Classes
class	DarcParticleSwarmMinimizer

struct	spherical_coor_triplet

struct	triplet_and_originnum

struct	ray_distance_derivs

class	FingerprintBase

class	NonPlaidFingerprint

class	PlaidFingerprint

class	FingerprintMultifunc
	Atom tree multifunction class. More...

class	SmallMol

class	UnionEdge

class	GenPharmacophore

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	PCluster
	@ Cluster of Pocket points More...

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

class	CCluster
	@ Cluster of exemplar points More...

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

class	PocketGrid
	@ More...

class	TargetPocketGrid
	@ More...

class	EggshellGrid
	@ More...

class	ElectrostaticpotentialGrid

class	ComparisonGrid
	@ More...

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
core::Real	dD_dv1 (const core::Real x0, const core::Real x2, const core::Real x3, const core::Real y0, const core::Real y2, const core::Real y3, const core::Real z0, const core::Real z2, const core::Real z3, const core::Real r)

core::Real	dD_dv2 (const core::Real x0, const core::Real x2, const core::Real x3, const core::Real y0, const core::Real y2, const core::Real y3, const core::Real z0, const core::Real z2, const core::Real z3, const core::Real r)

core::Real	dD_dv3 (const core::Real x0, const core::Real x2, const core::Real x3, const core::Real y0, const core::Real y2, const core::Real y3, const core::Real z0, const core::Real z2, const core::Real z3, const core::Real r)

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

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

core::Real	dD_dv6 (const core::Real x0, const core::Real x2, const core::Real x3, const core::Real y0, const core::Real y2, const core::Real y3, const core::Real z0, const core::Real z2, const core::Real z3, const core::Real r, const core::Real v4, const core::Real v5, const core::Real v6, const core::Real xc, const core::Real xs, const core::Real yc, const core::Real ys, const core::Real zc, const core::Real 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 basic::Tracer	TR ("core.scoring.constraints.PocketConstraint")

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

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)

Typedef Documentation

◆ DarcParticleSwarmMinimizerCOP

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

◆ DarcParticleSwarmMinimizerOP

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

◆ FingerprintManagerCOP

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

◆ FingerprintManagerOP

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

◆ NonPlaidFingerprintCOP

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

◆ NonPlaidFingerprintOP

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

◆ PlaidFingerprintCOP

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

◆ PlaidFingerprintOP

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

◆ PocketConstraintOP

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

◆ PocketGridCOP

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

◆ PocketGridOP

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

Function Documentation

◆ calDist()

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

References protocols::analysis::total.

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

◆ convert_cartesian_to_grid() [1/2]

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

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().

◆ convert_cartesian_to_grid() [2/2]

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

◆ convert_cartesian_to_spherical_coor_triplet()

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, and protocols::pockets::spherical_coor_triplet::rho.

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_().

◆ convert_grid_to_cartesian() [1/2]

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

◆ convert_grid_to_cartesian() [2/2]

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

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

◆ convert_spherical_coor_triplet_to_cartesian()

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, and protocols::pockets::spherical_coor_triplet::rho.

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().

◆ dD_dv1()

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

References core::pose::motif::a(), protocols::match::upstream::b, and protocols::hybridization::u.

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

◆ dD_dv2()

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

References core::pose::motif::a(), protocols::match::upstream::b, and protocols::hybridization::u.

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

◆ dD_dv3()

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

References core::pose::motif::a(), protocols::match::upstream::b, and protocols::hybridization::u.

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

◆ dD_dv4()

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

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

◆ dD_dv5()

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

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

◆ dD_dv6()

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

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

◆ Find_Closest_Intersect_SQ()

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 core::pose::motif::a(), and protocols::match::upstream::b.

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

◆ TR() [1/2]

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

static

◆ TR() [2/2]

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

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

Typedef Documentation

◆ DarcParticleSwarmMinimizerCOP

◆ DarcParticleSwarmMinimizerOP

◆ FingerprintManagerCOP

◆ FingerprintManagerOP

◆ NonPlaidFingerprintCOP

◆ NonPlaidFingerprintOP

◆ PlaidFingerprintCOP

◆ PlaidFingerprintOP

◆ PocketConstraintOP

◆ PocketGridCOP

◆ PocketGridOP

Function Documentation

◆ calDist()

◆ convert_cartesian_to_grid() [1/2]

◆ convert_cartesian_to_grid() [2/2]

◆ convert_cartesian_to_spherical_coor_triplet()

◆ convert_grid_to_cartesian() [1/2]

◆ convert_grid_to_cartesian() [2/2]

◆ convert_spherical_coor_triplet_to_cartesian()

◆ dD_dv1()

◆ dD_dv2()

◆ dD_dv3()

◆ dD_dv4()

◆ dD_dv5()

◆ dD_dv6()

◆ Find_Closest_Intersect_SQ()

◆ TR() [1/2]

◆ TR() [2/2]