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Public Types | Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
protocols::evaluation::PCA Class Reference

#include <PCA.hh>

Inheritance diagram for protocols::evaluation::PCA:
Inheritance graph
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Public Types

typedef utility::vector1< core::RealProjectionVector
 

Public Member Functions

 ~PCA () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
void read_eigvec_file (std::string fn, core::pose::Pose const &pose, int nvec=-1)
 read definition of PCA from file More...
 
void eval (core::pose::Pose const &pose, ProjectionVector &proj)
 compute projections for given pose More...
 
void show (std::ostream &)
 

Private Types

typedef ObjexxFCL::FArray2D< core::RealCoordVector
 
typedef utility::vector1< core::id::AtomIDIndexVector
 
typedef core::Real matrix[3][3]
 
typedef core::Real rvec[3]
 

Private Member Functions

void read_structure (std::istream &data, core::pose::Pose const &pose, IndexVector &ind, CoordVector &x, std::string endtag)
 helper to read_eigvec_file: reads a protein structure from input file More...
 
void fill_coordinates (core::pose::Pose const &pose, IndexVector const &ind, CoordVector &x)
 helper of eval: get the coordinates of interest from pose More...
 
void reset_x (core::Size n, CoordVector &x, rvec trans)
 
void jacobi (core::Real a[6][6], core::Real d[], core::Real v[6][6], int *nrot)
 
void calc_fit_R (int natoms, rvec *xp, rvec const *x, matrix R)
 
void rotate_vec (int natoms, rvec *x, matrix R)
 
void add_vec (int natoms, rvec *x, rvec const transvec)
 
void oprod (const rvec a, const rvec b, rvec c)
 

Private Attributes

CoordVector xref_
 
CoordVector xav_
 
IndexVector ifit_
 
IndexVector ipca_
 
ObjexxFCL::FArray3D< core::Realeigvec_
 
core::Size nfit_
 
core::Size npca_
 
core::Size nvec_
 

Member Typedef Documentation

◆ CoordVector

typedef ObjexxFCL::FArray2D< core::Real > protocols::evaluation::PCA::CoordVector
private

◆ IndexVector

typedef utility::vector1< core::id::AtomID > protocols::evaluation::PCA::IndexVector
private

◆ matrix

typedef core::Real protocols::evaluation::PCA::matrix[3][3]
private

◆ ProjectionVector

◆ rvec

typedef core::Real protocols::evaluation::PCA::rvec[3]
private

Constructor & Destructor Documentation

◆ ~PCA()

protocols::evaluation::PCA::~PCA ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

Member Function Documentation

◆ add_vec()

void protocols::evaluation::PCA::add_vec ( int  natoms,
rvec x,
rvec const  transvec 
)
private

References DIM.

◆ calc_fit_R()

void protocols::evaluation::PCA::calc_fit_R ( int  natoms,
rvec xp,
rvec const *  x,
matrix  R 
)
private

◆ eval()

void protocols::evaluation::PCA::eval ( core::pose::Pose const &  pose,
ProjectionVector proj 
)

◆ fill_coordinates()

void protocols::evaluation::PCA::fill_coordinates ( core::pose::Pose const &  pose,
IndexVector const &  ind,
CoordVector x 
)
private

helper of eval: get the coordinates of interest from pose

References core::pose::Pose::xyz().

◆ jacobi()

void protocols::evaluation::PCA::jacobi ( core::Real  a[6][6],
core::Real  d[],
core::Real  v[6][6],
int *  nrot 
)
private

◆ oprod()

void protocols::evaluation::PCA::oprod ( const rvec  a,
const rvec  b,
rvec  c 
)
private

◆ read_eigvec_file()

void protocols::evaluation::PCA::read_eigvec_file ( std::string  fn,
core::pose::Pose const &  pose,
int  nvec = -1 
)

read definition of PCA from file

◆ read_structure()

void protocols::evaluation::PCA::read_structure ( std::istream &  data,
core::pose::Pose const &  pose,
IndexVector ind,
CoordVector x,
std::string  endtag 
)
private

helper to read_eigvec_file: reads a protein structure from input file

References core::chemical::ResidueType::atom_index(), core::pose::Pose::residue_type(), and protocols::evaluation::tr().

◆ reset_x()

void protocols::evaluation::PCA::reset_x ( core::Size  n,
CoordVector x,
rvec  trans 
)
private

◆ rotate_vec()

void protocols::evaluation::PCA::rotate_vec ( int  natoms,
rvec x,
matrix  R 
)
private

References DIM.

◆ show()

void protocols::evaluation::PCA::show ( std::ostream &  os)

Member Data Documentation

◆ eigvec_

ObjexxFCL::FArray3D< core::Real > protocols::evaluation::PCA::eigvec_
private

◆ ifit_

IndexVector protocols::evaluation::PCA::ifit_
private

◆ ipca_

IndexVector protocols::evaluation::PCA::ipca_
private

◆ nfit_

core::Size protocols::evaluation::PCA::nfit_
private

◆ npca_

core::Size protocols::evaluation::PCA::npca_
private

◆ nvec_

core::Size protocols::evaluation::PCA::nvec_
private

◆ xav_

CoordVector protocols::evaluation::PCA::xav_
private

◆ xref_

CoordVector protocols::evaluation::PCA::xref_
private

The documentation for this class was generated from the following files: