protocols::evaluation::PCA Class Reference

#include <PCA.hh>

Inheritance diagram for protocols::evaluation::PCA:

Public Types
typedef utility::vector1 < core::Real >	ProjectionVector

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::Real >	CoordVector
typedef utility::vector1 < core::id::AtomID >	IndexVector
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::Real >	eigvec_
core::Size	nfit_
core::Size	npca_
core::Size	nvec_

Member Typedef Documentation

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

private

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

private

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

private

typedef utility::vector1< core::Real > protocols::evaluation::PCA::ProjectionVector

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

private

Constructor & Destructor Documentation

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

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

Member Function Documentation

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

private

References DIM.

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

private

References core::pack::dunbrack::c, DIM, protocols::evaluation::DIM6, protocols::evaluation::dump_matrix(), core::scoring::jacobi(), core::scoring::omega, protocols::toolbox::oprod(), protocols::evaluation::tr(), and protocols::hybridization::u.

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

compute projections for given pose

References protocols::toolbox::add_vec(), protocols::toolbox::calc_fit_R(), protocols::evaluation::dump_matrix(), protocols::toolbox::reset_x(), protocols::toolbox::rotate_vec(), and protocols::evaluation::tr().

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().

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

private

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

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

private

References protocols::evaluation::XX, protocols::evaluation::YY, and protocols::evaluation::ZZ.

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

read definition of PCA from file

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().

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

private

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

private

References core::pack::dunbrack::c, and DIM.

void protocols::evaluation::PCA::show

(

std::ostream &

os

)

Member Data Documentation

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

private

IndexVector protocols::evaluation::PCA::ifit_

private

IndexVector protocols::evaluation::PCA::ipca_

private

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

private

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

private

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

private

CoordVector protocols::evaluation::PCA::xav_

private

CoordVector protocols::evaluation::PCA::xref_

private

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

• src/protocols/evaluation/PCA.hh
• src/protocols/evaluation/PCA.cc