protocols::toolbox Namespace Reference

Namespaces
	match_enzdes_util
	pose_manipulation
	pose_metric_calculators
	rigid_body
	rotamer_set_operations
	sample_around
	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::shared_ptr < AllowInsert >	AllowInsertOP
typedef utility::pointer::shared_ptr < AllowInsert const >	AllowInsertCOP
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 < 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 < SelectResiduesByLayer >	SelectResiduesByLayerOP
typedef numeric::xyzMatrix < core::Real >	Matrix
typedef numeric::xyzVector < core::Real >	Vector

Functions
Size const	FIXED_DOMAIN (999)
static thread_local 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 thread_local basic::Tracer	_impl_tr ("protocols.toolbox.cluster")
static thread_local basic::Tracer	tr ("protocols.toolbox.DecoySetEvaluation", basic::t_info)
static thread_local 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)
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)
static thread_local 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, 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

Typedef Documentation

typedef utility::pointer::shared_ptr< AllowInsert const > protocols::toolbox::AllowInsertCOP

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Function Documentation

static thread_local 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().

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

References DIM.

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 a(), 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(), protocols::simple_filters::SSMotifFinder::superimpose_pose_on_template(), 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 protocols::simple_filters::coords(), fill_CA_coords(), fit_centered_coords(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::natoms(), 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 protocols::docking::membrane::MPDockingSetupMover::apply(), and CA_superimpose().

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

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

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(), jacobi(), 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, protocols::toolbox::ClusterOptions::cluster_radius, protocols::toolbox::DecoySetEvaluation::compute_distance_matrix(), 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
	)

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(), utility::file::FileName::local_name(), option, utility::file::FileName::path(), 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 protocols::simple_filters::coords(), and 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 protocols::simple_filters::coords(), xyz(), and core::pose::Pose::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(), protocols::simple_filters::coords(), numeric::xyzMatrix< class >::row_x(), numeric::xyzMatrix< class >::row_y(), numeric::xyzMatrix< class >::row_z(), and x().

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(), protocols::protein_interface_design::filters::RmsdSimpleFilter::superposition_transform(), superposition_transform(), and protocols::motif_grafting::movers::MotifGraftMover::superposition_transform().

std::string protocols::toolbox::fix_tag_suffix

(

string

str

)

References 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, ROTATE, runtime_assert, and z().

Referenced by 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().

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().

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

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 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(), protocols::protein_interface_design::filters::RmsdSimpleFilter::superposition_transform(), superposition_transform(), and protocols::motif_grafting::movers::MotifGraftMover::superposition_transform().

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

References c, and DIM.

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
	)

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

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

static

Referenced by protocols::toolbox::task_operations::InteractingRotamerExplosion::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), 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::task_operations::SeqprofConsensusOperation::parse_tag(), protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::position_untouchable(), protocols::toolbox::ClusterBase::print_summary(), protocols::toolbox::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::toolbox::DecoySetEvaluation::set_n_atom(), and protocols::toolbox::DecoySetEvaluation::wRMSD().

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

static

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

static

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

static

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

core::Size const protocols::toolbox::FIXED_DOMAIN

Referenced by protocols::toolbox::AllowInsert::append_residue().