#include <BumpGrid.hh>

Inheritance 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::VirtualBase	parent

Public Member Functions
	BumpGrid ()

	BumpGrid (BumpGrid const &)

	~BumpGrid () override

BumpGrid &	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...

Member Typedef Documentation

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

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

typedef utility::VirtualBase protocols::match::BumpGrid::parent

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

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

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

Constructor & Destructor Documentation

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

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

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

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

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

overridedefault

Member Function Documentation

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

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.

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

References 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

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.

References protocols::sparta::contains(), grids_, and protocols::match::ZERO.

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

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

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.

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
	)

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

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

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

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

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

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

References pair_permit_overlap_.

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

inlinestatic

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

References general_permit_overlap_, protocols::mean_field::max(), 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.

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.

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.

References pair_permit_overlap_.