#include <ActiveSiteGrid.hh>

Inheritance diagram for protocols::match::downstream::ActiveSiteGrid:

Public Types
typedef utility::VirtualBase	parent

typedef core::Size	Size

typedef core::Real	Real

typedef core::Vector	Vector

typedef numeric::geometry::BoundingBox < Vector >	BoundingBox

Public Member Functions
	~ActiveSiteGrid () override

	ActiveSiteGrid ()

	ActiveSiteGrid (ActiveSiteGrid const &)

ActiveSiteGrid &	operator= (ActiveSiteGrid const &rhs)

void	set_bounding_box (BoundingBox const &bb)
	Set the bounding box for this grid. More...

void	set_bin_width (Real width)

BoundingBox const &	bounding_box () const
	Accessor for the bounding box. More...

Bool3DGrid const &	grid () const

bool	occupied (Vector const &p) const
	Is a point in this grid active? False for a point outside the bounding box. More...

void	clear ()
	Reset all the voxels to false. More...

void	initialize_from_gridlig_file (std::string const &fname)

void	enlargen_to_capture_volume_within_radius_of_residue (core::conformation::Residue const &res, Real radius)
	Set the bounding box to be large enough to hold the volume within the radius of any atom in the given residue. This function has the side-effect of clearing the grid. More...

void	enlargen_to_capture_volume_within_radius_of_sidechain (core::conformation::Residue const &res, Real radius)
	Set the bounding box to be large enough to hold the volume within the radius of any sidechain atom in the given residue. This function has the side-effect of clearing the grid. More...

void	enlargen_to_capture_volume_within_radius_of_backbone (core::conformation::Residue const &res, Real radius)
	Set the bounding box to be large enough to hold the volume within the radius of any backbone atom in the given residue. This function has the side-effect of clearing the grid. More...

void	or_within_radius_of_residue (core::conformation::Residue const &res, Real radius)
	Set all the voxels within a certain radius of the residue atoms to true. More...

void	or_within_radius_of_sidechain (core::conformation::Residue const &res, Real radius)
	Set all the voxels within a certain radius of the sidechain atoms to true. More...

void	or_within_radius_of_backbone (core::conformation::Residue const &res, Real radius)
	Set all the voxels within a certain radius of the backbone atoms to true. More...

void	initialize ()
	Ensures the grid is up-to-date after any calls to enlargen_*. More...

Private Member Functions
void	swell_bounding_box (Vector lower, Vector upper, Real radius)
	Increase the size of the bounding box to contain a given volume. More...

void	prep_grid ()
	Ensure that the grid has the appropriate bounding box. This resets the grid if the object has modifications to its bounding box that have not yet been transfered to its grid. More...

Private Attributes
Real	bin_width_

BoundingBox	bb_

Bool3DGridOP	grid_

bool	reset_grid_bb_

Member Typedef Documentation

typedef numeric::geometry::BoundingBox< Vector > protocols::match::downstream::ActiveSiteGrid::BoundingBox

typedef utility::VirtualBase protocols::match::downstream::ActiveSiteGrid::parent

typedef core::Real protocols::match::downstream::ActiveSiteGrid::Real

typedef core::Size protocols::match::downstream::ActiveSiteGrid::Size

typedef core::Vector protocols::match::downstream::ActiveSiteGrid::Vector

Constructor & Destructor Documentation

protocols::match::downstream::ActiveSiteGrid::~ActiveSiteGrid ( )

overridedefault

protocols::match::downstream::ActiveSiteGrid::ActiveSiteGrid ( )

protocols::match::downstream::ActiveSiteGrid::ActiveSiteGrid ( ActiveSiteGrid const & other )

Member Function Documentation

BoundingBox const& protocols::match::downstream::ActiveSiteGrid::bounding_box ( ) const

inline

Accessor for the bounding box.

References bb_.

void protocols::match::downstream::ActiveSiteGrid::clear ( )

Reset all the voxels to false.

References grid_.

void protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_backbone	(	core::conformation::Residue const &	res,
		Real	radius
	)

Set the bounding box to be large enough to hold the volume within the radius of any backbone atom in the given residue. This function has the side-effect of clearing the grid.

References core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::nheavyatoms(), swell_bounding_box(), and core::conformation::Residue::xyz().

void protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_residue	(	core::conformation::Residue const &	res,
		Real	radius
	)

Set the bounding box to be large enough to hold the volume within the radius of any atom in the given residue. This function has the side-effect of clearing the grid.

References core::conformation::Residue::nheavyatoms(), swell_bounding_box(), and core::conformation::Residue::xyz().

void protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_sidechain	(	core::conformation::Residue const &	res,
		Real	radius
	)

Set the bounding box to be large enough to hold the volume within the radius of any sidechain atom in the given residue. This function has the side-effect of clearing the grid.

References core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::nheavyatoms(), swell_bounding_box(), and core::conformation::Residue::xyz().

Bool3DGrid const & protocols::match::downstream::ActiveSiteGrid::grid ( ) const

References grid_, and reset_grid_bb_.

void protocols::match::downstream::ActiveSiteGrid::initialize ( )

Ensures the grid is up-to-date after any calls to enlargen_*.

References prep_grid().

void protocols::match::downstream::ActiveSiteGrid::initialize_from_gridlig_file ( std::string const & fname )

References bb_, bin_width_, protocols::abinitio::filename(), grid_, occupied(), reset_grid_bb_, and core::id::to_string().

bool protocols::match::downstream::ActiveSiteGrid::occupied ( Vector const & p ) const

Is a point in this grid active? False for a point outside the bounding box.

References grid_.

Referenced by initialize_from_gridlig_file().

ActiveSiteGrid & protocols::match::downstream::ActiveSiteGrid::operator= ( ActiveSiteGrid const & rhs )

References bb_, bin_width_, grid_, and reset_grid_bb_.

void protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_backbone	(	core::conformation::Residue const &	res,
		Real	radius
	)

Set all the voxels within a certain radius of the backbone atoms to true.

References core::conformation::Residue::first_sidechain_atom(), grid_, prep_grid(), and core::conformation::Residue::xyz().

void protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_residue	(	core::conformation::Residue const &	res,
		Real	radius
	)

Set all the voxels within a certain radius of the residue atoms to true.

References grid_, core::conformation::Residue::nheavyatoms(), prep_grid(), and core::conformation::Residue::xyz().

void protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_sidechain	(	core::conformation::Residue const &	res,
		Real	radius
	)

Set all the voxels within a certain radius of the sidechain atoms to true.

References core::conformation::Residue::first_sidechain_atom(), grid_, core::conformation::Residue::nheavyatoms(), prep_grid(), and core::conformation::Residue::xyz().

void protocols::match::downstream::ActiveSiteGrid::prep_grid ( )

private

Ensure that the grid has the appropriate bounding box. This resets the grid if the object has modifications to its bounding box that have not yet been transfered to its grid.

References bb_, bin_width_, grid_, and reset_grid_bb_.

Referenced by initialize(), or_within_radius_of_backbone(), or_within_radius_of_residue(), and or_within_radius_of_sidechain().

void protocols::match::downstream::ActiveSiteGrid::set_bin_width ( Real width )

References bin_width_, and grid_.

void protocols::match::downstream::ActiveSiteGrid::set_bounding_box ( BoundingBox const & bb )

Set the bounding box for this grid.

References bb_, and grid_.