protocols::pockets::EggshellGrid Class Reference

@ More...

#include <PocketGrid.hh>

Inheritance diagram for protocols::pockets::EggshellGrid:

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 (core::pose::Pose const &protein_pose, const PocketGrid &pocket_grid, const PocketGrid &grid_for_extshell)
	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	get_connolly_eggshell (std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list, const PocketGrid &eggGrid, const PocketGrid &extGrid)
void	get_connolly_eggshell_on_grid (std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list, const PocketGrid &eggGrid, const PocketGrid &extGrid)
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
bool	operator== (PocketGrid const &rhs) const override
bool	same_type_as_me (PocketGrid const &other) const override
Public Member Functions inherited from protocols::pockets::PocketGrid
	PocketGrid ()
	~PocketGrid () override
	PocketGrid (const PocketGrid &gr)
PocketGrid &	operator= (const PocketGrid &gr)
numeric::xyzVector< core::Real >	dim () const
core::Real	spacing () const
	PocketGrid (core::conformation::Residue const &central_rsd)
	PocketGrid (std::vector< core::conformation::ResidueCOP > const &central_rsd)
	PocketGrid (core::conformation::Residue const &central_rsd, core::Real x, core::Real y, core::Real z)
	PocketGrid (std::vector< core::conformation::ResidueCOP > 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::ResidueCOP > 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::ResidueCOP > 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, int targetResi=0)
void	mark (core::Vector const &center, core::Real const &vdWd, core::Real const &buffer, bool polar=false, int targetResi=0)
void	findClusters ()
void	findExemplars (core::pose::Pose const &inPose, core::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, core::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::ResidueCOP > const &central_rsd, core::scoring::func::XYZ_Func const &xyz_func, core::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::ResidueCOP > 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 ()
core::Size	GetExemplarNumClusters () const
core::Size	GetExemplarNumAtoms () const
core::Size	GetExemplarNumPolarAtoms () const
void	write_pocketGrid_to_pdb (std::string const &output_filename)
void	alter_espGrid (std::string const &espGrid_filename)
void	alter_espGrid_with_bound_ligand (std::string const &espGrid_filename, core::pose::Pose const &protein_pose)
std::list< numeric::xyzVector< core::Real > >	get_connolly_surfacePoints (core::pose::Pose const &protein_pose) const
std::list< numeric::xyzVector< core::Real > >	get_connolly_surfacePoints_within_grid (std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list)

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::ResidueCOP >	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	spacing_
core::Real	stepSize_
numeric::xyzVector< core::Real >	mid_
numeric::xyzVector< core::Size >	dim_
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	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	filterExemplars_
bool	limitExemplars_
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

EggshellGrid() [1/5]

protocols::pockets::EggshellGrid::EggshellGrid

(

const PocketGrid &

gr

)

References calculate_center_xyz(), protocols::pockets::PocketGrid::EGGSHELL, eggshell_CoM_, eggshell_coord_list_, protocols::pockets::PocketGrid::grid_, protocols::pockets::PocketGrid::HSURFACE, protocols::pockets::PocketGrid::init(), protocols::pockets::PocketGrid::PSURFACE, protocols::pockets::PocketGrid::ST_SURFACE, protocols::pockets::PocketGrid::stepSize_, protocols::pockets::PocketGrid::T_SURFACE, protocols::pockets::PocketGrid::TP_BURIED, protocols::pockets::PocketGrid::TP_EDGE, protocols::pockets::PocketGrid::TP_POCKET, write_Grid_to_pdb(), 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_.

EggshellGrid() [2/5]

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

References protocols::cluster::calibur::aa, core::conformation::Residue::atom(), calculate_center_xyz(), core::pose::Pose::conformation(), eggshell_CoM_, eggshell_coord_list_, extra_coord_list_, protocols::pockets::PocketGrid::grid_, protocols::pockets::PocketGrid::HSURFACE, protocols::pockets::PocketGrid::init(), core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), protocols::pockets::PocketGrid::PSURFACE, core::pose::Pose::residue(), core::conformation::Conformation::residue(), core::pose::Pose::size(), protocols::pockets::PocketGrid::ST_SURFACE, protocols::pockets::PocketGrid::stepSize_, protocols::pockets::PocketGrid::T_SURFACE, protocols::pockets::TR(), write_Grid_to_pdb(), protocols::pockets::PocketGrid::xcorn_, protocols::pockets::PocketGrid::xdim_, core::conformation::Atom::xyz(), protocols::pockets::PocketGrid::ycorn_, protocols::pockets::PocketGrid::ydim_, protocols::pockets::PocketGrid::zcorn_, and protocols::pockets::PocketGrid::zdim_.

EggshellGrid() [3/5]

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

References eggshell_coord_list(), protocols::pockets::PocketGrid::EMPTY, extra_coord_list_, protocols::pockets::PocketGrid::grid_, protocols::pockets::PocketGrid::HSURFACE, protocols::pockets::PocketGrid::init(), protocols::pockets::PocketGrid::PO_BURIED, protocols::pockets::PocketGrid::PO_EDGE, protocols::pockets::PocketGrid::PO_SURF, protocols::pockets::PocketGrid::POCKET, protocols::pockets::PocketGrid::PSURFACE, protocols::pockets::PocketGrid::ST_SURFACE, protocols::pockets::PocketGrid::stepSize_, protocols::pockets::PocketGrid::T_SURFACE, protocols::pockets::PocketGrid::TP_BURIED, protocols::pockets::PocketGrid::TP_EDGE, protocols::pockets::PocketGrid::TP_POCKET, protocols::pockets::PocketGrid::TP_SURF, write_Grid_to_pdb(), 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_.

EggshellGrid() [4/5]

protocols::pockets::EggshellGrid::EggshellGrid	(	core::pose::Pose const &	protein_pose,
		const PocketGrid &	pocket_grid,
		const PocketGrid &	grid_for_extshell
	)

References protocols::pockets::PocketGrid::get_connolly_surfacePoints().

EggshellGrid() [5/5]

protocols::pockets::EggshellGrid::EggshellGrid

(

std::string const &

fname

)

References protocols::pockets::PocketGrid::EGGSHELL, eggshell_coord_list_, extra_coord_list_, protocols::pockets::PocketGrid::grid_, core::conformation::membrane::in, protocols::pockets::PocketGrid::init(), 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_.

Member Function Documentation

calculate_center_xyz()

numeric::xyzVector< core::Real > protocols::pockets::EggshellGrid::calculate_center_xyz

(

std::list< numeric::xyzVector< core::Real > > const &

pocketshell_coord_list

)

Referenced by EggshellGrid().

dump_eggshell() [1/2]

void protocols::pockets::EggshellGrid::dump_eggshell

(

std::string const &

fname

)

const

References protocols::pockets::PocketGrid::EGGSHELL, protocols::pockets::PocketGrid::grid_, core::conformation::membrane::out, 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_.

dump_eggshell() [2/2]

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 protocols::pockets::PocketGrid::EGGSHELL, eggshell_coord_list_, protocols::pockets::PocketGrid::grid_, core::conformation::membrane::out, protocols::jumping::rot1, protocols::jumping::rot2, 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_.

eggshell_coord_list()

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_ConnollySurface(), 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().

extra_coord_list()

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_ConnollySurface(), 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().

get_connolly_eggshell()

void protocols::pockets::EggshellGrid::get_connolly_eggshell	(	std::list< numeric::xyzVector< core::Real > > const &	surfacePoints_list,
		const PocketGrid &	eggGrid,
		const PocketGrid &	extGrid
	)

References protocols::pockets::convert_cartesian_to_grid(), protocols::pockets::PocketGrid::dim_, protocols::pockets::PocketGrid::mid_, and protocols::pockets::PocketGrid::spacing_.

get_connolly_eggshell_on_grid()

void protocols::pockets::EggshellGrid::get_connolly_eggshell_on_grid	(	std::list< numeric::xyzVector< core::Real > > const &	surfacePoints_list,
		const PocketGrid &	eggGrid,
		const PocketGrid &	extGrid
	)

References protocols::pockets::convert_grid_to_cartesian(), protocols::pockets::PocketGrid::dim_, protocols::pockets::PocketGrid::mid_, protocols::pockets::PocketGrid::spacing_, protocols::pockets::PocketGrid::xdim_, protocols::pockets::PocketGrid::ydim_, and protocols::pockets::PocketGrid::zdim_.

get_eggshell_distance() [1/2]

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

inline

References get_eggshell_distance().

Referenced by get_eggshell_distance().

get_eggshell_distance() [2/2]

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

References protocols::pockets::PocketGrid::EGGSHELL, eggshell_CoM_, eggshell_coord_list(), protocols::pockets::PocketGrid::grid_, core::conformation::membrane::out, protocols::pockets::PocketGrid::stepSize_, protocols::pockets::TR(), 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_.

operator==()

bool protocols::pockets::EggshellGrid::operator== ( PocketGrid const &  rhs ) const

overridevirtual

Reimplemented from protocols::pockets::PocketGrid.

References eggshell_CoM_, eggshell_coord_list_, and extra_coord_list_.

same_type_as_me()

bool protocols::pockets::EggshellGrid::same_type_as_me ( PocketGrid const &  other ) const

overridevirtual

Reimplemented from protocols::pockets::PocketGrid.

write_eggshell_to_pdb() [1/2]

void protocols::pockets::EggshellGrid::write_eggshell_to_pdb

(

std::string const &

output_pdbname

)

const

References eggshell_coord_list_, extra_coord_list_, and core::conformation::membrane::out.

write_eggshell_to_pdb() [2/2]

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

References eggshell_coord_list_, extra_coord_list_, core::conformation::membrane::out, protocols::jumping::rot1, and protocols::jumping::rot2.

write_Grid_to_pdb()

void protocols::pockets::EggshellGrid::write_Grid_to_pdb	(	const PocketGrid &	gr,
		std::string const &	output_pdbname
	)		const

References core::conformation::membrane::out, 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_.

Referenced by EggshellGrid().

Friends And Related Function Documentation

NonPlaidFingerprint

friend class NonPlaidFingerprint

friend

Member Data Documentation

eggshell_CoM_

numeric::xyzVector<core::Real> protocols::pockets::EggshellGrid::eggshell_CoM_

private

Referenced by EggshellGrid(), get_eggshell_distance(), operator==(), protocols::pockets::NonPlaidFingerprint::setup_from_ConnollySurface(), 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().

eggshell_coord_list_

std::list< numeric::xyzVector<core::Real> > protocols::pockets::EggshellGrid::eggshell_coord_list_

private

Referenced by dump_eggshell(), eggshell_coord_list(), EggshellGrid(), operator==(), and write_eggshell_to_pdb().

extra_coord_list_

std::list< numeric::xyzVector<core::Real> > protocols::pockets::EggshellGrid::extra_coord_list_

private

Referenced by EggshellGrid(), extra_coord_list(), operator==(), and write_eggshell_to_pdb().

---

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

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