Rosetta 3.4
Namespaces | Classes | Typedefs | Functions | Variables
protocols::toolbox Namespace Reference

Namespaces

namespace  match_enzdes_util
namespace  pose_manipulation
namespace  pose_metric_calculators
namespace  rotamer_set_operations
namespace  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)
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
void superimpose (Size natoms, FArray1_double const &weights, FArray2_double &ref_coords, FArray2_double &coords, Matrix &R)
 compute projections for given pose
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 nr, T const &a, basic::Tracer &tr)
 A function (not a macro) that will not print a square matrix to tr.Debug.
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.
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 &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 &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
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


Function Documentation

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

References DIM.

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

void protocols::toolbox::CA_superimpose ( 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 ( ObjexxFCL::FArray1_double const &  weights,
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 
)
void protocols::toolbox::dump_as_pdb ( std::string  filename,
Size  n,
FArray2_double &  x,
FArray1D_double  transvec 
)
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

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

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.

string protocols::toolbox::file_full_path ( string  tag)
void protocols::toolbox::fill_CA_coords ( core::pose::Pose const &  pose,
Size  n_atoms,
FArray2_double &  coords 
)
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::fit_centered_coords ( Size  natoms,
FArray1_double const &  weights,
FArray2_double &  ref_coords,
FArray2_double &  coords,
Matrix R 
)
void protocols::toolbox::fit_centered_coords ( core::Size  natoms,
ObjexxFCL::FArray1_double const &  weights,
ObjexxFCL::FArray2_double &  ref_coords,
ObjexxFCL::FArray2_double &  coords,
Matrix R 
)
string protocols::toolbox::fix_tag_suffix ( string  str)
KClusterOP protocols::toolbox::get_K_cluster_engine ( const string &  style)
void protocols::toolbox::jacobi ( double  a[6][6],
double  d[],
double  v[6][6],
int nrot 
)
std::ostream & protocols::toolbox::operator<< ( std::ostream &  out,
ClusterBase::ClusterList const &  cl 
)
std::ostream & protocols::toolbox::operator<< ( std::ostream &  out,
ClusterBase 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 calc_fit_R().

DummyClassAP protocols::toolbox::PyReturnValuePolicyTest_DummyClassAP ( void  )
DummyClassCAP protocols::toolbox::PyReturnValuePolicyTest_DummyClassCAP ( void  )
DummyClassCOP protocols::toolbox::PyReturnValuePolicyTest_DummyClassCOP ( void  )
DummyClassOP protocols::toolbox::PyReturnValuePolicyTest_DummyClassOP ( void  )
core::pose::PoseAP protocols::toolbox::PyReturnValuePolicyTest_PoseAP ( void  )
core::pose::PoseCAP protocols::toolbox::PyReturnValuePolicyTest_PoseCAP ( void  )
core::pose::PoseCOP protocols::toolbox::PyReturnValuePolicyTest_PoseCOP ( void  )
core::pose::PoseOP protocols::toolbox::PyReturnValuePolicyTest_PoseOP ( void  )
core::scoring::ScoreFunctionCOP protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionCOP ( void  )
core::scoring::ScoreFunctionCOP protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionCOP2 ( void  )
core::scoring::ScoreFunctionOP protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionOP ( void  )
SF_ReplicaAP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaAP ( void  )
SF_ReplicaCAP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaCAP ( void  )
SF_ReplicaCOP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaCOP ( void  )
SF_ReplicaOP protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaOP ( void  )
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 
)
void protocols::toolbox::rotate_vec ( int  natoms,
rvec *  x,
matrix  R 
)
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().

static basic::Tracer protocols::toolbox::tr ( "protocols.evaluation.PCA"  ,
basic::t_info   
) [static]
static basic::Tracer protocols::toolbox::tr ( "protocols.cluster"  ,
basic::t_info   
) [static]
static basic::Tracer protocols::toolbox::tr ( "protocols.toolbox.DecoySetEvaluation"  ,
basic::t_info   
) [static]

Variable Documentation

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