Uses of Class
org.biojava.nbio.structure.contact.BoundingBox

Packages that use BoundingBox

Package	Description
org.biojava.nbio.structure.contact
org.biojava.nbio.structure.xtal

Uses of BoundingBox in org.biojava.nbio.structure.contact

Methods in org.biojava.nbio.structure.contact with parameters of type BoundingBox

Modifier and Type	Method	Description
void	Grid.addAtoms(Atom[] atoms, BoundingBox bounds)	Adds a set of atoms, subsequent call to Grid.getIndicesContacts() or Grid.getAtomContacts() will produce the interatomic contacts.
void	Grid.addAtoms(Atom[] iAtoms, BoundingBox icoordbounds, Atom[] jAtoms, BoundingBox jcoordbounds)	Adds the i and j atoms and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
void	Grid.addCoords(javax.vecmath.Point3d[] atoms, BoundingBox bounds)	Adds a set of coordinates, subsequent call to Grid.getIndicesContacts() will produce the contacts, i.e. the set of points within distance cutoff.
void	Grid.addCoords(javax.vecmath.Point3d[] iAtoms, BoundingBox icoordbounds, javax.vecmath.Point3d[] jAtoms, BoundingBox jcoordbounds)	Adds the i and j coordinates and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
boolean	BoundingBox.overlaps(BoundingBox o, double cutoff)	Returns true if this bounding box overlaps given one, i.e. they are within one cutoff distance in one of their 3 dimensions.

Constructors in org.biojava.nbio.structure.contact with parameters of type BoundingBox

Modifier	Constructor	Description
	BoundingBox(BoundingBox bb)
	BoundingBox(BoundingBox[] boxes)	Given a set of bounding boxes returns a bounding box that bounds all of them.

Uses of BoundingBox in org.biojava.nbio.structure.xtal

Methods in org.biojava.nbio.structure.xtal that return BoundingBox

Modifier and Type	Method	Description
BoundingBox	UnitCellBoundingBox.getAuBoundingBox(int cellIdx)	Get the AU BoundingBox for the given cell index (cellIdx=0 would be original AU) The AU BoundingBox is the BoundingBox that bounds all chains belonging to the AU
BoundingBox	UnitCellBoundingBox.getChainBoundingBox(int cellIdx, int chainIdx)	Get the chain BoundingBox for the given cell index (cellIdx=0 would be original AU) and chain index