protocols::pockets::PocketGrid Class Reference

@ More...

#include <PocketGrid.hh>

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::conformation::Residue const &central_rsd, core::Real x, core::Real y, core::Real z)
	PocketGrid (std::vector< core::conformation::ResidueOP > const &central_rsd, 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)
	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::Real x, core::Real y, core::Real z, core::Real const &vdWd, core::Real const &buffer, bool polar=false, int targetResi=0)
void	mark (core::Vector const &center, 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, int targetResi=0)
void	clearSmallPockets (core::Size minsize)
void	findClusters ()
void	findExemplars (core::pose::Pose const &inPose, Size const total_residues)
void	findClustersByExemplars ()
void	linkExemplarsThroughSolvent ()
void	dumpGridToFile ()
void	dumpGridToFile (std::string const &output_filename)
void	dumpExemplarToFile ()
void	dumpExemplarToFile (std::string const &output_filename)
void	dumpTargetPocketsToFile (std::string const &output_filename)
void	dumpTargetPocketsToFile (std::string const &output_filename, numeric::xyzMatrix< core::Real > rot1, numeric::xyzMatrix< core::Real > rot2, numeric::xyzMatrix< core::Real > rot3)
void	dumpTargetPocketsToPDB (std::string const &output_filename, bool minipock=false)
void	dumpTargetPocketsToPDB (std::string const &output_filename, numeric::xyzMatrix< core::Real > rot1, numeric::xyzMatrix< core::Real > rot2, numeric::xyzMatrix< core::Real > rot3)
void	fillTargetPockets ()
void	print () const
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 ()
void	clusterCPockets ()
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::func::XYZ_Func const &xyz_func, Size const total_residues, bool center_target=true, core::Real x=0.0, core::Real y=0.0, core::Real z=0.0)
bool	autoexpanding_pocket_eval (std::vector< core::conformation::ResidueOP > const &central_rsd, core::scoring::func::XYZ_Func const &xyz_func, Size const total_residues, bool center_target=true, core::Real x=0.0, core::Real y=0.0, core::Real z=0.0)
bool	autoexpanding_pocket_eval (core::conformation::Residue const &central_rsd, core::pose::Pose const &inPose, bool center_target=true, core::Real x=0.0, core::Real y=0.0, core::Real z=0.0)
bool	autoexpanding_pocket_eval (std::vector< core::conformation::ResidueOP > const &central_rsd, core::pose::Pose const &inPose, bool center_target=true, core::Real x=0.0, core::Real y=0.0, core::Real z=0.0)
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
utility::vector1< core::Real >	getBounds ()

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, SUBTARGET,   HSURFACE, PSURFACE, POCKET, PO_SURF,   PO_BURIED, T_SURFACE, ST_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 thr3, core::Size max1, core::Size max2, core::Size max3, 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
bool	isSurfacePoint (core::Size x, core::Size y, core::Size z) const
bool	isTargetPocketPoint (core::Size x, core::Size y, core::Size z) const
bool	isDeepTargetPocketPoint (core::Size x, core::Size y, core::Size z) const
bool	isProteinPoint (core::Size x, core::Size y, core::Size z) 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< PtType > > >	c_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_
core::Size	expdbno_
core::Size	numTargets_
PClusterSet	clusters_
CClusterSet	c_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_
bool	ignoreBuriedPockets_
bool	ignoreExposedPockets_
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_
bool	exemplarRestriction_
bool	dumpExemplars_
bool	search13_
core::Real	minPockSize_
core::Real	maxPockSize_
numeric::xyzMatrix< core::Real >	rot_mat_
bool	static_grid_

Static Protected Attributes
static const core::Size	MAX_TARGETS =2

Friends
class	EggshellGrid
class	TargetPocketGrid
class	ComparisonGrid

Detailed Description

@

Member Enumeration Documentation

enum protocols::pockets::PocketGrid::PtType

protected

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

Constructor & Destructor Documentation

protocols::pockets::PocketGrid::PocketGrid

(

)

References core::pose::metrics::CalculatorFactory::Instance(), core::pose::metrics::CalculatorFactory::register_calculator(), and setup_default_options().

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

virtual

protocols::pockets::PocketGrid::PocketGrid

(

const PocketGrid &

gr

)

References c_grid_, dumpExemplars_, exemplarRestriction_, expdbno_, grid_, markpsp_, marksps_, minPockSize_, pdbno_, pockets_, search13_, setup_default_options(), static_grid_, stepSize_, tag_, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

protocols::pockets::PocketGrid::PocketGrid

(

core::conformation::Residue const &

central_rsd

)

References initialize(), core::pose::metrics::CalculatorFactory::Instance(), markpsp_, marksps_, option, core::pose::metrics::CalculatorFactory::register_calculator(), 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(), core::pose::metrics::CalculatorFactory::Instance(), markpsp_, marksps_, option, core::pose::metrics::CalculatorFactory::register_calculator(), setup_default_options(), size_x_, size_y_, size_z_, spacing_, and tag_.

protocols::pockets::PocketGrid::PocketGrid	(	core::conformation::Residue const &	central_rsd,
		core::Real	x,
		core::Real	y,
		core::Real	z
	)

References initialize(), core::pose::metrics::CalculatorFactory::Instance(), markpsp_, marksps_, option, core::pose::metrics::CalculatorFactory::register_calculator(), setup_default_options(), spacing_, and tag_.

protocols::pockets::PocketGrid::PocketGrid	(	std::vector< core::conformation::ResidueOP > const &	central_rsd,
		core::Real	x,
		core::Real	y,
		core::Real	z
	)

References initialize(), core::pose::metrics::CalculatorFactory::Instance(), markpsp_, marksps_, option, core::pose::metrics::CalculatorFactory::register_calculator(), 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
	)

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

Member Function Documentation

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval	(	core::conformation::Residue const &	central_rsd,
		core::scoring::func::XYZ_Func const &	xyz_func,
		Size const	total_residues,
		bool	center_target = true,
		core::Real	x = 0.0,
		core::Real	y = 0.0,
		core::Real	z = 0.0
	)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::clone(), core::scoring::func::XYZ_Func::residue(), and residues.

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::func::XYZ_Func const &	xyz_func,
		Size const	total_residues,
		bool	center_target = true,
		core::Real	x = 0.0,
		core::Real	y = 0.0,
		core::Real	z = 0.0
	)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), autoexpanding_pocket_eval(), and core::scoring::func::XYZ_Func::residue().

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval	(	core::conformation::Residue const &	central_rsd,
		core::pose::Pose const &	inPose,
		bool	center_target = true,
		core::Real	x = 0.0,
		core::Real	y = 0.0,
		core::Real	z = 0.0
	)

References autoexpanding_pocket_eval(), core::conformation::Residue::clone(), and residues.

bool protocols::pockets::PocketGrid::autoexpanding_pocket_eval	(	std::vector< core::conformation::ResidueOP > const &	central_rsd,
		core::pose::Pose const &	inPose,
		bool	center_target = true,
		core::Real	x = 0.0,
		core::Real	y = 0.0,
		core::Real	z = 0.0
	)

References bur_dist_, core::pose::Pose::conformation(), dumpExemplars_, exemplarRestriction_, findClusters(), findClustersByExemplars(), findExemplars(), findPockets(), findPSP(), findSPS(), initialize(), isTooSmall(), limit_x_, limit_y_, limit_z_, mark(), markPocketDepth(), markpsp_, marksps_, MAX_TARGETS, maxLen_, option, probe_rad_, recenter(), core::conformation::Conformation::residue(), rotatePoint(), side_chains_only_, size_x_, size_y_, size_z_, spacing_, static_grid_, stepSize_, surf_dist_, target, target_res, core::pose::Pose::total_residue(), whatIsTooSmall(), xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::clear

(

)

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

Referenced by init().

void protocols::pockets::PocketGrid::clearSmallPockets

(

core::Size

minsize

)

void protocols::pockets::PocketGrid::clusterCPockets

(

)

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

Referenced by findClustersByExemplars(), and linkExemplarsThroughSolvent().

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(), and protocols::pockets::TargetPocketGrid::findClusters().

void protocols::pockets::PocketGrid::dumpExemplarToFile

(

)

References expdbno_, filename(), and tag_.

void protocols::pockets::PocketGrid::dumpExemplarToFile

(

std::string const &

output_filename

)

References c_clusters_, utility::io::ozstream::clear(), utility::io::ozstream::close(), protocols::pockets::CClusterSet::clusters_, numTargets_, utility::io::ozstream::open(), stepSize_, xcorn_, ycorn_, and zcorn_.

void protocols::pockets::PocketGrid::dumpGridToFile

(

)

References filename(), pdbno_, and tag_.

void protocols::pockets::PocketGrid::dumpGridToFile

(

std::string const &

output_filename

)

References utility::io::ozstream::clear(), utility::io::ozstream::close(), protocols::pockets::PClusterSet::clusters_, clusters_, EMPTY, grid_, HSURFACE, minPockSize_, utility::io::ozstream::open(), PO_BURIED, PO_EDGE, PO_SURF, POCKET, PROTEIN, PSP, PSURFACE, ST_SURFACE, stepSize_, SUBTARGET, T_SURFACE, TARGET, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

void protocols::pockets::PocketGrid::dumpTargetPocketsToFile

(

std::string const &

output_filename

)

References utility::io::ozstream::clear(), utility::io::ozstream::close(), protocols::pockets::PClusterSet::clusters_, clusters_, grid_, minPockSize_, numTargets_, utility::io::ozstream::open(), stepSize_, TP_BURIED, TP_POCKET, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

void protocols::pockets::PocketGrid::dumpTargetPocketsToFile	(	std::string const &	output_filename,
		numeric::xyzMatrix< core::Real >	rot1,
		numeric::xyzMatrix< core::Real >	rot2,
		numeric::xyzMatrix< core::Real >	rot3
	)

References utility::io::ozstream::clear(), utility::io::ozstream::close(), protocols::pockets::PClusterSet::clusters_, clusters_, grid_, minPockSize_, numTargets_, utility::io::ozstream::open(), stepSize_, TP_BURIED, TP_POCKET, xcorn_, ycorn_, and zcorn_.

void protocols::pockets::PocketGrid::dumpTargetPocketsToPDB	(	std::string const &	output_filename,
		bool	minipock = false
	)

References utility::io::ozstream::clear(), utility::io::ozstream::close(), protocols::pockets::PClusterSet::clusters_, clusters_, EMPTY, grid_, minPockSize_, numTargets_, utility::io::ozstream::open(), stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

void protocols::pockets::PocketGrid::dumpTargetPocketsToPDB	(	std::string const &	output_filename,
		numeric::xyzMatrix< core::Real >	rot1,
		numeric::xyzMatrix< core::Real >	rot2,
		numeric::xyzMatrix< core::Real >	rot3
	)

References utility::io::ozstream::clear(), utility::io::ozstream::close(), protocols::pockets::PClusterSet::clusters_, clusters_, grid_, minPockSize_, numTargets_, utility::io::ozstream::open(), stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, ycorn_, and zcorn_.

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

protected

References EMPTY, grid_, POCKET, pockets_, TP_POCKET, xdim_, ydim_, z1, z2, and zdim_.

Referenced by fillTargetPockets().

void protocols::pockets::PocketGrid::fillTargetPockets

(

)

References EMPTY, fill(), grid_, pockets_, TP_POCKET, xdim_, ydim_, z1, z2, and zdim_.

void protocols::pockets::PocketGrid::findClusters

(

)

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

Referenced by autoexpanding_pocket_eval().

void protocols::pockets::PocketGrid::findClustersByExemplars

(

)

References c_clusters_, c_grid_, protocols::pockets::PClusterSet::clear(), clusterCPockets(), protocols::pockets::CClusterSet::clusters_, clusters_, grid_, numTargets_, stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, xdim_, ydim_, and zdim_.

Referenced by autoexpanding_pocket_eval().

void protocols::pockets::PocketGrid::findExemplars	(	core::pose::Pose const &	inPose,
		Size const	total_residues
	)

References protocols::pockets::CClusterSet::add(), c, c_clusters_, protocols::pockets::CClusterSet::clear(), protocols::pockets::PClusterSet::clusters_, protocols::pockets::CClusterSet::clusters_, clusters_, core::pose::Pose::conformation(), EMPTY, exit, protocols::pockets::CClusterSet::findClusters(), grid_, isDeepTargetPocketPoint(), isProteinPoint(), isTargetPocketPoint(), core::pose::Pose::metric(), minPockSize_, numTargets_, PO_SURF, numeric::conversions::radians(), core::conformation::Conformation::residue(), RING_HYBRID, rotatePoint(), SP2_HYBRID, SP3_HYBRID, core::kinematics::Stub::spherical(), ST_SURFACE, stepSize_, T_SURFACE, TP_SURF, protocols::pockets::TR, numeric::xyzVector< class >::x(), xcorn_, xdim_, numeric::xyzVector< class >::y(), ycorn_, ydim_, numeric::xyzVector< class >::z(), zcorn_, and zdim_.

Referenced by autoexpanding_pocket_eval().

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

References newSearch(), and stepSize_.

Referenced by autoexpanding_pocket_eval().

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

References newSearch(), and stepSize_.

Referenced by autoexpanding_pocket_eval().

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

References newSearch(), and stepSize_.

Referenced by autoexpanding_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 utility::io::ozstream::clear(), utility::io::ozstream::close(), protocols::pockets::PClusterSet::clusters_, clusters_, grid_, minPockSize_, utility::io::ozstream::open(), stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, protocols::pockets::TR, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

utility::vector1< core::Real > protocols::pockets::PocketGrid::getBounds

(

)

References protocols::pockets::PClusterSet::clusters_, clusters_, grid_, minPockSize_, numTargets_, stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, xcorn_, ycorn_, and zcorn_.

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

static

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

Referenced by protocols::pockets::PocketExemplarMultifunc::PocketExemplarMultifunc(), and protocols::pockets::PocketConstraint::read_def().

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

protected

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

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

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

Referenced by 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 expdbno_, init(), markpsp_, marksps_, numTargets_, 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 expdbno_, init(), markpsp_, marksps_, numTargets_, 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 expdbno_, init(), markpsp_, marksps_, numTargets_, 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 expdbno_, init(), markpsp_, marksps_, numTargets_, 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 expdbno_, init(), markpsp_, marksps_, numTargets_, pdbno_, recenter(), stepSize_, xdim_, ydim_, and zdim_.

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

inlineprotected

References grid_, TP_BURIED, and TP_POCKET.

Referenced by findExemplars().

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

inlineprotected

References grid_, PROTEIN, SUBTARGET, and TARGET.

Referenced by findExemplars().

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

protected

References grid_, HSURFACE, PSURFACE, ST_SURFACE, and T_SURFACE.

Referenced by markDepth(), newSearch(), and touchesPS().

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

inlineprotected

References grid_, TP_BURIED, TP_EDGE, TP_POCKET, and TP_SURF.

Referenced by findExemplars().

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().

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

(

)

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

void protocols::pockets::PocketGrid::linkExemplarsThroughSolvent

(

)

References c_clusters_, clusterCPockets(), protocols::pockets::PClusterSet::clusters_, protocols::pockets::CClusterSet::clusters_, clusters_, EMPTY, grid_, minPockSize_, numTargets_, POCKET, PROTEIN, stepSize_, TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, xcorn_, ycorn_, and zcorn_.

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 target.

Referenced by autoexpanding_pocket_eval(), and mark().

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,
		int	targetResi = 0
	)

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

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(), and target.

void protocols::pockets::PocketGrid::mark	(	core::Vector const &	center,
		core::Real const &	vdWd,
		core::Real const &	buffer,
		bool	polar = false,
		int	targetResi = 0
	)

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_, isSurfacePoint(), PO_BURIED, PO_EDGE, PO_SURF, POCKET, stepSize_, 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(), numTargets_, PO_EDGE, and TP_EDGE.

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().

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(), protocols::forge::remodel::rot_mat(), setup_default_options(), stepSize_, numeric::xyzMatrix< class >::to_identity(), TP_BURIED, TP_EDGE, TP_POCKET, TP_SURF, numeric::xyzVector< class >::x(), xcorn_, numeric::xyzMatrix< class >::xx(), numeric::xyzMatrix< class >::xy(), numeric::xyzMatrix< class >::xz(), numeric::xyzVector< class >::y(), ycorn_, numeric::xyzMatrix< class >::yx(), numeric::xyzMatrix< class >::yy(), numeric::xyzMatrix< class >::yz(), numeric::xyzVector< class >::z(), zcorn_, numeric::xyzVector< class >::zero(), numeric::xyzMatrix< class >::zx(), numeric::xyzMatrix< class >::zy(), and numeric::xyzMatrix< class >::zz().

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

(

)

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

void protocols::pockets::PocketGrid::newSearch ( core::Size  thr1, core::Size  thr2, core::Size  thr3, core::Size  max1, core::Size  max2, core::Size  max3, bool  psp = false, bool  sps = false  )

protected

References c, EMPTY, grid_, isSurfacePoint(), markpsp_, max(), POCKET, PSP, search13_, ST_SURFACE, T_SURFACE, TP_POCKET, protocols::pockets::TR, xdim_, ydim_, and zdim_.

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

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

(

const PocketGrid &

gr

)

References c_grid_, dumpExemplars_, exemplarRestriction_, expdbno_, grid_, markpsp_, marksps_, minPockSize_, pdbno_, pockets_, search13_, stepSize_, tag_, xcorn_, xdim_, ycorn_, ydim_, zcorn_, and zdim_.

void protocols::pockets::PocketGrid::print

(

)

const

References pockets_, protocols::pockets::TR, xdim_, ydim_, and zdim_.

void protocols::pockets::PocketGrid::randomAngle

(

)

References rot_mat_, numeric::random::uniform(), numeric::x_rotation_matrix_degrees(), numeric::y_rotation_matrix_degrees(), and numeric::z_rotation_matrix_degrees().

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_, numeric::xyzVector< class >::x(), xcorn_, xdim_, numeric::xyzVector< class >::y(), ycorn_, ydim_, numeric::xyzVector< class >::z(), zcorn_, and zdim_.

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

void protocols::pockets::PocketGrid::recenter

(

core::conformation::Residue const &

central_rsd

)

References core::conformation::Residue::atom(), center, 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 core::conformation::Residue::atom(), center, core::conformation::Residue::is_protein(), left, MAX_TARGETS, core::conformation::Residue::nheavyatoms(), recenter(), right, stepSize_, protocols::pockets::TR, core::conformation::Atom::type(), xdim_, core::conformation::Atom::xyz(), ydim_, and zdim_.

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(), findExemplars(), and recenter().

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

protected

References bur_dist_, bur_score_, dumpExemplars_, exemplarRestriction_, ignoreBuriedPockets_, ignoreExposedPockets_, limit_x_, limit_y_, limit_z_, markpsp_, marksps_, maxLen_, maxPockSize_, minPockSize_, option, probe_rad_, restrictSize_, rot_mat_, search13_, side_chains_only_, size_x_, size_y_, size_z_, spacing_, static_grid_, surf_dist_, surf_score_, and numeric::x_rotation_matrix_degrees().

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 isSurfacePoint(), 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().

void protocols::pockets::PocketGrid::zeroAngle

(

)

References rot_mat_, and numeric::x_rotation_matrix_degrees().

Friends And Related Function Documentation

friend class ComparisonGrid

friend

friend class EggshellGrid

friend

friend class TargetPocketGrid

friend

Member Data Documentation

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

protected

Referenced by autoexpanding_pocket_eval(), and setup_default_options().

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

protected

Referenced by setup_default_options().

CClusterSet protocols::pockets::PocketGrid::c_clusters_

protected

Referenced by dumpExemplarToFile(), findClustersByExemplars(), findExemplars(), and linkExemplarsThroughSolvent().

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

protected

Referenced by clear(), clusterCPockets(), findClustersByExemplars(), init(), operator=(), and PocketGrid().

PClusterSet protocols::pockets::PocketGrid::clusters_

protected

Referenced by clear(), clusterCPockets(), clusterPockets(), protocols::pockets::ComparisonGrid::compareCoverage(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), findClusters(), protocols::pockets::TargetPocketGrid::findClusters(), findClustersByExemplars(), findExemplars(), get_pocket_distance(), getBounds(), largestTargetPocketVolume(), linkExemplarsThroughSolvent(), markEdgeDepth(), move_pose_to_standard_orie(), netTargetPocketVolume(), and recenter().

bool protocols::pockets::PocketGrid::dumpExemplars_

protected

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

bool protocols::pockets::PocketGrid::exemplarRestriction_

protected

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

core::Size protocols::pockets::PocketGrid::expdbno_

protected

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

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

protected

Referenced by clear(), clusterPockets(), protocols::pockets::ComparisonGrid::compareCoverage(), protocols::pockets::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), findClustersByExemplars(), findExemplars(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), getBounds(), init(), isDeepTargetPocketPoint(), isProteinPoint(), isSurfacePoint(), isTargetPocketPoint(), isTooSmall(), linkExemplarsThroughSolvent(), mark(), protocols::pockets::ComparisonGrid::mark(), markDepth(), markEdgeDepth(), markOneEdgeDepth(), markPocketDepth(), move_pose_to_standard_orie(), newSearch(), operator=(), PocketGrid(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), targetPocketHeuristicScore(), targetPocketHydrophobicProteinSurface(), targetPocketPolarProteinSurface(), targetPocketProteinSurface(), targetPocketSolventSurface(), targetPocketVolume(), touchesSolvent(), touchesSS(), touchesSurface(), and whatIsTooSmall().

bool protocols::pockets::PocketGrid::ignoreBuriedPockets_

protected

Referenced by largestTargetPocketVolume(), netTargetPocketVolume(), and setup_default_options().

bool protocols::pockets::PocketGrid::ignoreExposedPockets_

protected

Referenced by largestTargetPocketVolume(), netTargetPocketVolume(), and setup_default_options().

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

protected

Referenced by autoexpanding_pocket_eval(), and setup_default_options().

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

protected

Referenced by autoexpanding_pocket_eval(), and setup_default_options().

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

protected

Referenced by autoexpanding_pocket_eval(), and setup_default_options().

bool protocols::pockets::PocketGrid::markpsp_

protected

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

bool protocols::pockets::PocketGrid::marksps_

protected

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

const core::Size protocols::pockets::PocketGrid::MAX_TARGETS =2

staticprotected

Referenced by autoexpanding_pocket_eval(), getRelaxResidues(), and recenter().

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

protected

Referenced by autoexpanding_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 protocols::pockets::ComparisonGrid::compareCoverage(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), findExemplars(), get_pocket_distance(), getBounds(), largestTargetPocketVolume(), linkExemplarsThroughSolvent(), move_pose_to_standard_orie(), netTargetPocketVolume(), operator=(), PocketGrid(), and setup_default_options().

core::Size protocols::pockets::PocketGrid::numTargets_

protected

Referenced by dumpExemplarToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), findClusters(), findClustersByExemplars(), findExemplars(), getBounds(), initialize(), largestTargetPocketVolume(), linkExemplarsThroughSolvent(), markEdgeDepth(), and netTargetPocketVolume().

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(), 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::search13_

protected

Referenced by newSearch(), operator=(), PocketGrid(), and setup_default_options().

bool protocols::pockets::PocketGrid::side_chains_only_

protected

Referenced by autoexpanding_pocket_eval(), and setup_default_options().

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

protected

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

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

protected

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

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

protected

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

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

protected

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

bool protocols::pockets::PocketGrid::static_grid_

protected

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

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

protected

Referenced by autoexpanding_pocket_eval(), clusterCPockets(), clusterPockets(), protocols::pockets::ComparisonGrid::compareCoverage(), protocols::pockets::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpExemplarToFile(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), findClustersByExemplars(), findExemplars(), findPockets(), findPSP(), findSPS(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), getBounds(), initialize(), largestTargetPocketVolume(), linkExemplarsThroughSolvent(), mark(), protocols::pockets::ComparisonGrid::mark(), markDepth(), markOneEdgeDepth(), move_pose_to_standard_orie(), netTargetPocketVolume(), operator=(), PocketGrid(), recenter(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), 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(), 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 dumpExemplarToFile(), dumpGridToFile(), operator=(), and PocketGrid().

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

protected

Referenced by protocols::pockets::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpExemplarToFile(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), findExemplars(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), getBounds(), linkExemplarsThroughSolvent(), mark(), protocols::pockets::ComparisonGrid::mark(), move_pose_to_standard_orie(), operator=(), PocketGrid(), recenter(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

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

protected

Referenced by autoexpanding_pocket_eval(), clusterCPockets(), clusterPockets(), protocols::pockets::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), findClustersByExemplars(), findExemplars(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), init(), initialize(), isTooSmall(), mark(), protocols::pockets::ComparisonGrid::mark(), markDepth(), markOneEdgeDepth(), markPocketDepth(), newSearch(), operator=(), PocketGrid(), print(), recenter(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), 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::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpExemplarToFile(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), findExemplars(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), getBounds(), linkExemplarsThroughSolvent(), mark(), protocols::pockets::ComparisonGrid::mark(), move_pose_to_standard_orie(), operator=(), PocketGrid(), recenter(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

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

protected

Referenced by autoexpanding_pocket_eval(), clusterCPockets(), clusterPockets(), protocols::pockets::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), fill(), fillTargetPockets(), findClusters(), findClustersByExemplars(), findExemplars(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), init(), initialize(), isTooSmall(), mark(), protocols::pockets::ComparisonGrid::mark(), markDepth(), markOneEdgeDepth(), markPocketDepth(), newSearch(), operator=(), PocketGrid(), print(), recenter(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), 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::ComparisonGrid::ComparisonGrid(), protocols::pockets::EggshellGrid::dump_eggshell(), dumpExemplarToFile(), dumpGridToFile(), dumpTargetPocketsToFile(), dumpTargetPocketsToPDB(), protocols::pockets::TargetPocketGrid::dumpTargetPocketsToPDB(), protocols::pockets::EggshellGrid::EggshellGrid(), findExemplars(), protocols::pockets::EggshellGrid::get_eggshell_distance(), get_pocket_distance(), getBounds(), linkExemplarsThroughSolvent(), mark(), protocols::pockets::ComparisonGrid::mark(), move_pose_to_standard_orie(), operator=(), PocketGrid(), recenter(), protocols::pockets::TargetPocketGrid::TargetPocketGrid(), and protocols::pockets::EggshellGrid::write_grid_to_pdb().

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

protected

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

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

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