Uses of Class
org.proteinshader.math.Vec3d

Packages that use Vec3d

org.proteinshader.gui.viewing	Holds important helper classes that the Renderer uses to control the view: Camera, Rotation, Lighting, etc.
org.proteinshader.math	The key classes in this package are Hermite and Quaternion, which are needed for generating the ribbons and tubes that are used to represent the backbone of a protein in a cartoon-type display.
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.

Uses of Vec3d in org.proteinshader.gui.viewing

Fields in org.proteinshader.gui.viewing declared as Vec3d

static Vec3d	Rotation.X_AXIS Vector representing an x-axis.
static Vec3d	Rotation.Y_AXIS Vector representing an y-axis.
static Vec3d	Rotation.Z_AXIS Vector representing an z-axis.

Uses of Vec3d in org.proteinshader.math

Methods in org.proteinshader.math that return Vec3d

Vec3d	Vec3d.add(Vec3d vec) Creates a new vector by adding the vector given as an argument to the calling vector (the existing vectors are NOT modified).
Vec3d	Hermite.calculateReverseTangent(double t) Gets the tangent from the calculateTangent() method and reverses its direction.
Vec3d	Hermite.calculateTangent(double t) Uses Hermite interpolation to calculate the tangent of a point on the cubic equation between the start and end points given the constructor.
Vec3d	Hermite.calculateTranslation(double t) If the xyz-point obtained by calculatePoint() is going to be used to translate an object from the origin to the point, then it is convenient for a vector to be returned instead of a point.
Vec3d	Vec3d.clone() Returns a clone of the calling vector.
Vec3d	Vec3d.cross(Vec3d vec) Creates a new vector by taking the cross product of the calling vector and the vector given as an argument.
Vec3d	Quaternion.getBinormal() Converts the Quaternion into a 3 x 3 rotation matrix and the returns the second column vector (the Binormal).
Vec3d	LocalFrame.getBinormal() Converts the rotation (a Quaternion) into a 3 x 3 rotation matrix and the returns the second column vector (the Binormal).
Vec3d	Quaternion.getNormal() Converts the Quaternion into a 3 x 3 rotation matrix and the returns the first column vector (the Normal).
Vec3d	LocalFrame.getNormal() Converts the rotation (a Quaternion) into a 3 x 3 rotation matrix and the returns the first column vector (the Normal).
Vec3d	LocalFrame.getReverseTangent() Converts the rotation (a Quaternion) into a 3 x 3 rotation matrix and the returns the third column vector (the Tangent) after reversing its direction.
Vec3d	Quaternion.getTangent() Converts the Quaternion into a 3 x 3 rotation matrix and the returns the third column vector (the Tangent).
Vec3d	LocalFrame.getTangent() Converts the rotation (a Quaternion) into a 3 x 3 rotation matrix and the returns the third column vector (the Tangent).
Vec3d	LocalFrame.getTranslation() Returns a copy of the translation vector held by this LocalFrame.
Vec3d	Point3d.minus(Point3d point) Returns the direction vector obtained by subtracting the point given as an argument from the calling point.
Vec3d	Vec3d.minus(Vec3d vec) Creates a new vector by subtracting the vector given as an argument from the calling vector (the existing vectors are NOT modified).
Vec3d	Quaternion.multiply(Vec3d v) Multiplies a vector by this quaternion and returns the resulting vector.
Vec3d	Vec3d.negate() Creates a new vector equal in magnitude but opposite in direction to the calling vector (the calling vector is NOT modified).
Vec3d	Vec3d.normalize() Creates a new vector that has the same direction as the calling vector, but is of unit length (the calling vector is NOT modified).
Vec3d	LocalFrame.rotate(Vec3d vector) Returns a new vector produced by rotating the vector given as an argument by the quaternion held in this local frame.
Vec3d	Vec3d.scale(double magnitude) Creates a new vector by scaling the calling vector by the magnitude given as an argument (the calling vector is NOT modified).

Methods in org.proteinshader.math with parameters of type Vec3d

Point3d	Point3d.add(Vec3d vec) Returns the point created by adding the vector given as an argument to the point that is the calling object.
Vec3d	Vec3d.add(Vec3d vec) Creates a new vector by adding the vector given as an argument to the calling vector (the existing vectors are NOT modified).
void	Point3d.addToMe(Vec3d vec) Tranlates the calling Point3d by adding the vector xyz-coordinates to it.
void	Vec3d.addToMe(Vec3d vec) Modifies the calling vector by adding the xyz-values of the vector given as an argument to the xyz-values of the calling vector.
void	Quaternion.adjustMyTangent(Vec3d tangent) Modifies this quaternion by rotating it such that if it is converted into a rotation matrix [N B T], the T vector will match the tangent given as an argument.
Quaternion	Quaternion.adjustTangent(Vec3d tangent) Returns a copy of this quaternion that has been rotated such that if it is converted into a rotation matrix [N B T], the T vector will match the tangent given as an argument.
void	QuaternionDemo.convertToQuaternionAndPrint(Vec3d N, Vec3d B, Vec3d T) Converts rotation matrix [N B T] to a quaternion and prints it.
Vec3d	Vec3d.cross(Vec3d vec) Creates a new vector by taking the cross product of the calling vector and the vector given as an argument.
void	Vec3d.crossMe(Vec3d vec) Modifies the calling vector by calculating the cross product of the calling vector and the vector given as an argument and storing the result in the calling vector.
double	Vec3d.dot(Vec3d vec) Returns the dot product of the calling vector and the vector given as an argument.
double	Quaternion.generateAxisAndAngle(Vec3d axis) Converts the Quaternion to an axis of rotation and an angle.
void	Quaternion.generateMatrix(Vec3d N, Vec3d B, Vec3d T) Generates a 3 x 3 rotation matrix (actually 3 column vectors) that is equivalent to this quaternion, assuming that the quaternion has already been normalized (such that x^2 + y^2 + z^2 + w^2 = 1).
void	LocalFrame.generateMatrix(Vec3d N, Vec3d B, Vec3d T) Generates a 3 x 3 rotation matrix (actually 3 column vectors) that is equivalent to the rotation quaternion.
Vec3d	Vec3d.minus(Vec3d vec) Creates a new vector by subtracting the vector given as an argument from the calling vector (the existing vectors are NOT modified).
void	Vec3d.minusFromMe(Vec3d vec) The x, y, and z values of the vector given as an argument are subtracted from the x, y, and z values of the calling vector.
Vec3d	Quaternion.multiply(Vec3d v) Multiplies a vector by this quaternion and returns the resulting vector.
void	QuaternionDemo.printColumnVectors(Vec3d N, Vec3d B, Vec3d T) Prints the 3 column vectors to standard out.
void	SlerpDemo.printColumnVectors(Vec3d N, Vec3d B, Vec3d T) Prints the 3 column vectors to standard out.
static void	HermiteDemo.printStartAndEndPoints(Point3d p1, Point3d p2, Vec3d tan1, Vec3d tan2) Prints the start and end points along with their tangents.
Vec3d	LocalFrame.rotate(Vec3d vector) Returns a new vector produced by rotating the vector given as an argument by the quaternion held in this local frame.
void	LocalFrame.setTranslation(Vec3d translation) Holds on the the vector given as an argument so that it can be used as the translation for the local coordinate frame.
void	Vec3d.setXYZ(Vec3d vec) Sets the xyz-values of the vector to the xyz-values of the vector given as an argument.
void	Quaternion.setXYZW(Vec3d axis, double angle) Calculates and sets (x, y, z, w) of this quaternion based on the axis and angle (in radians) given as aguments.
void	Quaternion.setXYZW(Vec3d N, Vec3d B, Vec3d T) Calculates and sets (x, y, z, w) of this quaternion based on the rotation contained in the 3 x 3 matrix [N B T].

Constructors in org.proteinshader.math with parameters of type Vec3d

Hermite(Point3d p1, Point3d p2, Vec3d tan1, Vec3d tan2)
Constructs a Hermite object by using the input points and vectors to calculate and store the coefficients needed for the cubic equations for x(t), y(t), and z(t).

Hermite(Vec3d p1, Vec3d p2, Vec3d tan1, Vec3d tan2)
Constructs a Hermite object by using the input vectors to calculate and store the coefficients needed for the cubic equations for x(t), y(t), and z(t).

LocalFrame(Quaternion rotation, Vec3d translation)
Constructs a LocalFrame that holds on to the Quaternion and Vec3d given as arguments.

LocalFrame(Vec3d N, Vec3d B, Vec3d T, double x, double y, double z)
Constructs a LocalFrame equivalent to the rotation matrix [N B T] and the translation (x, y, z).

Quaternion(Vec3d axis, double angle)
Creates a quaternion that is equivalent to the rotation specified by the axis and angle (in radians) given as aguments.

Quaternion(Vec3d N, Vec3d B, Vec3d T)
Creates a quaternion that is equivalent to the rotation contained in the 3 x 3 matrix [N B T].

Uses of Vec3d in org.proteinshader.structure

Methods in org.proteinshader.structure that return Vec3d

Vec3d	Segment.getMiddleBinormal() Converts the middle rotation (a Quaternion) into a 3 x 3 rotation matrix and then returns the third column vector, the Binormal.
Vec3d	Segment.getMiddleNormal() Converts the middle rotation (a Quaternion) into a 3 x 3 rotation matrix and then returns the first column vector, the Normal.
Vec3d	Segment.getMiddleTangent() Converts the middle rotation (a Quaternion) into a 3 x 3 rotation matrix and then returns the third column vector, the Tangent.
Vec3d	Segment.getMiddleXYZ() Copies the xyz-coordinates for the center of this Segment into a new Vec3d and returns it.
Vec3d	AminoAcid.getTranslation() Returns a new Ved3d object based on the xyz-coordinates of the alpha-carbon.
Vec3d	Drawable.getTranslation() Returns the xyz-center of the Drawable as a vector.
Vec3d	Drawable.minus(Drawable other) Returns a vector created by subtracting the xyz-center of the Drawable given as an argument from the xyz-center of the calling Drawable object.