Uses of Interface
org.simtk.geometry3d.Vector3D

Packages that use Vector3D

org.simtk.geometry3d
org.simtk.molecularstructure
org.simtk.molecularstructure.atom
org.simtk.molecularstructure.nucleicacid

Uses of Vector3D in org.simtk.geometry3d

Subinterfaces of Vector3D in org.simtk.geometry3d

interface

MutableVector3D

Classes in org.simtk.geometry3d that implement Vector3D

class	Vector3DClass
class	Vector3DFloatArrayWrapper

Fields in org.simtk.geometry3d declared as Vector3D

Vector3D	Line3D.direction
Vector3D	Line3D.origin
static Vector3D	Vector3DClass.X_AXIS
static Vector3D	Vector3DClass.Y_AXIS
static Vector3D	Vector3DClass.Z_AXIS

Methods in org.simtk.geometry3d that return Vector3D

static Vector3D	Vector3DClass.centroid(java.util.Collection<Vector3D> bagOfPoints) Compute the centroid or mean point
static Vector3D	Vector3DClass.centroid(Vector3D[] coordinates, double[] weights)
Vector3D	Vector2DClass.cross(Vector2D v2)
Vector3D	Vector2D.cross(Vector2D v2)
Vector3D	Vector3DClass.cross(Vector3D v2)
Vector3D	Vector3D.cross(Vector3D v2)
Vector3D	MassBodyClass.getCenterOfMass()
Vector3D	MassBody.getCenterOfMass()
Vector3D	Line3D.getClosestPoint(Vector3D v)
Vector3D	Matrix3DClass.getColumn(int j)
Vector3D	Matrix3D.getColumn(int j)
Vector3D	Matrix3DClass.getDiagonal()
Vector3D	Matrix3D.getDiagonal()
Vector3D	Line3D.getDirection()
Vector3D	Cylinder.getHead()
Vector3D	Cylinder.getMidpoint()
Vector3D	Plane3D.getNormal()
Vector3D	Line3D.getOrigin()
Vector3D	Matrix3DClass.getRow(int i)
Vector3D	Matrix3D.getRow(int i)
Vector3D	Cylinder.getTail()
Vector3D	HomogeneousTransformClass.getTranslation()
Vector3D	HomogeneousTransform.getTranslation()
Vector3D	Vector3DClass.minus(MathVector v2)
Vector3D	Vector3D.minus(MathVector v2)
Vector3D	Vector3DClass.plus(MathVector v2)
Vector3D	Vector3D.plus(MathVector v2)
Vector3D	Vector3DClass.rotate(Vector3D axis, double angle)
Vector3D	Vector3D.rotate(Vector3D axis, double angle)
Vector3D	Vector3DClass.times(double s)
Vector3D	Vector3D.times(double s)
Vector3D	Matrix3DClass.times(MathVector v)
Vector3D	Matrix3D.times(MathVector v)
Vector3D	HomogeneousTransformClass.times(Vector3D v)
Vector3D	HomogeneousTransform.times(Vector3D v)
Vector3D	Vector3DClass.unit()
Vector3D	Vector3D.unit()

Methods in org.simtk.geometry3d that return types with arguments of type Vector3D

java.util.Collection<Vector3D>

Hash3D.neighborKeys(Vector3D position, double radius) Find positions of all objects within a specified radius of a specified point.

Methods in org.simtk.geometry3d with parameters of type Vector3D

static Matrix3D	Matrix3DClass.axisAngle(Vector3D axis, double angle)
static Plane3D	Plane3D.bestPlane3D(Vector3D[] coordinates, double[] weights)
static Vector3D	Vector3DClass.centroid(Vector3D[] coordinates, double[] weights)
Vector3D	Vector3DClass.cross(Vector3D v2)
Vector3D	Vector3D.cross(Vector3D v2)
double	Plane3D.distance(Vector3D p) Distance between a point and a plane
V	Hash3D.getClosest(Vector3D position, double radius) Return the closest object to a particular position If no object is within the specified radius, return null.
Vector3D	Line3D.getClosestPoint(Vector3D v)
protected void	Vector3DClass.initialize(Vector3D v2)
static HomogeneousTransform	Superposition.kabsch78(Vector3D[] v1, Vector3D[] v2, double[] weights) Return a transformation that can place one set of vectors onto another while minimizing the least-squares distance between the corresponding points.
static HomogeneousTransform	Superposition.kabsch78(Vector3D[] v1, Vector3D[] v2, double[] weights) Return a transformation that can place one set of vectors onto another while minimizing the least-squares distance between the corresponding points.
java.util.Collection<Vector3D>	Hash3D.neighborKeys(Vector3D position, double radius) Find positions of all objects within a specified radius of a specified point.
java.util.Collection<V>	Hash3D.neighborValues(Vector3D position, double radius) Find all objects within a specified radius of a specified point This method has constant asymptotic time complexity.
V	Hash3D.put(Vector3D position, V object) Inserts an object into the data structure at a particular position.
java.lang.Object	Hash3D.remove(Vector3D vec) Remove the object at a particular position
Vector3D	Vector3DClass.rotate(Vector3D axis, double angle)
Vector3D	Vector3D.rotate(Vector3D axis, double angle)
void	MutableHomogeneousTransform.setTranslation(Vector3D t)
void	HomogeneousTransformClass.setTranslation(Vector3D t)
Vector3D	HomogeneousTransformClass.times(Vector3D v)
Vector3D	HomogeneousTransform.times(Vector3D v)

Method parameters in org.simtk.geometry3d with type arguments of type Vector3D

static Line3D	Line3D.bestLine3D(java.util.Vector<Vector3D> bagOfPoints)
static Plane3D	Plane3D.bestPlane3D(java.util.Collection<Vector3D> bagOfPoints) Create a plane that minimizes the sum of squared distances to a set of points
static Vector3D	Vector3DClass.centroid(java.util.Collection<Vector3D> bagOfPoints) Compute the centroid or mean point

Constructors in org.simtk.geometry3d with parameters of type Vector3D

Cylinder(Vector3D hd, Vector3D tl, double rd)

Line3D(Vector3D d, Vector3D o)

SemiCylinder(Vector3D head, Vector3D tail, double radius, Vector3DClass normalArg)

Uses of Vector3D in org.simtk.molecularstructure

Methods in org.simtk.molecularstructure that return Vector3D

Vector3D	ResidueClass.getBackbonePosition() Return preferred location of backbone trace in molecular representations
Vector3D	Residue.getBackbonePosition()
Vector3D	MoleculeCollection.getCenterOfMass()
Vector3D	MolecularClass.getCenterOfMass()
Vector3D	ResidueClass.getSideChainPosition()
Vector3D	Residue.getSideChainPosition()

Uses of Vector3D in org.simtk.molecularstructure.atom

Methods in org.simtk.molecularstructure.atom that return Vector3D

Vector3D	AtomClass.getCenterOfMass()
Vector3D	AtomPosition.getCoordinates()
Vector3D	AtomClass.getCoordinates()
Vector3D	Atom.getCoordinates()

Methods in org.simtk.molecularstructure.atom with parameters of type Vector3D

void	AtomPosition.setCoordinates(Vector3D v)
void	AtomClass.setCoordinates(Vector3D v)
void	Atom.setCoordinates(Vector3D coordinates)

Constructors in org.simtk.molecularstructure.atom with parameters of type Vector3D

AtomPosition(Vector3D coordinates)

Uses of Vector3D in org.simtk.molecularstructure.nucleicacid

Methods in org.simtk.molecularstructure.nucleicacid that return Vector3D

Vector3D

BasePair.getHelixCenter() Estimate position at center of a double helix containing this base pair