#include <PocketGrid.hh>

Inheritance diagram for protocols::pockets::ElectrostaticpotentialGrid:

Public Types
enum	PtType { PROTEIN, SURFACE, SOLVENT, PSEUDO_PROTEIN }

Public Member Functions
	ElectrostaticpotentialGrid ()

void	initialize_espGrid ()

void	initialize_typGrid ()

	ElectrostaticpotentialGrid (std::string const &input_espGrid_filename, core::pose::Pose const &protein_pose, PocketGrid const &pocket_grid, bool delphi=false)

void	mark_protein_espGrid_points (core::pose::Pose const &protein_pose)

void	mark_atom_espGrid_points (numeric::xyzVector< core::Real > atom_coord, core::Real const &vdWd)

std::list< utility::vector1 < core::Real > > const &	espGrid_point_list () const

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

void	write_connollySurface_to_pdb (std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list, std::string const &output_pdbname) const

void	get_oegrid_dimensions (std::string const &input_OEgrid_filename)

void	fill_espGrid_values (std::string const &input_OEgrid_filename)

void	fill_espGrid_values_with_type (std::string const &input_OEgrid_filename)

void	print_to_oegrid (std::string const &output_OEgrid_filename)

void	resize_espGrid_to_match_pocketGrid (std::string const &espGrid_filename, PocketGrid const &pg)

void	assign_esp_for_protein_grid_points (core::pose::Pose const &protein_pose, std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list)

void	assign_esp_for_atom_grid_points (numeric::xyzVector< core::Real > atom_coord, core::Real const &inflated_radius)

void	assign_esp_for_surface_grid_points (std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list)

void	assign_esp_for_surface_grid_points_by_nn (std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list)

core::Real	get_atom_dist_from_connolly_surface (numeric::xyzVector< core::Real > atom_coord, std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list)

void	mark_buried_solvent_points (core::pose::Pose const &protein_pose, std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list)

void	get_ZAP_espGrid_values (std::string const &input_espGrid_filename)

void	get_ZAP_espGrid_values_with_type (std::string const &input_espGrid_filename)

void	get_DELPHI_espGrid_values (std::string const &input_espGrid_filename)

void	change_espGrid_for_darc (std::string const &espGrid_filename, core::pose::Pose const &protein_pose, PocketGrid const &pocket_grid)

void	set_surface_esp_to_zero ()

void	set_protein_esp_to_zero ()

void	cap_espGrid ()

bool	operator== (PocketGrid const &other) 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	clearSmallPockets (core::Size minsize)

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)

Public Attributes
std::vector< std::vector < std::vector< core::Real > > >	espGrid_

std::vector< std::vector < std::vector< PtType > > >	typGrid_

Private Attributes
numeric::xyzVector< core::Size >	espGrid_dim_

numeric::xyzVector< core::Real >	espGrid_mid_

core::Real	espGrid_spacing_

std::list< utility::vector1 < core::Real > >	espGrid_points_list_

Friends
class	NonPlaidFingerprint

class	PocketGrid

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

Member Enumeration Documentation

enum protocols::pockets::ElectrostaticpotentialGrid::PtType

Enumerator
PROTEIN
SURFACE
SOLVENT
PSEUDO_PROTEIN

Constructor & Destructor Documentation

protocols::pockets::ElectrostaticpotentialGrid::ElectrostaticpotentialGrid ( )

inline

protocols::pockets::ElectrostaticpotentialGrid::ElectrostaticpotentialGrid	(	std::string const &	input_espGrid_filename,
		core::pose::Pose const &	protein_pose,
		PocketGrid const &	pocket_grid,
		bool	delphi = `false`
	)

References get_DELPHI_espGrid_values(), and get_ZAP_espGrid_values().

Member Function Documentation

void protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_atom_grid_points	(	numeric::xyzVector< core::Real >	atom_coord,
		core::Real const &	inflated_radius
	)

References espGrid_dim_, espGrid_mid_, espGrid_spacing_, PROTEIN, SURFACE, and typGrid_.

Referenced by assign_esp_for_protein_grid_points().

void protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_protein_grid_points	(	core::pose::Pose const &	protein_pose,
		std::list< numeric::xyzVector< core::Real > > const &	surfacePoints_list
	)

References assign_esp_for_atom_grid_points(), core::pose::Pose::conformation(), protocols::pockets::convert_cartesian_to_grid(), espGrid_dim_, espGrid_mid_, espGrid_spacing_, get_atom_dist_from_connolly_surface(), core::conformation::Conformation::residue(), and core::pose::Pose::size().

Referenced by change_espGrid_for_darc().

void protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_surface_grid_points ( std::list< numeric::xyzVector< core::Real > > const & surfacePoints_list )

References espGrid_dim_, espGrid_mid_, espGrid_spacing_, SURFACE, and typGrid_.

Referenced by change_espGrid_for_darc().

void protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_surface_grid_points_by_nn ( std::list< numeric::xyzVector< core::Real > > const & surfacePoints_list )

References protocols::pockets::convert_cartesian_to_grid(), espGrid_dim_, espGrid_mid_, espGrid_spacing_, SURFACE, and typGrid_.

void protocols::pockets::ElectrostaticpotentialGrid::cap_espGrid ( )

References espGrid_, and espGrid_dim_.

Referenced by change_espGrid_for_darc().

void protocols::pockets::ElectrostaticpotentialGrid::change_espGrid_for_darc	(	std::string const &	espGrid_filename,
		core::pose::Pose const &	protein_pose,
		PocketGrid const &	pocket_grid
	)

References assign_esp_for_protein_grid_points(), assign_esp_for_surface_grid_points(), cap_espGrid(), protocols::pockets::PocketGrid::get_connolly_surfacePoints(), initialize_typGrid(), mark_buried_solvent_points(), print_to_oegrid(), resize_espGrid_to_match_pocketGrid(), set_protein_esp_to_zero(), set_surface_esp_to_zero(), write_connollySurface_to_pdb(), and write_espGrid_to_pdb().

std::list< utility::vector1<core::Real> > const& protocols::pockets::ElectrostaticpotentialGrid::espGrid_point_list ( ) const

inline

References espGrid_points_list_.

void protocols::pockets::ElectrostaticpotentialGrid::fill_espGrid_values ( std::string const & input_OEgrid_filename )

References espGrid_, espGrid_dim_, and initialize_espGrid().

Referenced by protocols::pockets::PocketGrid::alter_espGrid(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), get_ZAP_espGrid_values(), and resize_espGrid_to_match_pocketGrid().

void protocols::pockets::ElectrostaticpotentialGrid::fill_espGrid_values_with_type ( std::string const & input_OEgrid_filename )

References core::pose::motif::a(), protocols::match::upstream::b, espGrid_, espGrid_dim_, initialize_espGrid(), initialize_typGrid(), and typGrid_.

Referenced by get_ZAP_espGrid_values_with_type().

core::Real protocols::pockets::ElectrostaticpotentialGrid::get_atom_dist_from_connolly_surface	(	numeric::xyzVector< core::Real >	atom_coord,
		std::list< numeric::xyzVector< core::Real > > const &	surfacePoints_list
	)

Referenced by assign_esp_for_protein_grid_points().

void protocols::pockets::ElectrostaticpotentialGrid::get_DELPHI_espGrid_values ( std::string const & input_espGrid_filename )

References espGrid_, espGrid_dim_, espGrid_mid_, espGrid_spacing_, protocols::pockets::PocketGrid::init(), and protocols::pockets::PocketGrid::spacing().

Referenced by ElectrostaticpotentialGrid(), and protocols::pockets::NonPlaidFingerprint::setup_from_espGrid().

void protocols::pockets::ElectrostaticpotentialGrid::get_oegrid_dimensions ( std::string const & input_OEgrid_filename )

References espGrid_dim_, espGrid_mid_, espGrid_spacing_, and protocols::pockets::PocketGrid::spacing().

Referenced by protocols::pockets::PocketGrid::alter_espGrid(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), get_ZAP_espGrid_values(), get_ZAP_espGrid_values_with_type(), and resize_espGrid_to_match_pocketGrid().

void protocols::pockets::ElectrostaticpotentialGrid::get_ZAP_espGrid_values ( std::string const & input_espGrid_filename )

References fill_espGrid_values(), and get_oegrid_dimensions().

Referenced by ElectrostaticpotentialGrid(), and protocols::pockets::NonPlaidFingerprint::get_surface_esp().

void protocols::pockets::ElectrostaticpotentialGrid::get_ZAP_espGrid_values_with_type ( std::string const & input_espGrid_filename )

References fill_espGrid_values_with_type(), and get_oegrid_dimensions().

Referenced by protocols::pockets::NonPlaidFingerprint::setup_from_espGrid().

void protocols::pockets::ElectrostaticpotentialGrid::initialize_espGrid ( )

References espGrid_, and espGrid_dim_.

Referenced by fill_espGrid_values(), and fill_espGrid_values_with_type().

void protocols::pockets::ElectrostaticpotentialGrid::initialize_typGrid ( )

References espGrid_dim_, SOLVENT, and typGrid_.

Referenced by change_espGrid_for_darc(), and fill_espGrid_values_with_type().

void protocols::pockets::ElectrostaticpotentialGrid::mark_atom_espGrid_points	(	numeric::xyzVector< core::Real >	atom_coord,
		core::Real const &	vdWd
	)

References espGrid_, espGrid_dim_, espGrid_mid_, espGrid_spacing_, protocols::mean_field::max(), and protocols::mean_field::min().

Referenced by mark_protein_espGrid_points().

void protocols::pockets::ElectrostaticpotentialGrid::mark_buried_solvent_points	(	core::pose::Pose const &	protein_pose,
		std::list< numeric::xyzVector< core::Real > > const &	surfacePoints_list
	)

References espGrid_dim_, PROTEIN, PSEUDO_PROTEIN, SURFACE, and typGrid_.

Referenced by change_espGrid_for_darc().

void protocols::pockets::ElectrostaticpotentialGrid::mark_protein_espGrid_points ( core::pose::Pose const & protein_pose )

References core::pose::Pose::conformation(), mark_atom_espGrid_points(), core::conformation::Conformation::residue(), and core::pose::Pose::size().

bool protocols::pockets::ElectrostaticpotentialGrid::operator== ( PocketGrid const & other ) const

overridevirtual

Reimplemented from protocols::pockets::PocketGrid.

References espGrid_dim_, espGrid_mid_, espGrid_points_list_, and espGrid_spacing_.

void protocols::pockets::ElectrostaticpotentialGrid::print_to_oegrid ( std::string const & output_OEgrid_filename )

References espGrid_, espGrid_dim_, espGrid_mid_, espGrid_spacing_, core::conformation::membrane::out, and typGrid_.

Referenced by protocols::pockets::PocketGrid::alter_espGrid(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), and change_espGrid_for_darc().

void protocols::pockets::ElectrostaticpotentialGrid::resize_espGrid_to_match_pocketGrid	(	std::string const &	espGrid_filename,
		PocketGrid const &	pg
	)

References protocols::pockets::PocketGrid::dim_, espGrid_, espGrid_dim_, espGrid_mid_, espGrid_spacing_, fill_espGrid_values(), get_oegrid_dimensions(), 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 change_espGrid_for_darc().

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

overridevirtual

Reimplemented from protocols::pockets::PocketGrid.

void protocols::pockets::ElectrostaticpotentialGrid::set_protein_esp_to_zero ( )

References espGrid_, espGrid_dim_, PROTEIN, and typGrid_.

Referenced by change_espGrid_for_darc().

void protocols::pockets::ElectrostaticpotentialGrid::set_surface_esp_to_zero ( )

References espGrid_, espGrid_dim_, SURFACE, and typGrid_.

Referenced by change_espGrid_for_darc().

void protocols::pockets::ElectrostaticpotentialGrid::write_connollySurface_to_pdb	(	std::list< numeric::xyzVector< core::Real > > const &	surfacePoints_list,
		std::string const &	output_pdbname
	)		const