Uses of Class
edu.sdsc.mbt.Bond

Packages that use Bond

edu.sdsc.mbt
edu.sdsc.mbt.viewables	This package provides classes which enable molecular biology data to be represented as visible/renderable viewable objects, plus, this package defines a top-level StructureDocument object to encapsulate the complete state of these objects and properties.
edu.sdsc.mbt.viewers.GLViewerImpl
edu.sdsc.sirius.util

Uses of Bond in edu.sdsc.mbt

Methods in edu.sdsc.mbt that return Bond

Bond	StructureMap.getBond(int bondIndex) Get the Bond at the specified index.

Methods in edu.sdsc.mbt with parameters of type Bond

int	StructureMap.getBondIndex(Bond bond) Get the index of the specified Bond.
void	StructureMap.addBond(Bond bond) Add a Bond to the StructureMap.
void	StructureMap.addAtom(Atom added, Atom bonded, Bond b, boolean assignName)
void	StructureMap.addAtom(Atom added, Atom bonded, Bond b, int number)
void	StructureMap.removeBond(Bond bond) Remove a Bond from the StructureMap.
java.util.Vector	StructureMap.getBonds(Bond bond) Return a Vector of bonds that are neighbors of the argument

Uses of Bond in edu.sdsc.mbt.viewables

Methods in edu.sdsc.mbt.viewables with parameters of type Bond

double	BondRadiusByScaledAtomRadius.getBondRadius(Bond bond) Produce the primary radius based upon the first atom radius.
double	BondRadiusByScaledAtomRadius.getSplitBondRadius(Bond bond) Produce the secondary radius based upon the second atom radius.
double	BondRadiusByAtomRadius.getBondRadius(Bond bond) Produce the primary radius based upon the first atom radius.
double	BondRadiusByAtomRadius.getSplitBondRadius(Bond bond) Produce the secondary radius based upon the second atom radius.
double	BondRadiusAsWire.getBondRadius(Bond bond) Produce the primary radius (in pixel units) as a constant value.
double	BondRadiusAsWire.getSplitBondRadius(Bond bond) Produce the secondary radius (in pixel units) as a constant value.
double	BondRadiusAsStick.getBondRadius(Bond bond) Produce the primary radius (in pixel units) as a constant value.
double	BondRadiusAsStick.getSplitBondRadius(Bond bond) Produce the secondary radius (in pixel units) as a constant value.
double	BondRadius.getBondRadius(Bond bond) Provides the primary radius for a bond.
double	BondRadius.getSplitBondRadius(Bond bond) Provides the secondary radius for a SPLIT bond (@see BondForm).
java.lang.String	BondLabelNone.getBondLabel(Bond bond) Produce a null label.
java.lang.String	BondLabelByDistance.getBondLabel(Bond bond) Produce a label based upon the bond atom distance.
java.lang.String	BondLabel.getBondLabel(Bond bond)
int	BondFormSplit.getBondForm(Bond bond)
int	BondFormSimple.getBondForm(Bond bond)
int	BondFormOrder.getBondForm(Bond bond)
int	BondForm.getBondForm(Bond bond)
void	BondColorByElement.getBondColor(Bond bond, float[] color)
void	BondColorByElement.getSplitBondColor(Bond bond, float[] color)
void	BondColorByAtomColor.getBondColor(Bond bond, float[] color)
void	BondColorByAtomColor.getSplitBondColor(Bond bond, float[] color)
void	BondColor.getBondColor(Bond bond, float[] color) Provides the primary color for a bond.
void	BondColor.getSplitBondColor(Bond bond, float[] color) Provides the secondary color for a SPLIT bond (@see BondForm).

Uses of Bond in edu.sdsc.mbt.viewers.GLViewerImpl

Methods in edu.sdsc.mbt.viewers.GLViewerImpl with parameters of type Bond

static double[]	BondGeometryUtils.getDisplacementVector(Bond bond, double[] direction, double spacing)
static boolean	BondGeometryUtils.isTerminalBond(Bond bond)
void	BondGeometry.draw(Bond bond, StructureStyles structureStyles, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut) Please complete the missing tags for main

Uses of Bond in edu.sdsc.sirius.util

Methods in edu.sdsc.sirius.util with parameters of type Bond

static Location	StructureMath.getBondLocation(Bond bond) Returns a location of the bond, with the lookAt vector pointed along the bond and the up vector being orthogonal to the plane of the bond and one of the atoms the third vector is computed automatically The position is at the heavy atom
static java.util.Vector	StructureMath.getRotatedAtoms(StructureMap map, Bond bond, Atom atom)