#include <PCA.hh>

Inheritance diagram for protocols::evaluation::PCA:

Collaboration diagram for protocols::evaluation::PCA:

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

Public Member Functions
virtual	~PCA ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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 (Size n, CoordVector &x, rvec trans)

void	jacobi (double a[6][6], double d[], double 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 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_

Size	nfit_

Size	npca_

Size	nvec_

Detailed Description

Definition at line 51 of file PCA.hh.

Member Typedef Documentation

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

private

Definition at line 52 of file PCA.hh.

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

private

Definition at line 53 of file PCA.hh.

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

private

Definition at line 55 of file PCA.hh.

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

Definition at line 60 of file PCA.hh.

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

private

Definition at line 56 of file PCA.hh.

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 49 of file PCA.cc.

Member Function Documentation

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

private

Definition at line 91 of file PCA.cc.

References DIM.

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

private

Definition at line 298 of file PCA.cc.

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

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

compute projections for given pose

Definition at line 182 of file PCA.cc.

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

Definition at line 263 of file PCA.cc.

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

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

private

Definition at line 395 of file PCA.cc.

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

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

private

Definition at line 289 of file PCA.cc.

References XX, YY, and 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

Definition at line 102 of file PCA.cc.

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

Definition at line 139 of file PCA.cc.

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

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

private

Definition at line 165 of file PCA.cc.

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

private

Definition at line 74 of file PCA.cc.

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

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

Definition at line 242 of file PCA.cc.

Member Data Documentation

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

private

Definition at line 78 of file PCA.hh.

IndexVector protocols::evaluation::PCA::ifit_

private

Definition at line 76 of file PCA.hh.

IndexVector protocols::evaluation::PCA::ipca_

private

Definition at line 77 of file PCA.hh.

Size protocols::evaluation::PCA::nfit_

private

Definition at line 79 of file PCA.hh.

Size protocols::evaluation::PCA::npca_

private

Definition at line 79 of file PCA.hh.

Size protocols::evaluation::PCA::nvec_

private

Definition at line 79 of file PCA.hh.

CoordVector protocols::evaluation::PCA::xav_

private

Definition at line 75 of file PCA.hh.

CoordVector protocols::evaluation::PCA::xref_

private

Definition at line 74 of file PCA.hh.

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

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

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation