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#include <PocketGrid.hh>

Public Member Functions
	EggshellGrid (const PocketGrid &gr)

	EggshellGrid (const PocketGrid &grd, core::pose::Pose const &ligand_pose)

	EggshellGrid (const PocketGrid &ext_grd, std::list< numeric::xyzVector< core::Real > > const &eggshell_coord_list)

	EggshellGrid (std::string const &fname)

std::list< numeric::xyzVector < core::Real > > const &	eggshell_coord_list () const

std::list< numeric::xyzVector < core::Real > > const &	extra_coord_list () const

void	dump_eggshell (std::string const &fname) const

void	dump_eggshell (std::string const &fname, numeric::xyzMatrix< core::Real > rot1, numeric::xyzMatrix< core::Real > rot2, numeric::xyzMatrix< core::Real > rot3) const

void	write_eggshell_to_pdb (std::string const &output_pdbname) const

void	write_eggshell_to_pdb (std::string const &output_pdbname, numeric::xyzMatrix< core::Real > rot1, numeric::xyzMatrix< core::Real > rot2, numeric::xyzMatrix< core::Real > rot3) const

void	write_grid_to_pdb (const PocketGrid &gr, std::string const &output_pdbname) const

numeric::xyzVector< core::Real >	calculate_center_xyz (std::list< numeric::xyzVector< core::Real > > const &pocketshell_coord_list)

core::Real	get_eggshell_distance (EggshellGrid const &template_eggshell) const

core::Real	get_eggshell_distance (EggshellGrid const &template_eggshell, std::string const &comparison_pdbname) const

Public Member Functions inherited from protocols::pockets::PocketGrid
	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 ()

Private Attributes
std::list< numeric::xyzVector < core::Real > >	eggshell_coord_list_

std::list< numeric::xyzVector < core::Real > >	extra_coord_list_

numeric::xyzVector< core::Real >	eggshell_CoM_

Friends
class	NonPlaidFingerprint

Additional Inherited Members
Static Public Member Functions inherited from protocols::pockets::PocketGrid
static std::vector < core::conformation::ResidueOP >	getRelaxResidues (core::pose::Pose const &input_pose, std::string const &resids)

Protected Types inherited from protocols::pockets::PocketGrid
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 inherited from protocols::pockets::PocketGrid
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 inherited from protocols::pockets::PocketGrid
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 inherited from protocols::pockets::PocketGrid
static const core::Size	MAX_TARGETS =2

Detailed Description

@

Constructor & Destructor Documentation

protocols::pockets::EggshellGrid::EggshellGrid ( const PocketGrid & gr )

protocols::pockets::EggshellGrid::EggshellGrid	(	const PocketGrid &	grd,
		core::pose::Pose const &	ligand_pose
	)

protocols::pockets::EggshellGrid::EggshellGrid	(	const PocketGrid &	ext_grd,
		std::list< numeric::xyzVector< core::Real > > const &	eggshell_coord_list
	)

protocols::pockets::EggshellGrid::EggshellGrid ( std::string const & fname )

Member Function Documentation

numeric::xyzVector< core::Real > protocols::pockets::EggshellGrid::calculate_center_xyz ( std::list< numeric::xyzVector< core::Real > > const & pocketshell_coord_list )

References numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by EggshellGrid().

void protocols::pockets::EggshellGrid::dump_eggshell ( std::string const & fname ) const

References utility::io::ozstream::clear(), utility::io::ozstream::close(), protocols::pockets::PocketGrid::EGGSHELL, protocols::pockets::PocketGrid::grid_, utility::io::ozstream::open(), protocols::pockets::PocketGrid::stepSize_, protocols::pockets::PocketGrid::xcorn_, protocols::pockets::PocketGrid::xdim_, protocols::pockets::PocketGrid::ycorn_, protocols::pockets::PocketGrid::ydim_, protocols::pockets::PocketGrid::zcorn_, and protocols::pockets::PocketGrid::zdim_.

void protocols::pockets::EggshellGrid::dump_eggshell	(	std::string const &	fname,
		numeric::xyzMatrix< core::Real >	rot1,
		numeric::xyzMatrix< core::Real >	rot2,
		numeric::xyzMatrix< core::Real >	rot3
	)		const

References utility::io::ozstream::clear(), utility::io::ozstream::close(), protocols::pockets::PocketGrid::EGGSHELL, eggshell_coord_list_, protocols::pockets::PocketGrid::grid_, utility::io::ozstream::open(), protocols::pockets::PocketGrid::stepSize_, protocols::pockets::PocketGrid::xcorn_, protocols::pockets::PocketGrid::xdim_, protocols::pockets::PocketGrid::ycorn_, protocols::pockets::PocketGrid::ydim_, protocols::pockets::PocketGrid::zcorn_, and protocols::pockets::PocketGrid::zdim_.

std::list< numeric::xyzVector<core::Real> > const& protocols::pockets::EggshellGrid::eggshell_coord_list ( ) const

inline

References eggshell_coord_list_.

Referenced by EggshellGrid(), get_eggshell_distance(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_and_known_ligand(), and protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_using_bound_ligand().

std::list< numeric::xyzVector<core::Real> > const& protocols::pockets::EggshellGrid::extra_coord_list ( ) const

inline

References extra_coord_list_.

Referenced by protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_and_known_ligand(), and protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_using_bound_ligand().

core::Real protocols::pockets::EggshellGrid::get_eggshell_distance ( EggshellGrid const & template_eggshell ) const

inline

References get_eggshell_distance().

Referenced by get_eggshell_distance().

core::Real protocols::pockets::EggshellGrid::get_eggshell_distance	(	EggshellGrid const &	template_eggshell,
		std::string const &	comparison_pdbname
	)		const

void protocols::pockets::EggshellGrid::write_eggshell_to_pdb ( std::string const & output_pdbname ) const

References utility::io::ozstream::clear(), utility::io::ozstream::close(), eggshell_coord_list_, extra_coord_list_, and utility::io::ozstream::open().

void protocols::pockets::EggshellGrid::write_eggshell_to_pdb	(	std::string const &	output_pdbname,
		numeric::xyzMatrix< core::Real >	rot1,
		numeric::xyzMatrix< core::Real >	rot2,
		numeric::xyzMatrix< core::Real >	rot3
	)		const