Rosetta Protocols  2014.35
Namespaces | Classes | Typedefs | Functions | Variables
protocols::toolbox Namespace Reference

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
utility::pointer::owning_ptr
< AllowInsert const > 
AllowInsertCOP
 
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< NodeOPAdjacentRemainingNodes (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 core::Real protocols::toolbox::matrix
typedef core::Real protocols::toolbox::rvec

Function Documentation

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

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
DummyClassCAP protocols::toolbox::PyReturnValuePolicyTest_DummyClassCAP ( void  )
inline
DummyClassCOP protocols::toolbox::PyReturnValuePolicyTest_DummyClassCOP ( void  )
inline
DummyClassOP protocols::toolbox::PyReturnValuePolicyTest_DummyClassOP ( void  )
inline
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
core::scoring::ScoreFunctionCOP protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionCOP2 ( void  )
inline
core::scoring::ScoreFunctionOP protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionOP ( void  )
inline
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 
)
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 
)
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 
)
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

basic::Tracer protocols::toolbox::_impl_tr("protocols.toolbox.cluster")
static
core::Size const protocols::toolbox::FIXED_DOMAIN
basic::Tracer protocols::toolbox::tr("protocols.cluster", basic::t_info)
static
basic::Tracer protocols::toolbox::tr("protocols.evaluation.PCA", basic::t_info)
static
basic::Tracer protocols::toolbox::tr("protocols.evaluation.PCA", basic::t_info)
static
basic::Tracer protocols::toolbox::tr("protocols.toolbox.DecoySetEvaluation", basic::t_info)
static