protocols::pockets::PocketGrid Class Reference

@ More...

#include <PocketGrid.hh>

Inheritance diagram for protocols::pockets::PocketGrid:

Collaboration diagram for protocols::pockets::PocketGrid:

Public Member Functions
	PocketGrid ()
virtual	~PocketGrid ()
	PocketGrid (const PocketGrid &gr)
PocketGrid &	operator= (const PocketGrid &gr)
	PocketGrid (core::conformation::Residue const &central_rsd)
	PocketGrid (std::vector< core::conformation::ResidueOP > const &central_rsd)
	PocketGrid (core::Real const &xc, core::Real const &yc, core::Real const &zc, core::Real x, core::Real y, core::Real z, core::Real const &stepSize)
	PocketGrid (core::Real const &xc, core::Real const &yc, core::Real const &zc, core::Real x, core::Real y, core::Real z)
	PocketGrid (core::Real const &xc, core::Real const &yc, core::Real const &zc, core::Real x, core::Real y, core::Real z, core::Real const &stepSize, bool psp, bool sps)
	PocketGrid (core::Real const &xc, core::Real const &yc, core::Real const &zc, core::Real x, core::Real const &stepSize=1, bool psp=false, bool sps=false)
	PocketGrid (core::Vector const &center, core::Real x, core::Real const &stepSize=1, bool psp=false, bool sps=false)
	PocketGrid (core::Vector const &center, core::Real const &x, core::Real const &y, core::Real const &z, core::Real const &stepSize=1, bool psp=false, bool sps=false)
void	initialize (core::Real const &xc, core::Real const &yc, core::Real const &zc, core::Real const size_x, core::Real const size_y, core::Real const size_z, core::Real const &stepSize=1, bool psp=false, bool sps=false)
void	initialize (core::Real const &xc, core::Real const &yc, core::Real const &zc, core::Real x, core::Real const &stepSize=1, bool psp=false, bool sps=false)
void	initialize (core::Vector const &center, core::Real x, core::Real const &stepSize=1, bool psp=false, bool sps=false)
void	initialize (core::Vector const &center, core::Real const &x, core::Real const &y, core::Real const &z, core::Real const &stepSize=1, bool psp=false, bool sps=false)
void	initialize (core::conformation::Residue const &central_rsd, core::Real const &x, core::Real const &y, core::Real const &z, core::Real const &stepSize=1, bool psp=false, bool sps=false)
void	initialize (std::vector< core::conformation::ResidueOP > const &central_rsd, core::Real const &x, core::Real const &y, core::Real const &z, core::Real const &stepSize=1, bool psp=false, bool sps=false)
void	clear ()
void	recenter (core::Real const &xc, core::Real const &yc, core::Real const &zc)
void	recenter (core::conformation::Residue const &central_rsd)
void	recenter (std::vector< core::conformation::ResidueOP > const &central_rsds)
void	recenter (core::Vector const &center)
void	findPockets (core::Size thr, core::Real max)
void	findPSP (core::Size thr, core::Real max)
void	findSPS (core::Size thr, core::Real max)
void	mark (core::Real x, core::Real y, core::Real z, core::Real const &vdWd, core::Real const &buffer, bool polar=false, bool targetResi=false)
void	mark (core::Vector const &center, core::Real const &vdWd, core::Real const &buffer, bool polar=false, bool targetResi=false)
void	clearSmallPockets (core::Size minsize)
void	findClusters ()
void	dumpGridToFile ()
void	dumpGridToFile (std::string const &output_filename)
void	fillTargetPockets ()
void	print ()
core::Real	targetPocketVolume (core::Real const &surf_sc, core::Real const &bur_sc) const
core::Real	largestTargetPocketVolume ()
void	markPocketDepth (core::Real const &surf_d, core::Real const &bur_d)
void	markEdgeDepth (core::Real const &surf_d, core::Real const &bur_d)
core::Real	netTargetPocketVolume ()
void	markDepth (core::Size x, core::Size y, core::Size z, core::Real const &surf_d, core::Real const &bur_d)
bool	markOneEdgeDepth (core::Size x, core::Size y, core::Size z, core::Real const &surf_d, core::Real const &bur_d, bool isTarget)
void	clusterPockets ()
core::Real	targetPocketSolventSurface () const
core::Real	targetPocketProteinSurface () const
core::Real	targetPocketHydrophobicProteinSurface () const
core::Real	targetPocketPolarProteinSurface () const
core::Real	targetPocketHeuristicScore () const
bool	isTooSmall () const
core::Vector	whatIsTooSmall () const
bool	autoexpanding_pocket_eval (core::conformation::Residue const &central_rsd, core::scoring::constraints::XYZ_Func const &xyz_func, Size const total_residues)
bool	autoexpanding_pocket_eval (std::vector< core::conformation::ResidueOP > const &central_rsd, core::scoring::constraints::XYZ_Func const &xyz_func, Size const total_residues)
bool	autoexpanding_pocket_eval (core::conformation::Residue const &central_rsd, core::pose::Pose const &inPose)
bool	autoexpanding_pocket_eval (std::vector< core::conformation::ResidueOP > const &central_rsd, core::pose::Pose const &inPose)
bool	DARC_autoexpanding_pocket_eval (core::conformation::Residue const &central_rsd, core::pose::Pose const &inPose, numeric::xyzVector< core::Real > grid_center)
bool	DARC_autoexpanding_pocket_eval (core::conformation::Residue const &central_rsd, core::scoring::constraints::XYZ_Func const &xyz_func, Size const total_residues, numeric::xyzVector< core::Real > grid_center)
bool	DARC_pocket_eval (core::conformation::Residue const &central_rsd, core::pose::Pose const &inPose, numeric::xyzVector< core::Real > grid_center)
bool	DARC_pocket_eval (core::conformation::Residue const &central_rsd, core::scoring::constraints::XYZ_Func const &xyz_func, Size const total_residues, numeric::xyzVector< core::Real > grid_center)
void	move_pose_to_standard_orie (core::Size const &central_seqpos, core::pose::Pose &pose)
void	randomAngle ()
void	zeroAngle ()
core::Real	get_pocket_distance (PocketGrid const &template_pocket) const
core::Real	get_pocket_distance (PocketGrid const &template_pocket, std::string const &comparison_pdbname) const

Static Public Member Functions
static std::vector < core::conformation::ResidueOP >	getRelaxResidues (core::pose::Pose const &input_pose, std::string const &resids)

Protected Types
enum	PtType {   EMPTY, PROTEIN, TARGET, HSURFACE,   PSURFACE, POCKET, PO_SURF, PO_BURIED,   T_SURFACE, TP_POCKET, TP_SURF, TP_BURIED,   PO_EDGE, TP_EDGE, PSP, EGGSHELL,   EGGSHELL_SURROUNDING }

Protected Member Functions
void	init ()
void	setup_default_options ()
void	newSearch (core::Size thr1, core::Size thr2, core::Size max1, core::Size max2, bool psp=false, bool sps=false)
bool	fill (core::Size x, core::Size y, core::Size z)
bool	touchesSolvent (core::Size x, core::Size y, core::Size z) const
bool	touchesSS (core::Size x, core::Size y, core::Size z) const
bool	touchesPS (core::Size x, core::Size y, core::Size z) const
bool	touchesSurface (core::Size x, core::Size y, core::Size z, bool polar, bool either=false) const
numeric::xyzVector< core::Real >	rotatePoint (core::Real x, core::Real y, core::Real z)

Protected Attributes
std::vector< std::vector < std::vector< PtType > > >	grid_
std::vector< std::vector < std::vector< core::Size > > >	pockets_
core::Size	xdim_
core::Size	ydim_
core::Size	zdim_
core::Real	xcorn_
core::Real	ycorn_
core::Real	zcorn_
core::Real	stepSize_
core::Real	maxLen_
std::string	tag_
core::Size	pdbno_
PClusterSet	clusters_
core::Real	size_x_
core::Real	size_y_
core::Real	size_z_
core::Real	spacing_
core::Real	limit_x_
core::Real	limit_y_
core::Real	limit_z_
bool	restrictSize_
core::Real	probe_rad_
core::Real	surf_score_
core::Real	surf_dist_
core::Real	bur_score_
core::Real	bur_dist_
bool	side_chains_only_
bool	markpsp_
bool	marksps_
core::Real	minPockSize_
core::Real	maxPockSize_
numeric::xyzMatrix< core::Real >	rot_mat_

Friends
class	EggshellGrid

Detailed Description

@

Member Enumeration Documentation

enum protocols::pockets::PocketGrid::PtType

protected

Enumerator
EMPTY
PROTEIN
TARGET
HSURFACE
PSURFACE
POCKET
PO_SURF
PO_BURIED
T_SURFACE
TP_POCKET
TP_SURF
TP_BURIED
PO_EDGE
TP_EDGE
PSP
EGGSHELL
EGGSHELL_SURROUNDING

Constructor & Destructor Documentation

protocols::pockets::PocketGrid::PocketGrid

(

)

References setup_default_options().

protocols::pockets::PocketGrid::~PocketGrid ( )

virtual

protocols::pockets::PocketGrid::PocketGrid

(

const PocketGrid &

gr)

References grid_, markpsp_, marksps_, minPockSize_, pdbno_, pockets_, setup_default_options(), stepSize_, tag_, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

protocols::pockets::PocketGrid::PocketGrid

(

core::conformation::Residue const &

central_rsd)

References initialize(), markpsp_, marksps_, setup_default_options(), size_x_, size_y_, size_z_, spacing_, and tag_.

protocols::pockets::PocketGrid::PocketGrid

(

std::vector< core::conformation::ResidueOP > const &

central_rsd)

References initialize(), markpsp_, marksps_, setup_default_options(), size_x_, size_y_, size_z_, spacing_, and tag_.

protocols::pockets::PocketGrid::PocketGrid	(	core::Real const &	xc,
		core::Real const &	yc,
		core::Real const &	zc,
		core::Real	x,
		core::Real	y,
		core::Real	z,
		core::Real const &	stepSize
	)

References initialize(), markpsp_, marksps_, setup_default_options(), and tag_.

protocols::pockets::PocketGrid::PocketGrid	(	core::Real const &	xc,
		core::Real const &	yc,
		core::Real const &	zc,
		core::Real	x,
		core::Real	y,
		core::Real	z
	)

References initialize(), markpsp_, marksps_, setup_default_options(), spacing_, and tag_.

protocols::pockets::PocketGrid::PocketGrid	(	core::Real const &	xc,
		core::Real const &	yc,
		core::Real const &	zc,
		core::Real	x,
		core::Real	y,
		core::Real	z,
		core::Real const &	stepSize,
		bool	psp,
		bool	sps
	)

References initialize(), setup_default_options(), and tag_.

protocols::pockets::PocketGrid::PocketGrid	(	core::Real const &	xc,
		core::Real const &	yc,
		core::Real const &	zc,
		core::Real	x,
		core::Real const &	stepSize = 1,
		bool	psp = false,
		bool	sps = false
	)

References initialize(), setup_default_options(), and tag_.

protocols::pockets::PocketGrid::PocketGrid	(	core::Vector const &	center,
		core::Real	x,
		core::Real const &	stepSize = 1,
		bool	psp = false,
		bool	sps = false
	)

References initialize(), setup_default_options(), and tag_.

protocols::pockets::PocketGrid::PocketGrid	(	core::Vector const &	center,
		core::Real const &	x,
		core::Real const &	y,
		core::Real const &	z,
		core::Real const &	stepSize = 1,
		bool	psp = false,
		bool	sps = false
	)

References initialize(), setup_default_options(), and tag_.

Member Function Documentation

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval	(	core::conformation::Residue const &	central_rsd,
		core::scoring::constraints::XYZ_Func const &	xyz_func,
		Size const	total_residues
	)

References core::conformation::Residue::atom(), bur_dist_, findClusters(), findPockets(), findPSP(), findSPS(), initialize(), isTooSmall(), limit_x_, limit_y_, limit_z_, mark(), markEdgeDepth(), markPocketDepth(), markpsp_, marksps_, maxLen_, probe_rad_, recenter(), core::scoring::constraints::XYZ_Func::residue(), rotatePoint(), core::conformation::Residue::seqpos(), side_chains_only_, size_x_, size_y_, size_z_, spacing_, stepSize_, surf_dist_, core::conformation::Atom::type(), whatIsTooSmall(), xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval(), and move_pose_to_standard_orie().

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval	(	std::vector< core::conformation::ResidueOP > const &	central_rsd,
		core::scoring::constraints::XYZ_Func const &	xyz_func,
		Size const	total_residues
	)

References autoexpanding_pocket_eval().

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval	(	core::conformation::Residue const &	central_rsd,
		core::pose::Pose const &	inPose
	)

References autoexpanding_pocket_eval(), core::pose::Pose::conformation(), and core::pose::Pose::total_residue().

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval	(	std::vector< core::conformation::ResidueOP > const &	central_rsd,
		core::pose::Pose const &	inPose
	)

References autoexpanding_pocket_eval(), core::pose::Pose::conformation(), and core::pose::Pose::total_residue().

void protocols::pockets::PocketGrid::clear

(

)

References protocols::pockets::PClusterSet::clear(), clusters_, grid_, and pockets_.

Referenced by init().

void protocols::pockets::PocketGrid::clearSmallPockets

(

core::Size

minsize)

void protocols::pockets::PocketGrid::clusterPockets

(

)

References protocols::pockets::PClusterSet::add(), protocols::pockets::PClusterSet::clusters_, clusters_, grid_, protocols::pockets::PClusterSet::join(), PO_BURIED, PO_EDGE, POCKET, stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, xdim_, ydim_, and zdim_.

Referenced by findClusters().

bool protocols::pockets::PocketGrid::DARC_autoexpanding_pocket_eval	(	core::conformation::Residue const &	central_rsd,
		core::pose::Pose const &	inPose,
		numeric::xyzVector< core::Real >	grid_center
	)

References core::pose::Pose::conformation(), and core::pose::Pose::total_residue().

bool protocols::pockets::PocketGrid::DARC_autoexpanding_pocket_eval	(	core::conformation::Residue const &	central_rsd,
		core::scoring::constraints::XYZ_Func const &	xyz_func,
		Size const	total_residues,
		numeric::xyzVector< core::Real >	grid_center
	)

References core::conformation::Residue::atom(), bur_dist_, findClusters(), findPockets(), findPSP(), findSPS(), initialize(), isTooSmall(), limit_x_, limit_y_, limit_z_, mark(), markEdgeDepth(), markPocketDepth(), markpsp_, marksps_, maxLen_, probe_rad_, recenter(), core::scoring::constraints::XYZ_Func::residue(), rotatePoint(), core::conformation::Residue::seqpos(), side_chains_only_, size_x_, size_y_, size_z_, spacing_, stepSize_, surf_dist_, core::conformation::Atom::type(), whatIsTooSmall(), xdim_, ydim_, and zdim_.

bool protocols::pockets::PocketGrid::DARC_pocket_eval	(	core::conformation::Residue const &	central_rsd,
		core::pose::Pose const &	inPose,
		numeric::xyzVector< core::Real >	grid_center
	)

References core::pose::Pose::conformation(), and core::pose::Pose::total_residue().

bool protocols::pockets::PocketGrid::DARC_pocket_eval	(	core::conformation::Residue const &	central_rsd,
		core::scoring::constraints::XYZ_Func const &	xyz_func,
		Size const	total_residues,
		numeric::xyzVector< core::Real >	grid_center
	)

References core::conformation::Residue::atom(), bur_dist_, findClusters(), findPockets(), findPSP(), findSPS(), mark(), markEdgeDepth(), markPocketDepth(), markpsp_, marksps_, maxLen_, probe_rad_, core::scoring::constraints::XYZ_Func::residue(), rotatePoint(), core::conformation::Residue::seqpos(), side_chains_only_, stepSize_, surf_dist_, core::conformation::Atom::type(), xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::dumpGridToFile

(

)

References protocols::abinitio::filename(), pdbno_, and tag_.

void protocols::pockets::PocketGrid::dumpGridToFile

(

std::string const &

output_filename)

References protocols::pockets::PClusterSet::clusters_, clusters_, EMPTY, grid_, HSURFACE, minPockSize_, PO_BURIED, PO_EDGE, PO_SURF, POCKET, PROTEIN, PSP, PSURFACE, stepSize_, T_SURFACE, TARGET, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

bool protocols::pockets::PocketGrid::fill ( core::Size  x, core::Size  y, core::Size  z  )

protected

References EMPTY, grid_, POCKET, pockets_, TP_POCKET, xdim_, ydim_, and zdim_.

Referenced by fillTargetPockets().

void protocols::pockets::PocketGrid::fillTargetPockets

(

)

References EMPTY, fill(), grid_, pockets_, TP_POCKET, xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::findClusters

(

)

References clusterPockets(), protocols::pockets::PClusterSet::clusters_, clusters_, grid_, PO_BURIED, PO_EDGE, PO_SURF, POCKET, T_SURFACE, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and DARC_pocket_eval().

void protocols::pockets::PocketGrid::findPockets	(	core::Size	thr,
		core::Real	max
	)

References newSearch(), and stepSize_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and DARC_pocket_eval().

void protocols::pockets::PocketGrid::findPSP	(	core::Size	thr,
		core::Real	max
	)

References newSearch(), and stepSize_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and DARC_pocket_eval().

void protocols::pockets::PocketGrid::findSPS	(	core::Size	thr,
		core::Real	max
	)

References newSearch(), and stepSize_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and DARC_pocket_eval().

core::Real protocols::pockets::PocketGrid::get_pocket_distance ( PocketGrid const &  template_pocket) const

inline

References get_pocket_distance().

Referenced by get_pocket_distance().

core::Real protocols::pockets::PocketGrid::get_pocket_distance	(	PocketGrid const &	template_pocket,
		std::string const &	comparison_pdbname
	)		const

References protocols::pockets::PClusterSet::clusters_, clusters_, grid_, minPockSize_, stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, protocols::pockets::TR(), xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

std::vector< core::conformation::ResidueOP > protocols::pockets::PocketGrid::getRelaxResidues ( core::pose::Pose const &  input_pose, std::string const &  resids  )

static

References core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::pose::Pose::pdb_info(), core::conformation::Conformation::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::pockets::PocketConstraint::read_def().

void protocols::pockets::PocketGrid::init ( void  )

protected

References clear(), EMPTY, grid_, pockets_, xdim_, ydim_, and zdim_.

Referenced by protocols::pockets::EggshellGrid::EggshellGrid(), initialize(), move_pose_to_standard_orie(), and recenter().

void protocols::pockets::PocketGrid::initialize	(	core::Real const &	xc,
		core::Real const &	yc,
		core::Real const &	zc,
		core::Real const	size_x,
		core::Real const	size_y,
		core::Real const	size_z,
		core::Real const &	stepSize = 1,
		bool	psp = false,
		bool	sps = false
	)

References init(), markpsp_, marksps_, pdbno_, recenter(), stepSize_, xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and PocketGrid().

void protocols::pockets::PocketGrid::initialize	(	core::Real const &	xc,
		core::Real const &	yc,
		core::Real const &	zc,
		core::Real	x,
		core::Real const &	stepSize = 1,
		bool	psp = false,
		bool	sps = false
	)

References init(), markpsp_, marksps_, pdbno_, recenter(), stepSize_, xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::initialize	(	core::Vector const &	center,
		core::Real	x,
		core::Real const &	stepSize = 1,
		bool	psp = false,
		bool	sps = false
	)

References init(), markpsp_, marksps_, pdbno_, recenter(), stepSize_, xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::initialize	(	core::Vector const &	center,
		core::Real const &	x,
		core::Real const &	y,
		core::Real const &	z,
		core::Real const &	stepSize = 1,
		bool	psp = false,
		bool	sps = false
	)

References init(), markpsp_, marksps_, pdbno_, recenter(), stepSize_, xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::initialize	(	core::conformation::Residue const &	central_rsd,
		core::Real const &	x,
		core::Real const &	y,
		core::Real const &	z,
		core::Real const &	stepSize = 1,
		bool	psp = false,
		bool	sps = false
	)

References init(), markpsp_, marksps_, pdbno_, recenter(), stepSize_, xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::initialize	(	std::vector< core::conformation::ResidueOP > const &	central_rsd,
		core::Real const &	x,
		core::Real const &	y,
		core::Real const &	z,
		core::Real const &	stepSize = 1,
		bool	psp = false,
		bool	sps = false
	)

References init(), markpsp_, marksps_, pdbno_, recenter(), stepSize_, xdim_, ydim_, and zdim_.

bool protocols::pockets::PocketGrid::isTooSmall

(

)

const

References grid_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval(), and DARC_autoexpanding_pocket_eval().

core::Real protocols::pockets::PocketGrid::largestTargetPocketVolume

(

)

References clusters_, protocols::pockets::PClusterSet::getLargestClusterSize(), minPockSize_, and stepSize_.

void protocols::pockets::PocketGrid::mark	(	core::Real	x,
		core::Real	y,
		core::Real	z,
		core::Real const &	vdWd,
		core::Real const &	buffer,
		bool	polar = false,
		bool	targetResi = false
	)

References grid_, HSURFACE, PROTEIN, PSURFACE, stepSize_, T_SURFACE, TARGET, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and mark().

void protocols::pockets::PocketGrid::mark	(	core::Vector const &	center,
		core::Real const &	vdWd,
		core::Real const &	buffer,
		bool	polar = false,
		bool	targetResi = false
	)

References mark().

void protocols::pockets::PocketGrid::markDepth	(	core::Size	x,
		core::Size	y,
		core::Size	z,
		core::Real const &	surf_d,
		core::Real const &	bur_d
	)

References EMPTY, grid_, HSURFACE, PO_BURIED, PO_EDGE, PO_SURF, POCKET, PSURFACE, stepSize_, T_SURFACE, TP_BURIED, TP_EDGE, TP_SURF, xdim_, ydim_, and zdim_.

Referenced by markPocketDepth().

void protocols::pockets::PocketGrid::markEdgeDepth	(	core::Real const &	surf_d,
		core::Real const &	bur_d
	)

References protocols::pockets::PClusterSet::clusters_, clusters_, grid_, markOneEdgeDepth(), PO_EDGE, and TP_EDGE.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and DARC_pocket_eval().

bool protocols::pockets::PocketGrid::markOneEdgeDepth	(	core::Size	x,
		core::Size	y,
		core::Size	z,
		core::Real const &	surf_d,
		core::Real const &	bur_d,
		bool	isTarget
	)

References EMPTY, grid_, HSURFACE, PO_BURIED, PO_EDGE, PO_SURF, POCKET, PSURFACE, stepSize_, TP_BURIED, TP_POCKET, TP_SURF, xdim_, ydim_, and zdim_.

Referenced by markEdgeDepth().

void protocols::pockets::PocketGrid::markPocketDepth	(	core::Real const &	surf_d,
		core::Real const &	bur_d
	)

References grid_, markDepth(), POCKET, TP_POCKET, xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and DARC_pocket_eval().

void protocols::pockets::PocketGrid::move_pose_to_standard_orie	(	core::Size const &	central_seqpos,
		core::pose::Pose &	pose
	)

References core::pose::Pose::apply_transform_Rx_plus_v(), autoexpanding_pocket_eval(), protocols::pockets::PClusterSet::clusters_, clusters_, core::pose::Pose::conformation(), grid_, init(), minPockSize_, core::conformation::Conformation::residue(), setup_default_options(), stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, ycorn_, and zcorn_.

core::Real protocols::pockets::PocketGrid::netTargetPocketVolume

(

)

References clusters_, protocols::pockets::PClusterSet::getNetClusterSize(), maxPockSize_, minPockSize_, and stepSize_.

void protocols::pockets::PocketGrid::newSearch ( core::Size  thr1, core::Size  thr2, core::Size  max1, core::Size  max2, bool  psp = false, bool  sps = false  )

protected

References core::pack::dunbrack::c, EMPTY, grid_, HSURFACE, markpsp_, POCKET, PSP, PSURFACE, T_SURFACE, TP_POCKET, xdim_, ydim_, and zdim_.

Referenced by findPockets(), findPSP(), and findSPS().

PocketGrid & protocols::pockets::PocketGrid::operator=

(

const PocketGrid &

gr)

References grid_, markpsp_, marksps_, minPockSize_, pdbno_, pockets_, stepSize_, tag_, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

void protocols::pockets::PocketGrid::print

(

)

References pockets_, xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::randomAngle

(

)

References rot_mat_.

void protocols::pockets::PocketGrid::recenter	(	core::Real const &	xc,
		core::Real const &	yc,
		core::Real const &	zc
	)

References protocols::pockets::PClusterSet::clear(), clusters_, init(), rotatePoint(), stepSize_, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), initialize(), and recenter().

void protocols::pockets::PocketGrid::recenter

(

core::conformation::Residue const &

central_rsd)

References core::conformation::Residue::atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), recenter(), core::conformation::Atom::type(), and core::conformation::Atom::xyz().

void protocols::pockets::PocketGrid::recenter

(

std::vector< core::conformation::ResidueOP > const &

central_rsds)

References recenter().

void protocols::pockets::PocketGrid::recenter

(

core::Vector const &

center)

References recenter().

numeric::xyzVector< core::Real > protocols::pockets::PocketGrid::rotatePoint ( core::Real  x, core::Real  y, core::Real  z  )

protected

References rot_mat_.

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and recenter().

void protocols::pockets::PocketGrid::setup_default_options ( )

protected

References bur_dist_, bur_score_, limit_x_, limit_y_, limit_z_, markpsp_, marksps_, maxLen_, maxPockSize_, minPockSize_, probe_rad_, restrictSize_, rot_mat_, side_chains_only_, size_x_, size_y_, size_z_, spacing_, surf_dist_, and surf_score_.

Referenced by move_pose_to_standard_orie(), and PocketGrid().

core::Real protocols::pockets::PocketGrid::targetPocketHeuristicScore

(

)

const

References grid_, stepSize_, touchesPS(), touchesSS(), TP_POCKET, xdim_, ydim_, and zdim_.

core::Real protocols::pockets::PocketGrid::targetPocketHydrophobicProteinSurface

(

)

const

References grid_, stepSize_, touchesSurface(), TP_POCKET, xdim_, ydim_, and zdim_.

core::Real protocols::pockets::PocketGrid::targetPocketPolarProteinSurface

(

)

const

References grid_, stepSize_, touchesSurface(), TP_POCKET, xdim_, ydim_, and zdim_.

core::Real protocols::pockets::PocketGrid::targetPocketProteinSurface

(

)

const

References grid_, stepSize_, touchesSurface(), TP_POCKET, xdim_, ydim_, and zdim_.

core::Real protocols::pockets::PocketGrid::targetPocketSolventSurface

(

)

const

References grid_, stepSize_, touchesSolvent(), TP_POCKET, xdim_, ydim_, and zdim_.

core::Real protocols::pockets::PocketGrid::targetPocketVolume	(	core::Real const &	surf_sc,
		core::Real const &	bur_sc
	)		const

References grid_, stepSize_, TP_BURIED, TP_POCKET, TP_SURF, xdim_, ydim_, and zdim_.

bool protocols::pockets::PocketGrid::touchesPS ( core::Size  x, core::Size  y, core::Size  z  ) const

protected

References grid_, HSURFACE, PSURFACE, T_SURFACE, xdim_, ydim_, and zdim_.

Referenced by targetPocketHeuristicScore().

bool protocols::pockets::PocketGrid::touchesSolvent ( core::Size  x, core::Size  y, core::Size  z  ) const

protected

References EMPTY, grid_, xdim_, ydim_, and zdim_.

Referenced by targetPocketSolventSurface().

bool protocols::pockets::PocketGrid::touchesSS ( core::Size  x, core::Size  y, core::Size  z  ) const

protected

References EMPTY, grid_, xdim_, ydim_, and zdim_.

Referenced by targetPocketHeuristicScore().

bool protocols::pockets::PocketGrid::touchesSurface ( core::Size  x, core::Size  y, core::Size  z, bool  polar, bool  either = false  ) const

protected

References grid_, HSURFACE, PSURFACE, xdim_, ydim_, and zdim_.

Referenced by targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), and targetPocketProteinSurface().

core::Vector protocols::pockets::PocketGrid::whatIsTooSmall

(

)

const

References grid_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval(), and DARC_autoexpanding_pocket_eval().

void protocols::pockets::PocketGrid::zeroAngle

(

)

References rot_mat_.

Friends And Related Function Documentation

friend class EggshellGrid

friend

Member Data Documentation

core::Real protocols::pockets::PocketGrid::bur_dist_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and setup_default_options().

core::Real protocols::pockets::PocketGrid::bur_score_

protected

Referenced by setup_default_options().

PClusterSet protocols::pockets::PocketGrid::clusters_

protected

Referenced by clear(), clusterPockets(), dumpGridToFile(), findClusters(), get_pocket_distance(), largestTargetPocketVolume(), markEdgeDepth(), move_pose_to_standard_orie(), netTargetPocketVolume(), and recenter().

std::vector< std::vector < std::vector <PtType> > > protocols::pockets::PocketGrid::grid_

protected

Referenced by clear(), clusterPockets(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), init(), isTooSmall(), mark(), markDepth(), markEdgeDepth(), markOneEdgeDepth(), markPocketDepth(), move_pose_to_standard_orie(), newSearch(), operator=(), PocketGrid(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), touchesPS(), touchesSolvent(), touchesSS(), touchesSurface(), and whatIsTooSmall().

core::Real protocols::pockets::PocketGrid::limit_x_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and setup_default_options().

core::Real protocols::pockets::PocketGrid::limit_y_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and setup_default_options().

core::Real protocols::pockets::PocketGrid::limit_z_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), and setup_default_options().

bool protocols::pockets::PocketGrid::markpsp_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), initialize(), newSearch(), operator=(), PocketGrid(), and setup_default_options().

bool protocols::pockets::PocketGrid::marksps_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), initialize(), operator=(), PocketGrid(), and setup_default_options().

core::Real protocols::pockets::PocketGrid::maxLen_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and setup_default_options().

core::Real protocols::pockets::PocketGrid::maxPockSize_

protected

Referenced by netTargetPocketVolume(), and setup_default_options().

core::Real protocols::pockets::PocketGrid::minPockSize_

protected

Referenced by dumpGridToFile(), get_pocket_distance(), largestTargetPocketVolume(), move_pose_to_standard_orie(), netTargetPocketVolume(), operator=(), PocketGrid(), and setup_default_options().

core::Size protocols::pockets::PocketGrid::pdbno_

protected

Referenced by dumpGridToFile(), initialize(), operator=(), and PocketGrid().

std::vector< std::vector < std::vector <core::Size> > > protocols::pockets::PocketGrid::pockets_

protected

Referenced by clear(), fill(), fillTargetPockets(), init(), operator=(), PocketGrid(), and print().

core::Real protocols::pockets::PocketGrid::probe_rad_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and setup_default_options().

bool protocols::pockets::PocketGrid::restrictSize_

protected

Referenced by setup_default_options().

numeric::xyzMatrix<core::Real> protocols::pockets::PocketGrid::rot_mat_

protected

Referenced by randomAngle(), rotatePoint(), setup_default_options(), and zeroAngle().

bool protocols::pockets::PocketGrid::side_chains_only_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and setup_default_options().

core::Real protocols::pockets::PocketGrid::size_x_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), PocketGrid(), and setup_default_options().

core::Real protocols::pockets::PocketGrid::size_y_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), PocketGrid(), and setup_default_options().

core::Real protocols::pockets::PocketGrid::size_z_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), PocketGrid(), and setup_default_options().

core::Real protocols::pockets::PocketGrid::spacing_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), PocketGrid(), and setup_default_options().

core::Real protocols::pockets::PocketGrid::stepSize_

protected

Referenced by autoexpanding_pocket_eval(), clusterPockets(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), findPockets(), findPSP(), findSPS(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), initialize(), largestTargetPocketVolume(), mark(), markDepth(), markOneEdgeDepth(), move_pose_to_standard_orie(), netTargetPocketVolume(), operator=(), PocketGrid(), recenter(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

core::Real protocols::pockets::PocketGrid::surf_dist_

protected

Referenced by autoexpanding_pocket_eval(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), and setup_default_options().

core::Real protocols::pockets::PocketGrid::surf_score_

protected

Referenced by setup_default_options().

std::string protocols::pockets::PocketGrid::tag_

protected

Referenced by dumpGridToFile(), operator=(), and PocketGrid().

core::Real protocols::pockets::PocketGrid::xcorn_

protected

Referenced by protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), mark(), move_pose_to_standard_orie(), operator=(), PocketGrid(), recenter(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

core::Size protocols::pockets::PocketGrid::xdim_

protected

Referenced by autoexpanding_pocket_eval(), clusterPockets(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), init(), initialize(), isTooSmall(), mark(), markDepth(), markOneEdgeDepth(), markPocketDepth(), newSearch(), operator=(), PocketGrid(), print(), recenter(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), touchesPS(), touchesSolvent(), touchesSS(), touchesSurface(), whatIsTooSmall(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

core::Real protocols::pockets::PocketGrid::ycorn_

protected

Referenced by protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), mark(), move_pose_to_standard_orie(), operator=(), PocketGrid(), recenter(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

core::Size protocols::pockets::PocketGrid::ydim_

protected

Referenced by autoexpanding_pocket_eval(), clusterPockets(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), init(), initialize(), isTooSmall(), mark(), markDepth(), markOneEdgeDepth(), markPocketDepth(), newSearch(), operator=(), PocketGrid(), print(), recenter(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), touchesPS(), touchesSolvent(), touchesSS(), touchesSurface(), whatIsTooSmall(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

core::Real protocols::pockets::PocketGrid::zcorn_

protected

Referenced by protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), mark(), move_pose_to_standard_orie(), operator=(), PocketGrid(), recenter(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

core::Size protocols::pockets::PocketGrid::zdim_

protected

Referenced by autoexpanding_pocket_eval(), clusterPockets(), DARC_autoexpanding_pocket_eval(), DARC_pocket_eval(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), init(), initialize(), isTooSmall(), mark(), markDepth(), markOneEdgeDepth(), markPocketDepth(), newSearch(), operator=(), PocketGrid(), print(), recenter(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), touchesPS(), touchesSolvent(), touchesSS(), touchesSurface(), whatIsTooSmall(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

---

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

• src/protocols/pockets/PocketGrid.hh
• src/protocols/pockets/PocketGrid.cc