Classes
class	DarcElectrostaticsBase

class	DelphiElectrostatics

class	DarcParticleSwarmMinimizer

struct	spherical_coor_triplet

struct	ray_distance_derivs

class	FingerprintBase

class	NonPlaidFingerprint

class	PlaidFingerprint

class	FingerprintMultifunc
	Atom tree multifunction class. More...

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

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

class	PCluster
	@ More...

class	PClusterSet
	@ More...

class	PocketGrid
	@ More...

class	EggshellGrid
	@ More...

Typedefs
typedef utility::pointer::owning_ptr < DelphiElectrostatics >	DelphiElectrostaticsOP

typedef utility::pointer::owning_ptr < DelphiElectrostatics const >	DelphiElectrostaticsCOP

typedef utility::pointer::owning_ptr < DarcParticleSwarmMinimizer >	DarcParticleSwarmMinimizerOP

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

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

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

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

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

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

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

typedef utility::pointer::owning_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)

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

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

Typedef Documentation

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

Definition at line 30 of file DarcParticleSwarmMinimizer.fwd.hh.

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

Definition at line 28 of file DarcParticleSwarmMinimizer.fwd.hh.

typedef utility::pointer::owning_ptr< DelphiElectrostatics const > protocols::pockets::DelphiElectrostaticsCOP

Definition at line 32 of file DarcElectrostatics.fwd.hh.

typedef utility::pointer::owning_ptr< DelphiElectrostatics > protocols::pockets::DelphiElectrostaticsOP

Definition at line 28 of file DarcElectrostatics.fwd.hh.

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

Definition at line 33 of file Fingerprint.fwd.hh.

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

Definition at line 29 of file Fingerprint.fwd.hh.

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

Definition at line 35 of file Fingerprint.fwd.hh.

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

Definition at line 34 of file Fingerprint.fwd.hh.

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

Definition at line 27 of file PocketConstraint.fwd.hh.

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

Definition at line 35 of file PocketGrid.fwd.hh.

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

Definition at line 31 of file PocketGrid.fwd.hh.

Function Documentation

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

inline

Definition at line 222 of file Fingerprint.hh.

References protocols::pockets::spherical_coor_triplet::phi, protocols::pockets::spherical_coor_triplet::psi, and protocols::pockets::spherical_coor_triplet::rho.

Referenced by 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_spherical_coor_triplet_to_cartesian	(	spherical_coor_triplet const &	triplet,
		numeric::xyzVector< core::Real > &	coord
	)

inline

Definition at line 229 of file Fingerprint.hh.

References protocols::pockets::spherical_coor_triplet::phi, protocols::pockets::spherical_coor_triplet::psi, and protocols::pockets::spherical_coor_triplet::rho.

Referenced by 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
	)

Definition at line 1480 of file Fingerprint.cc.

References protocols::match::upstream::b, and core::pack::dunbrack::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
	)

Definition at line 1519 of file Fingerprint.cc.

References protocols::match::upstream::b, and core::pack::dunbrack::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
	)

Definition at line 1556 of file Fingerprint.cc.

References protocols::match::upstream::b, and core::pack::dunbrack::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
	)

Definition at line 1593 of file Fingerprint.cc.

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
	)

Definition at line 1608 of file Fingerprint.cc.

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
	)

Definition at line 1623 of file Fingerprint.cc.

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
	)

Definition at line 1638 of file Fingerprint.cc.

References protocols::match::upstream::b, and core::pack::dunbrack::c.

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

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

static

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

static

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

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation