Classes
class	CCluster
	@ Cluster of exemplar points More...

class	CClusterSet
	@ Set of clusters of exemplar points More...

class	ComparisonGrid
	@ More...

class	DarcParticleSwarmMinimizer

class	EggshellGrid
	@ More...

class	ElectrostaticpotentialGrid

class	FingerprintBase

class	FingerprintMultifunc
	Atom tree multifunction class. More...

class	GenPharmacophore

class	NonPlaidFingerprint

class	PCluster
	@ Cluster of Pocket points More...

class	PClusterSet
	@ Set of cluster of pocket points More...

class	PlaidFingerprint

class	PocketConstraint
	This constraint favors creating a pocket suitable for a small-molecule. More...

class	PocketConstraintCreator
	Mover creator for the PocketConstraint constraint. More...

class	PocketExemplarMultifunc
	Pocket multifunction class, does objective function of optimization. More...

class	PocketGrid
	@ More...

struct	ray_distance_derivs

class	SmallMol

struct	spherical_coor_triplet

class	TargetPocketGrid
	@ More...

struct	triplet_and_originnum

class	UnionEdge

Typedefs
typedef utility::pointer::shared_ptr < DarcParticleSwarmMinimizer >	DarcParticleSwarmMinimizerOP

typedef utility::pointer::shared_ptr < DarcParticleSwarmMinimizer const >	DarcParticleSwarmMinimizerCOP

typedef utility::pointer::shared_ptr < NonPlaidFingerprint >	NonPlaidFingerprintOP

typedef utility::pointer::shared_ptr < NonPlaidFingerprint const >	NonPlaidFingerprintCOP

typedef utility::pointer::shared_ptr < PlaidFingerprint >	PlaidFingerprintOP

typedef utility::pointer::shared_ptr < PlaidFingerprint const >	PlaidFingerprintCOP

typedef utility::pointer::shared_ptr < FingerprintManager >	FingerprintManagerOP

typedef utility::pointer::shared_ptr < FingerprintManager const >	FingerprintManagerCOP

typedef utility::pointer::shared_ptr < PocketConstraint >	PocketConstraintOP

typedef utility::pointer::shared_ptr < PocketGrid >	PocketGridOP

typedef utility::pointer::shared_ptr < PocketGrid const >	PocketGridCOP

Functions
double	dD_dv1 (const double x0, const double x2, const double x3, const double y0, const double y2, const double y3, const double z0, const double z2, const double z3, const double r)

double	dD_dv2 (const double x0, const double x2, const double x3, const double y0, const double y2, const double y3, const double z0, const double z2, const double z3, const double r)

double	dD_dv3 (const double x0, const double x2, const double x3, const double y0, const double y2, const double y3, const double z0, const double z2, const double z3, const double r)

double	dD_dv4 (const double x0, const double x2, const double x3, const double y0, const double y2, const double y3, const double z0, const double z2, const double z3, const double r, const double v4, const double v5, const double v6, const double, const double, const double yc, const double ys, const double zc, const double zs)

double	dD_dv5 (const double x0, const double x2, const double x3, const double y0, const double y2, const double y3, const double z0, const double z2, const double z3, const double r, const double v4, const double v5, const double v6, const double xc, const double xs, const double yc, const double ys, const double zc, const double zs)

double	dD_dv6 (const double x0, const double x2, const double x3, const double y0, const double y2, const double y3, const double z0, const double z2, const double z3, const double r, const double v4, const double v5, const double v6, const double xc, const double xs, const double yc, const double ys, const double zc, const double zs)

core::Real	Find_Closest_Intersect_SQ (core::Real const &phiAngle, core::Real const &psiAngle, core::Real const &atomX, core::Real const &atomY, core::Real const &atomZ, core::Real const &atom_radius)

void	convert_cartesian_to_spherical_coor_triplet (numeric::xyzVector< core::Real > const &coord, spherical_coor_triplet &triplet)

void	convert_spherical_coor_triplet_to_cartesian (spherical_coor_triplet const &triplet, numeric::xyzVector< core::Real > &coord)

void	convert_cartesian_to_grid (numeric::xyzVector< core::Real > const &cart_coord, numeric::xyzVector< core::Real > const &mid, numeric::xyzVector< core::Real > const &dim, core::Real const &spacing, numeric::xyzVector< core::Real > &grid_coord)

void	convert_grid_to_cartesian (numeric::xyzVector< core::Real > const &grid_coord, numeric::xyzVector< core::Real > const &mid, numeric::xyzVector< core::Real > const &dim, core::Real const &spacing, numeric::xyzVector< core::Real > &cart_coord)

core::Real	calDist (vector< core::Real > const &a1, vector< core::Real > const &a2)

static thread_local basic::Tracer	TR ("core.scoring.constraints.PocketConstraint")

void	convert_cartesian_to_grid (numeric::xyzVector< core::Real > const &cart_coord, numeric::xyzVector< core::Real > const &mid, numeric::xyzVector< core::Size > const &dim, core::Real const &spacing, numeric::xyzVector< core::Real > &grid_coord)

void	convert_grid_to_cartesian (numeric::xyzVector< core::Real > &grid_coord, numeric::xyzVector< core::Real > const &mid, numeric::xyzVector< core::Size > const &dim, core::Real const &spacing, numeric::xyzVector< core::Real > &cart_coord)

Variables
static basic::Tracer	TR ("core.grid.Pockets.PocketGrid")

Typedef Documentation

typedef utility::pointer::shared_ptr< DarcParticleSwarmMinimizer const > protocols::pockets::DarcParticleSwarmMinimizerCOP

typedef utility::pointer::shared_ptr< DarcParticleSwarmMinimizer > protocols::pockets::DarcParticleSwarmMinimizerOP

typedef utility::pointer::shared_ptr< FingerprintManager const > protocols::pockets::FingerprintManagerCOP

typedef utility::pointer::shared_ptr< FingerprintManager > protocols::pockets::FingerprintManagerOP

typedef utility::pointer::shared_ptr< NonPlaidFingerprint const > protocols::pockets::NonPlaidFingerprintCOP

typedef utility::pointer::shared_ptr< NonPlaidFingerprint > protocols::pockets::NonPlaidFingerprintOP

typedef utility::pointer::shared_ptr< PlaidFingerprint const > protocols::pockets::PlaidFingerprintCOP

typedef utility::pointer::shared_ptr< PlaidFingerprint > protocols::pockets::PlaidFingerprintOP

typedef utility::pointer::shared_ptr< PocketConstraint > protocols::pockets::PocketConstraintOP

typedef utility::pointer::shared_ptr< PocketGrid const > protocols::pockets::PocketGridCOP

typedef utility::pointer::shared_ptr< PocketGrid > protocols::pockets::PocketGridOP

Function Documentation

core::Real protocols::pockets::calDist	(	vector< core::Real > const &	a1,
		vector< core::Real > const &	a2
	)

References cout, exit, and protocols::analysis::total.

Referenced by protocols::pockets::SmallMol::cal_min_dist(), and protocols::pockets::SmallMol::calRMSD().

void protocols::pockets::convert_cartesian_to_grid	(	numeric::xyzVector< core::Real > const &	cart_coord,
		numeric::xyzVector< core::Real > const &	mid,
		numeric::xyzVector< core::Real > const &	dim,
		core::Real const &	spacing,
		numeric::xyzVector< core::Real > &	grid_coord
	)

inline

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

Referenced by protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_protein_grid_points(), protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_surface_grid_points_by_nn(), protocols::pockets::EggshellGrid::get_connolly_eggshell(), protocols::pockets::PocketGrid::get_connolly_surfacePoints_within_grid(), protocols::pockets::NonPlaidFingerprint::get_interpolated_esp_energy(), and protocols::pockets::NonPlaidFingerprint::get_interpolated_esp_energy_with_type().

void protocols::pockets::convert_cartesian_to_grid	(	numeric::xyzVector< core::Real > const &	cart_coord,
		numeric::xyzVector< core::Real > const &	mid,
		numeric::xyzVector< core::Size > const &	dim,
		core::Real const &	spacing,
		numeric::xyzVector< core::Real > &	grid_coord
	)

inline

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

void protocols::pockets::convert_cartesian_to_spherical_coor_triplet	(	numeric::xyzVector< core::Real > const &	coord,
		spherical_coor_triplet &	triplet
	)

inline

References protocols::pockets::spherical_coor_triplet::phi, protocols::pockets::spherical_coor_triplet::psi, protocols::pockets::spherical_coor_triplet::rho, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by protocols::pockets::NonPlaidFingerprint::convert_cart_to_spherical_and_round(), protocols::pockets::DarcParticleSwarmMinimizer::fill_atom_arrays_(), protocols::pockets::NonPlaidFingerprint::get_Rvalue(), protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_pdb_file(), protocols::pockets::NonPlaidFingerprint::setup_from_EggshellGrid(), and protocols::pockets::PlaidFingerprint::update_rhos_().

void protocols::pockets::convert_grid_to_cartesian	(	numeric::xyzVector< core::Real > const &	grid_coord,
		numeric::xyzVector< core::Real > const &	mid,
		numeric::xyzVector< core::Real > const &	dim,
		core::Real const &	spacing,
		numeric::xyzVector< core::Real > &	cart_coord
	)

inline

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

Referenced by protocols::pockets::EggshellGrid::get_connolly_eggshell_on_grid().

void protocols::pockets::convert_grid_to_cartesian	(	numeric::xyzVector< core::Real > &	grid_coord,
		numeric::xyzVector< core::Real > const &	mid,
		numeric::xyzVector< core::Size > const &	dim,
		core::Real const &	spacing,
		numeric::xyzVector< core::Real > &	cart_coord
	)

inline

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

void protocols::pockets::convert_spherical_coor_triplet_to_cartesian	(	spherical_coor_triplet const &	triplet,
		numeric::xyzVector< core::Real > &	coord
	)

inline

References protocols::pockets::spherical_coor_triplet::phi, protocols::pockets::spherical_coor_triplet::psi, protocols::pockets::spherical_coor_triplet::rho, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by protocols::pockets::NonPlaidFingerprint::convert_spherical_list_to_cartesian_list(), protocols::pockets::FingerprintBase::print_to_pdb(), and protocols::pockets::NonPlaidFingerprint::trim_based_on_known_ligand().

double protocols::pockets::dD_dv1	(	const double	x0,
		const double	x2,
		const double	x3,
		const double	y0,
		const double	y2,
		const double	y3,
		const double	z0,
		const double	z2,
		const double	z3,
		const double	r
	)

References a(), protocols::match::upstream::b, and c.

Referenced by dD_dv4(), dD_dv5(), and dD_dv6().

double protocols::pockets::dD_dv2	(	const double	x0,
		const double	x2,
		const double	x3,
		const double	y0,
		const double	y2,
		const double	y3,
		const double	z0,
		const double	z2,
		const double	z3,
		const double	r
	)

References a(), protocols::match::upstream::b, and c.

Referenced by dD_dv4(), dD_dv5(), and dD_dv6().

double protocols::pockets::dD_dv3	(	const double	x0,
		const double	x2,
		const double	x3,
		const double	y0,
		const double	y2,
		const double	y3,
		const double	z0,
		const double	z2,
		const double	z3,
		const double	r
	)

References a(), protocols::match::upstream::b, and c.

Referenced by dD_dv4(), dD_dv5(), and dD_dv6().

double protocols::pockets::dD_dv4	(	const double	x0,
		const double	x2,
		const double	x3,
		const double	y0,
		const double	y2,
		const double	y3,
		const double	z0,
		const double	z2,
		const double	z3,
		const double	r,
		const double	v4,
		const double	v5,
		const double	v6,
		const double	,
		const double	,
		const double	yc,
		const double	ys,
		const double	zc,
		const double	zs
	)

References dD_dv1(), dD_dv2(), and dD_dv3().

double protocols::pockets::dD_dv5	(	const double	x0,
		const double	x2,
		const double	x3,
		const double	y0,
		const double	y2,
		const double	y3,
		const double	z0,
		const double	z2,
		const double	z3,
		const double	r,
		const double	v4,
		const double	v5,
		const double	v6,
		const double	xc,
		const double	xs,
		const double	yc,
		const double	ys,
		const double	zc,
		const double	zs
	)

References dD_dv1(), dD_dv2(), and dD_dv3().

double protocols::pockets::dD_dv6	(	const double	x0,
		const double	x2,
		const double	x3,
		const double	y0,
		const double	y2,
		const double	y3,
		const double	z0,
		const double	z2,
		const double	z3,
		const double	r,
		const double	v4,
		const double	v5,
		const double	v6,
		const double	xc,
		const double	xs,
		const double	yc,
		const double	ys,
		const double	zc,
		const double	zs
	)

References dD_dv1(), dD_dv2(), and dD_dv3().

core::Real protocols::pockets::Find_Closest_Intersect_SQ	(	core::Real const &	phiAngle,
		core::Real const &	psiAngle,
		core::Real const &	atomX,
		core::Real const &	atomY,
		core::Real const &	atomZ,
		core::Real const &	atom_radius
	)

References a(), protocols::match::upstream::b, and c.

Referenced by protocols::pockets::DarcParticleSwarmMinimizer::DarcPSO_fp_compare_(), and protocols::pockets::PlaidFingerprint::update_rhos_().

static thread_local basic::Tracer protocols::pockets::TR ( "core.scoring.constraints.PocketConstraint" )

static

Variable Documentation

basic::Tracer protocols::pockets::TR("core.grid.Pockets.PocketGrid")

static

Referenced by protocols::pockets::EggshellGrid::EggshellGrid(), protocols::pockets::PocketConstraint::fill_f1_f2(), protocols::pockets::EggshellGrid::get_eggshell_distance(), protocols::pockets::PocketGrid::get_pocket_distance(), protocols::pockets::PocketGrid::newSearch(), protocols::pockets::PocketGrid::print(), protocols::pockets::PocketGrid::recenter(), and protocols::pockets::PocketConstraint::score().

Classes

Typedefs

Functions

Variables

Typedef Documentation

Function Documentation

Variable Documentation