols::toolbox::DummyClassAP

typedef utility::pointer::access_ptr< DummyClass const > protocols::toolbox::DummyClassCAP

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::owning_ptr< SelectResiduesByLayer > protocols::toolbox::SelectResiduesByLayerOP

typedef utility::pointer::access_ptr< SF_Replica > protocols::toolbox::SF_ReplicaAP

typedef utility::pointer::access_ptr< SF_Replica const > protocols::toolbox::SF_ReplicaCAP

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

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

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

Function Documentation

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

References DIM, and j.

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

std::list< NodeOP > protocols::toolbox::AdjacentRemainingNodes ( NodeOP node )

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

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

References core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by protocols::simple_moves::AlignChainMover::apply(), and protocols::simple_moves::AddChainMover::swap_chain().

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(), numeric::xyzVector< class >::length(), numeric::xyzVector< class >::normalized(), core::pose::Pose::set_jump(), core::kinematics::Jump::translation_along_axis(), and core::conformation::Conformation::upstream_jump_stub().

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

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

References fill_CA_coords(), fit_centered_coords(), core::chemical::ResidueType::is_protein(), j, core::chemical::ResidueType::natoms(), nres, reset_x(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), tr, and core::pose::Pose::xyz().

Referenced by CA_superimpose().

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

References CA_superimpose(), core::pose::Pose::total_residue(), and weights.

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

References c, DIM, DIM6, dump_matrix(), j, jacobi(), protocols::stepwise::sampling::protein::omega(), oprod(), and tr.

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

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().

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, core::io::silent::SilentStruct::clone(), cluster, protocols::toolbox::ClusterOptions::cluster_radius, protocols::toolbox::DecoySetEvaluation::compute_distance_matrix(), j, protocols::toolbox::ClusterOptions::keep_center, protocols::toolbox::ClusterOptions::limit_cluster_size, protocols::toolbox::DecoySetEvaluation::n_decoys(), and runtime_assert.

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().

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

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

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

References out.

template<class T >

void protocols::toolbox::dump_matrix	(	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().

template<class T >

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

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

NodeOP protocols::toolbox::ExtractSmallest ( std::list< NodeOP > & nodes )

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

std::string protocols::toolbox::file_full_path ( string tag )

References utility::file::FileName::base(), mc::hierarchical_pool, cluster::K_n_sub, utility::file::FileName::local_name(), option, utility::file::FileName::path(), s, out::file::silent, and user.

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

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

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

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

References core::pose::Pose::total_residue().

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().

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

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

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
	)

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

References calc_fit_R(), numeric::xyzMatrix< class >::row_x(), numeric::xyzMatrix< class >::row_y(), and numeric::xyzMatrix< class >::row_z().

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

std::string protocols::toolbox::fix_tag_suffix ( string str )

References cluster::K_level, option, and protocols::kinmatch::str().

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

Size const protocols::toolbox::FIXED_DOMAIN ( 999 )

KClusterOP protocols::toolbox::get_K_cluster_engine ( const string & style )

References utility_exit_with_message.

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

References protocols::match::upstream::b, c, DIM6, j, ROTATE, runtime_assert, s, and t.

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

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

References protocols::toolbox::ClusterBase::show().

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

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

References protocols::toolbox::ClusterBase::read().

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

References size(), and tag.

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

References XX, YY, and ZZ.

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

DummyClassAP protocols::toolbox::PyReturnValuePolicyTest_DummyClassAP ( void )

inline

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

DummyClassCAP protocols::toolbox::PyReturnValuePolicyTest_DummyClassCAP ( void )

inline

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

DummyClassCOP protocols::toolbox::PyReturnValuePolicyTest_DummyClassCOP ( void )

inline

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

DummyClassOP protocols::toolbox::PyReturnValuePolicyTest_DummyClassOP ( void )

inline

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

core::pose::PoseAP protocols::toolbox::PyReturnValuePolicyTest_PoseAP ( void )

inline

core::pose::PoseCAP protocols::toolbox::PyReturnValuePolicyTest_PoseCAP ( void )

inline

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

inline

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

inline

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

inline

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

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

inline

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

inline

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

SF_ReplicaAP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaAP ( void )

inline

SF_ReplicaCAP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaCAP ( void )

inline

SF_ReplicaCOP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaCOP ( void )

inline

SF_ReplicaOP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaOP ( void )

inline

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

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

References j, and 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(), and protocols::motif_grafting::movers::MotifGraftMover::superposition_transform().

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

References c, DIM, and j.

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

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

compute projections for given pose

References fit_centered_coords(), and reset_x().

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

compute projections for given pose

References fit_centered_coords(), and reset_x().

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
	)

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

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
	)

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 runtime_assert, superposition_transform(), and vector_vector_to_FArray2().

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
	)