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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  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  EnergyLandscapeEvaluator
 Evaluates a set of score/rms points. More...
 
class  GreedyKCenter
 Greedy K-Center Clustering Algorithm. More...
 
class  IGInterfaceEdgeUpweighter
 
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  MulliganPNearEvaluator
 Evaluates a set of score/rms points using Vikram's pnear method. More...
 
struct  Node
 
class  OP_const_iterator
 const_iterator class for SilentFileData container. More...
 
class  ResidueGroupIGEdgeUpweighter
 
class  ResidueNetwork
 residuenetwork base class More...
 
class  RotamerBoltzmannWeightEvaluator
 Evaluates a set of score/rms points using the RotamerBoltzmann original method. More...
 
class  SamplerPlusPlus
 
class  ScoreRmsPoint
 
class  ScoreRmsPoints
 
class  SF_Replica
 

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< NodeOPAdjacentRemainingNodes (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

typedef utility::pointer::shared_ptr< CalcInterNeighborGroup const > protocols::toolbox::CalcInterNeighborGroupCOP
typedef utility::pointer::shared_ptr< CovalentResidueNetwork const > protocols::toolbox::CovalentResidueNetworkCOP
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< DummyClass const > protocols::toolbox::DummyClassCOP
typedef utility::pointer::shared_ptr< DummyClass > protocols::toolbox::DummyClassOP
typedef utility::pointer::shared_ptr< EnergyLandscapeEvaluator const > protocols::toolbox::EnergyLandscapeEvaluatorCOP
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< SamplerPlusPlus > protocols::toolbox::SamplerPlusPlusOP
typedef utility::pointer::shared_ptr< ScoreRmsPoint const > protocols::toolbox::ScoreRmsPointCOP
typedef utility::pointer::shared_ptr< ScoreRmsPoint > protocols::toolbox::ScoreRmsPointOP
typedef utility::pointer::shared_ptr< ScoreRmsPoints const > protocols::toolbox::ScoreRmsPointsCOP
typedef utility::pointer::shared_ptr< ScoreRmsPoints > protocols::toolbox::ScoreRmsPointsOP
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

Enumeration Type Documentation

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

static basic::Tracer protocols::toolbox::_impl_tr ( "protocols.toolbox.cluster"  )
static
void protocols::toolbox::add_vec ( int  natoms,
rvec *  x,
const rvec  transvec 
)

References DIM.

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

std::list< NodeOP > protocols::toolbox::AdjacentRemainingNodes ( NodeOP  node)
void protocols::toolbox::apply_superposition_transform ( core::pose::Pose pose,
Matrix  rotation,
Vector  to_init_center,
Vector  to_fit_center 
)
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 
)
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 
)
void protocols::toolbox::CA_superimpose ( core::pose::Pose const &  ref_pose,
core::pose::Pose fit_pose 
)
void protocols::toolbox::calc_fit_R ( int  natoms,
Real const *  weights,
rvec const *  xp,
rvec const *  x,
matrix  R 
)
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 
)
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 
)
bool protocols::toolbox::compareIndexEnergyPair ( const std::pair< int, float > &  p1,
const std::pair< int, float > &  p2 
)
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,
core::Size  n,
FArray2_double &  x,
FArray1D_double  transvec 
)
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().

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.

NodeOP protocols::toolbox::ExtractSmallest ( std::list< NodeOP > &  nodes)
std::string protocols::toolbox::file_full_path ( string  tag)
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 
)
void protocols::toolbox::fill_CA_coords ( core::pose::Pose const &  pose,
core::Size  n_atoms,
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 ( core::Size  natoms,
FArray1_double const &  weights,
FArray2_double const &  ref_coords,
FArray2_double &  coords,
Matrix R 
)
std::string protocols::toolbox::fix_tag_suffix ( string  str)
KClusterOP protocols::toolbox::get_K_cluster_engine ( const string &  style)
void protocols::toolbox::jacobi ( core::Real  a[6][6],
core::Real  d[],
core::Real  v[6][6],
int *  nrot 
)
std::ostream& protocols::toolbox::operator<< ( std::ostream &  os,
ScoreRmsPoint const &  score 
)
std::ostream & protocols::toolbox::operator<< ( std::ostream &  out,
ClusterBase const &  cl 
)
std::ostream & protocols::toolbox::operator<< ( std::ostream &  out,
ClusterBase::ClusterList const &  cl 
)
std::istream & protocols::toolbox::operator>> ( std::istream &  in,
ClusterBase &  cl 
)
std::istream & protocols::toolbox::operator>> ( std::istream &  in,
ClusterBase::ClusterList &  cl 
)
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().

void protocols::toolbox::out_of_bounds_memory_access ( )
DummyClassCOP protocols::toolbox::PyReturnValuePolicyTest_DummyClassCOP ( void  )
inline
DummyClassOP protocols::toolbox::PyReturnValuePolicyTest_DummyClassOP ( 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
core::scoring::ScoreFunctionCOP protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionCOP2 ( void  )
inline
core::scoring::ScoreFunctionOP protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionOP ( 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 ( core::Size  n,
FArray2_double &  x,
FArray1_double const &  wts,
FArray1_double &  transvec 
)
template<class T >
void protocols::toolbox::ROTATE ( T &  a,
int  i,
int  j,
int  k,
int  l,
core::Real  s,
core::Real  tau 
)

Referenced by jacobi().

void protocols::toolbox::rotate_vec ( int  natoms,
rvec *  x,
matrix  R 
)
void protocols::toolbox::superimpose ( core::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 ( core::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 
)
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 
)
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 
)
void protocols::toolbox::take_pose_op ( core::pose::PoseOP const &  )
inline
static basic::Tracer protocols::toolbox::tr ( "protocols.cluster"  ,
basic::t_info   
)
static
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
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

constexpr int protocols::toolbox::DIM6 = 6

Referenced by calc_fit_R(), and jacobi().

constexpr int protocols::toolbox::XX = 0

Referenced by oprod().

constexpr int protocols::toolbox::YY = 1

Referenced by oprod().

constexpr int protocols::toolbox::ZZ = 2

Referenced by oprod().