#include <ActiveSiteGrid.hh>

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

Collaboration diagram for protocols::match::downstream::ActiveSiteGrid:

Public Types
typedef utility::pointer::ReferenceCount	parent

typedef core::Size	Size

typedef core::Real	Real

typedef core::Vector	Vector

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

Public Member Functions
virtual	~ActiveSiteGrid ()

	ActiveSiteGrid ()

	ActiveSiteGrid (ActiveSiteGrid const &)

ActiveSiteGrid const &	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_

Detailed Description

Definition at line 43 of file ActiveSiteGrid.hh.

Member Typedef Documentation

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

Definition at line 49 of file ActiveSiteGrid.hh.

typedef utility::pointer::ReferenceCount protocols::match::downstream::ActiveSiteGrid::parent

Definition at line 45 of file ActiveSiteGrid.hh.

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

Definition at line 47 of file ActiveSiteGrid.hh.

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

Definition at line 46 of file ActiveSiteGrid.hh.

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

Definition at line 48 of file ActiveSiteGrid.hh.

Constructor & Destructor Documentation

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

virtual

Definition at line 41 of file ActiveSiteGrid.cc.

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

Definition at line 43 of file ActiveSiteGrid.cc.

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

Definition at line 51 of file ActiveSiteGrid.cc.

Member Function Documentation

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

inline

Accessor for the bounding box.

Definition at line 69 of file ActiveSiteGrid.hh.

References bb_.

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

Reset all the voxels to false.

Definition at line 218 of file ActiveSiteGrid.cc.

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.

Definition at line 256 of file ActiveSiteGrid.cc.

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.

Definition at line 224 of file ActiveSiteGrid.cc.

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.

Definition at line 240 of file ActiveSiteGrid.cc.

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

Definition at line 202 of file ActiveSiteGrid.cc.

References grid_, and reset_grid_bb_.

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

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

Definition at line 309 of file ActiveSiteGrid.cc.

References prep_grid().

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

Definition at line 73 of file ActiveSiteGrid.cc.

References bb_, bin_width_, protocols::abinitio::filename(), grid_, occupied(), reset_grid_bb_, and core::io::serialization::size().

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.

Definition at line 211 of file ActiveSiteGrid.cc.

References grid_.

Referenced by initialize_from_gridlig_file().

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

Definition at line 61 of file ActiveSiteGrid.cc.

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.

Definition at line 298 of file ActiveSiteGrid.cc.

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.

Definition at line 272 of file ActiveSiteGrid.cc.

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.

Definition at line 285 of file ActiveSiteGrid.cc.

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.

Definition at line 343 of file ActiveSiteGrid.cc.

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)

Definition at line 195 of file ActiveSiteGrid.cc.

References bin_width_, and grid_.

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

Set the bounding box for this grid.

Definition at line 188 of file ActiveSiteGrid.cc.

References bb_, and grid_.