protocols::toolbox Namespace Reference

Namespaces
	match_enzdes_util
	pose_manipulation
	pose_metric_calculators
	rotamer_set_operations
	task_operations

Classes
class	AllowInsert
class	ClusterBase
class	ClusterPhilStyle
class	ClusterOptions
class	OP_const_iterator
	const_iterator class for SilentFileData container. More...
class	DecoySetEvaluation
class	IGLigandDesignEdgeUpweighter
class	ResidueGroupIGEdgeUpweighter
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	DummyClass
class	SF_Replica
class	SelectResiduesByLayer

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 < 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)
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)
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)
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)
static basic::Tracer	tr ("protocols.evaluation.PCA", basic::t_info)
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	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	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::owning_ptr< AllowInsert > protocols::toolbox::AllowInsertOP

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

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

Definition at line 32 of file DecoySetEvaluation.fwd.hh.

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

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

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

Definition at line 33 of file PyReturnValuePolicyTest.hh.

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

Definition at line 34 of file PyReturnValuePolicyTest.hh.

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

Definition at line 31 of file PyReturnValuePolicyTest.hh.

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

Definition at line 28 of file PyReturnValuePolicyTest.hh.

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

Definition at line 37 of file KCluster.fwd.hh.

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

Definition at line 35 of file KCluster.fwd.hh.

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

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

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

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

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

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

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

Definition at line 21 of file KCluster.fwd.hh.

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

Definition at line 19 of file KCluster.fwd.hh.

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

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

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

Definition at line 33 of file KCluster.fwd.hh.

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

Definition at line 31 of file KCluster.fwd.hh.

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

Definition at line 34 of file superimpose.hh.

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

Definition at line 102 of file DecoySetEvaluation.cc.

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

Definition at line 103 of file DecoySetEvaluation.cc.

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

Definition at line 22 of file SelectResiduesByLayer.fwd.hh.

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

Definition at line 67 of file PyReturnValuePolicyTest.hh.

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

Definition at line 68 of file PyReturnValuePolicyTest.hh.

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

Definition at line 65 of file PyReturnValuePolicyTest.hh.

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

Definition at line 62 of file PyReturnValuePolicyTest.hh.

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

Definition at line 35 of file superimpose.hh.

Function Documentation

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().

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

Definition at line 209 of file superimpose.cc.

References DIM.

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

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
	)

Definition at line 76 of file superimpose.cc.

References 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 CA_superimpose().

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

Definition at line 151 of file superimpose.cc.

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
	)

Definition at line 309 of file superimpose.cc.

References core::pack::dunbrack::c, DIM, DIM6, dump_matrix(), jacobi(), core::scoring::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
	)

Definition at line 39 of file Cluster.impl.hh.

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
	)

Definition at line 55 of file Cluster.impl.hh.

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, and protocols::toolbox::DecoySetEvaluation::n_decoys().

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

Definition at line 220 of file Cluster.cc.

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

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
	)

Definition at line 240 of file superimpose.cc.

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.

Definition at line 161 of file superimpose.cc.

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.

Definition at line 164 of file superimpose.cc.

string protocols::toolbox::file_full_path

(

string

tag)

Definition at line 77 of file KCluster.cc.

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,
		FArray2_double &	coords
	)

Definition at line 61 of file superimpose.cc.

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
	)

Definition at line 66 of file superimpose.cc.

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

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::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
	)

Definition at line 254 of file superimpose.cc.

References calc_fit_R().

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(), and superimpose().

string protocols::toolbox::fix_tag_suffix

(

string

str)

Definition at line 142 of file KCluster.cc.

References 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)

Definition at line 64 of file KCluster.cc.

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

Definition at line 415 of file superimpose.cc.

References protocols::match::upstream::b, core::pack::dunbrack::c, DIM6, ROTATE, and core::scoring::hbonds::t().

Referenced by calc_fit_R().

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

Definition at line 55 of file Cluster.cc.

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

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

Definition at line 60 of file Cluster.cc.

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

Definition at line 76 of file Cluster.cc.

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

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

Definition at line 82 of file Cluster.cc.

References core::io::serialization::size().

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

Definition at line 300 of file superimpose.cc.

References XX, YY, and ZZ.

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

DummyClassAP protocols::toolbox::PyReturnValuePolicyTest_DummyClassAP ( void  )

inline

Definition at line 58 of file PyReturnValuePolicyTest.hh.

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

DummyClassCAP protocols::toolbox::PyReturnValuePolicyTest_DummyClassCAP ( void  )

inline

Definition at line 59 of file PyReturnValuePolicyTest.hh.

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

DummyClassCOP protocols::toolbox::PyReturnValuePolicyTest_DummyClassCOP ( void  )

inline

Definition at line 57 of file PyReturnValuePolicyTest.hh.

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

DummyClassOP protocols::toolbox::PyReturnValuePolicyTest_DummyClassOP ( void  )

inline

Definition at line 56 of file PyReturnValuePolicyTest.hh.

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

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

inline

Definition at line 106 of file PyReturnValuePolicyTest.hh.

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

inline

Definition at line 107 of file PyReturnValuePolicyTest.hh.

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

inline

Definition at line 105 of file PyReturnValuePolicyTest.hh.

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

inline

Definition at line 104 of file PyReturnValuePolicyTest.hh.

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

inline

Definition at line 110 of file PyReturnValuePolicyTest.hh.

References core::scoring::ScoreFunctionFactory::create_score_function().

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

inline

Definition at line 111 of file PyReturnValuePolicyTest.hh.

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

inline

Definition at line 109 of file PyReturnValuePolicyTest.hh.

References core::scoring::ScoreFunctionFactory::create_score_function().

SF_ReplicaAP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaAP ( void  )

inline

Definition at line 100 of file PyReturnValuePolicyTest.hh.

SF_ReplicaCAP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaCAP ( void  )

inline

Definition at line 101 of file PyReturnValuePolicyTest.hh.

SF_ReplicaCOP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaCOP ( void  )

inline

Definition at line 99 of file PyReturnValuePolicyTest.hh.

SF_ReplicaOP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaOP ( void  )

inline

Definition at line 98 of file PyReturnValuePolicyTest.hh.

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
	)

Definition at line 217 of file superimpose.cc.

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(), and superimpose().

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

Definition at line 192 of file superimpose.cc.

References core::pack::dunbrack::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

Definition at line 131 of file superimpose.cc.

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

Definition at line 142 of file superimpose.cc.

References fit_centered_coords(), and reset_x().

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

static

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

static

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

static

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

static

Variable Documentation

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

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