#include <BumpGrid.hh>

Inheritance diagram for protocols::match::BumpGrid:

Collaboration diagram for protocols::match::BumpGrid:

Public Types
typedef Bool3DGrid::BoundingBox	BoundingBox

typedef Bool3DGrid::Bin3D	Bin3D

typedef Bool3DGrid::Vector	Vector

typedef std::pair< Vector, core::Real >	Sphere

typedef core::Real	Real

typedef utility::pointer::ReferenceCount	parent

Public Member Functions
	BumpGrid ()

	BumpGrid (BumpGrid const &)

virtual	~BumpGrid ()

BumpGrid const &	operator= (BumpGrid const &)

void	set_bounding_box (BoundingBox const &bb)
	Initialization. More...

void	set_general_overlap_tolerance (Real tolerated_overlap)
	Set the tolerance for sphere overlap between all sphere types. All tolerances must be set before any spheres are ORed into the grid. More...

void	set_pair_overlap_tolerance (ProbeRadius rad1, ProbeRadius rad2, Real tolerated_overlap)
	Set the overlap tolerance for a specific pair of sphere types (e.g. OXY/NIT) The specific tolerance is combined with the general overlap tolerance. All tolerances must be set before any spheres are ORed into the grid. More...

BumpGrid	create_bump_grid_for_bb (BoundingBox const &bb) const

BumpGridOP	create_new_bump_grid_for_bb (BoundingBox const &bb) const

void	or_with (BumpGrid const &)

void	and_with (BumpGrid const &)

void	or_by_sphere (Sphere const &)

void	or_by_sphere (Vector const &center, ProbeRadius radius_type)

bool	overlaps (BumpGrid const &) const

bool	occupied (ProbeRadius radius_type, Vector const &p) const
	Collision detection by a point p with a given (fixed) radius type. Collision detection is performed in "configuration space", where the obstacles have been convolved with a spherical probe of a given radius. This collision detection is conservative: it will not report a collision to exist that does not, but may miss a collision that does exist. More...

Real	pair_overlap_tolerance (ProbeRadius rad1, ProbeRadius rad2) const

Bool3DGrid const &	grid (ProbeRadius radtype) const

Real	required_separation_distance (ProbeRadius rad1, ProbeRadius rad2) const

Static Public Member Functions
static Real	probe_radius (ProbeRadius radtype)

Private Attributes
utility::vector1< Bool3DGridOP >	grids_

utility::vector1 < utility::vector1< Real > >	pair_permit_overlap_
	allow some pairs of atom types to overlap by a certain amount – e.g. O and N More...

Real	general_permit_overlap_
	allow all pairs of atom types to overlap by a certain amount More...

Detailed Description

Definition at line 203 of file BumpGrid.hh.

Member Typedef Documentation

typedef Bool3DGrid::Bin3D protocols::match::BumpGrid::Bin3D

Definition at line 207 of file BumpGrid.hh.

typedef Bool3DGrid::BoundingBox protocols::match::BumpGrid::BoundingBox

Definition at line 206 of file BumpGrid.hh.

typedef utility::pointer::ReferenceCount protocols::match::BumpGrid::parent

Definition at line 211 of file BumpGrid.hh.

typedef core::Real protocols::match::BumpGrid::Real

Definition at line 210 of file BumpGrid.hh.

typedef std::pair< Vector, core::Real > protocols::match::BumpGrid::Sphere

Definition at line 209 of file BumpGrid.hh.

typedef Bool3DGrid::Vector protocols::match::BumpGrid::Vector

Definition at line 208 of file BumpGrid.hh.

Constructor & Destructor Documentation

protocols::match::BumpGrid::BumpGrid ( )

Definition at line 926 of file BumpGrid.cc.

References core::sequence::end, grids_, protocols::match::n_probe_radii, and pair_permit_overlap_.

Referenced by create_new_bump_grid_for_bb().

protocols::match::BumpGrid::BumpGrid ( BumpGrid const & rhs)

Definition at line 956 of file BumpGrid.cc.

References grids_, and protocols::match::n_probe_radii.

protocols::match::BumpGrid::~BumpGrid ( )

virtual

Definition at line 967 of file BumpGrid.cc.

Member Function Documentation

void protocols::match::BumpGrid::and_with ( BumpGrid const & other)

Definition at line 1038 of file BumpGrid.cc.

References grids_, and protocols::match::n_probe_radii.

BumpGrid protocols::match::BumpGrid::create_bump_grid_for_bb ( BoundingBox const & bb) const

The input bounding box is assumed to hold all of the (real space) spheres that should be represented. Create a larger bounding box big enough to hold all of the configuration space spheres.

Definition at line 1006 of file BumpGrid.cc.

References general_permit_overlap_, pair_permit_overlap_, and set_bounding_box().

BumpGridOP protocols::match::BumpGrid::create_new_bump_grid_for_bb ( BoundingBox const & bb) const

Definition at line 1019 of file BumpGrid.cc.

References BumpGrid(), general_permit_overlap_, and pair_permit_overlap_.

Referenced by protocols::match::bump_grid_to_enclose_residue(), and protocols::match::bump_grid_to_enclose_residue_backbone().

Bool3DGrid const& protocols::match::BumpGrid::grid ( ProbeRadius radtype) const

inline

Definition at line 273 of file BumpGrid.hh.

References grids_.

bool protocols::match::BumpGrid::occupied	(	ProbeRadius	radius_type,
		Vector const &	p
	)		const

Collision detection by a point p with a given (fixed) radius type. Collision detection is performed in "configuration space", where the obstacles have been convolved with a spherical probe of a given radius. This collision detection is conservative: it will not report a collision to exist that does not, but may miss a collision that does exist.

Definition at line 1084 of file BumpGrid.cc.

References contains, grids_, and protocols::match::ZERO.

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::atom_coordinate_unacceptable().

BumpGrid const & protocols::match::BumpGrid::operator= ( BumpGrid const & rhs)

Definition at line 969 of file BumpGrid.cc.

References general_permit_overlap_, grids_, protocols::match::n_probe_radii, and pair_permit_overlap_.

void protocols::match::BumpGrid::or_by_sphere ( Sphere const & input)

Input sphere is a real-space sphere – it's radius will be increased by the varying probe radii to create the varying configuration-space spheres.

Definition at line 1049 of file BumpGrid.cc.

References grids_, protocols::match::n_probe_radii, and probe_radius().

Referenced by protocols::match::fill_grid_with_backbone_heavyatom_spheres(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), and protocols::match::fill_grid_with_residue_spheres().

void protocols::match::BumpGrid::or_by_sphere	(	Vector const &	center,
		ProbeRadius	radius_type
	)

Definition at line 1057 of file BumpGrid.cc.

References grids_, protocols::match::n_probe_radii, required_separation_distance(), and protocols::match::ZERO.

void protocols::match::BumpGrid::or_with ( BumpGrid const & other)

Definition at line 1030 of file BumpGrid.cc.

References grids_, and protocols::match::n_probe_radii.

bool protocols::match::BumpGrid::overlaps ( BumpGrid const & other) const

Definition at line 1069 of file BumpGrid.cc.

References grids_, and protocols::match::n_probe_radii.

BumpGrid::Real protocols::match::BumpGrid::pair_overlap_tolerance	(	ProbeRadius	rad1,
		ProbeRadius	rad2
	)		const

Definition at line 1107 of file BumpGrid.cc.

References pair_permit_overlap_.

static Real protocols::match::BumpGrid::probe_radius ( ProbeRadius radtype)

inlinestatic

Definition at line 256 of file BumpGrid.hh.

References protocols::match::C_ALA, protocols::match::C_CAR, protocols::match::H_ALA, protocols::match::H_ARO, protocols::match::NIT, protocols::match::OXY, protocols::match::SULPH, and protocols::match::ZERO.

Referenced by protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue(), protocols::match::bump_grid_to_enclose_residue_backbone(), protocols::match::initialize_atomtype_2_probe_radius_map(), or_by_sphere(), required_separation_distance(), and set_bounding_box().

Real protocols::match::BumpGrid::required_separation_distance	(	ProbeRadius	rad1,
		ProbeRadius	rad2
	)		const

inline

Definition at line 279 of file BumpGrid.hh.

References general_permit_overlap_, pair_permit_overlap_, probe_radius(), and protocols::match::ZERO.

Referenced by protocols::match::downstream::DownstreamAlgorithm::are_colliding(), protocols::match::upstream::ProteinUpstreamBuilder::atom_coordinate_unacceptable(), protocols::match::downstream::RigidLigandBuilder::initialize_upstream_nonbonded_min_separation_d2(), protocols::match::downstream::LigandConformerBuilder::initialize_upstream_nonbonded_min_separation_d2(), and or_by_sphere().

void protocols::match::BumpGrid::set_bounding_box ( BoundingBox const & bb)

Initialization.

Definition at line 985 of file BumpGrid.cc.

References grids_, protocols::match::n_probe_radii, and probe_radius().

Referenced by create_bump_grid_for_bb().

void protocols::match::BumpGrid::set_general_overlap_tolerance ( Real tolerated_overlap)

Set the tolerance for sphere overlap between all sphere types. All tolerances must be set before any spheres are ORed into the grid.

Definition at line 1094 of file BumpGrid.cc.

References general_permit_overlap_.

void protocols::match::BumpGrid::set_pair_overlap_tolerance	(	ProbeRadius	rad1,
		ProbeRadius	rad2,
		Real	tolerated_overlap
	)

Set the overlap tolerance for a specific pair of sphere types (e.g. OXY/NIT) The specific tolerance is combined with the general overlap tolerance. All tolerances must be set before any spheres are ORed into the grid.

Definition at line 1100 of file BumpGrid.cc.

References pair_permit_overlap_.