Uses of Class
org.proteinshader.structure.Bond

Packages that use Bond

org.proteinshader.graphics.adapter	Holds the StructureToGraphics class, which is used to manage the use of the drawing classes and OpenGL display lists.
org.proteinshader.structure	Holds the classes that store information from a Protein Data Bank file: Structure, Model, Chain, AminoAcid, Heterogen, Water, Atom, Bond, Helix, BetaStrand, Loop, etc.
org.proteinshader.structure.visitor	Holds Visitor classes that know how to traverse the hierarchy of objects held by class Structure.

Uses of Bond in org.proteinshader.graphics.adapter

Methods in org.proteinshader.graphics.adapter with parameters of type Bond

void	StructureToGraphics.draw(GL gl, Bond bond) Draws the Bond as a single cylinder for a Balls-and-Sticks style display, but two cylinders for a Sticks style display.

Uses of Bond in org.proteinshader.structure

Methods in org.proteinshader.structure that return Bond

Bond	Atom.getBond(Atom dstAtom) Returns the Bond from this Atom (the source) to the destination Atom.

Methods in org.proteinshader.structure that return types with arguments of type Bond

Iterator<Bond>

Atom.iteratorBonds() Returns an Iterator for the Bonds held by this Atom.

Methods in org.proteinshader.structure with parameters of type Bond

void	Atom.removeBond(Bond bond) Removes the Bond if it exists.

Uses of Bond in org.proteinshader.structure.visitor

Methods in org.proteinshader.structure.visitor with parameters of type Bond

void	ModifierVisitor.visit(Bond bond) If a BondModifier has been added, it will be used to modify the Bond.
void	Visitor.visit(Bond bond) If debug is true, the atomID of both the source Atom and the destination Atom will be printed to standard out.
void	SFWriterVisitor.visit(Bond bond) Writes all information held by a Bond.
void	VisibilityVisitor.visit(Bond bond) Tests the visiblity of the Bond in order to determine if it should be transferred to the opaque Atoms and Bonds or translucent Drawables list.
void	BondGeneratorVisitor.visit(Bond bond) NO OPERATION: This Visitor method is not needed by the bond generator.