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protocols::match::downstream::ActiveSiteGrid Class Reference

#include <ActiveSiteGrid.hh>

Inheritance diagram for protocols::match::downstream::ActiveSiteGrid:
Inheritance graph
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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 &)
 
ActiveSiteGridoperator= (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

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)
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_.

void protocols::match::downstream::ActiveSiteGrid::swell_bounding_box ( Vector  lower,
Vector  upper,
Real  radius 
)
private

Member Data Documentation

BoundingBox protocols::match::downstream::ActiveSiteGrid::bb_
private
Real protocols::match::downstream::ActiveSiteGrid::bin_width_
private
Bool3DGridOP protocols::match::downstream::ActiveSiteGrid::grid_
private
bool protocols::match::downstream::ActiveSiteGrid::reset_grid_bb_
private

The documentation for this class was generated from the following files: