Uses of Class
org.proteinshader.math.Quaternion

Packages that use Quaternion

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.
org.proteinshader.structure.visitor	Holds Visitor classes that know how to traverse the hierarchy of objects held by class Structure.

Uses of Quaternion in org.proteinshader.math

Methods in org.proteinshader.math that return Quaternion

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.
Quaternion	Quaternion.clone() Creates a clone of this quaternion and returns it.
Quaternion	Quaternion.conjugate() Creates a clone of the calling Quaternion and then converts it to the conjugate, q'.
Quaternion	Quaternion.invert() Creates a clone of the calling Quaternion and inverts it.
Quaternion	Quaternion.multiply(Quaternion quat) Creates a clone of the calling Quaternion and multiplies it by the Quaternion given as an argument.
Quaternion	Quaternion.normalize() Creates and returns a new quaternion that is equivalent to the calling quaternion, but is guaranteed to be of unit length.
Quaternion	Quaternion.slerp(Quaternion end, double t) Uses SLERP (Spherical Linear intERPolation) to calculate a Quaternion (a rotation) at any point t between the calling Quaternion and the argument Quaternion.

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

double	Quaternion.angleBetweenNormals(Quaternion quat) Returns the angle between the normals of the calling and argument quaternions, where the normal is the first column vector of the rotation matrix [N B T] that is the equivalent of a quaternion.
void	SlerpDemo.interpolateAndPrint(Quaternion quat1, Quaternion quat2, double t) Interpolates between the two quaternions given as arguments and then prints the result quaterion along with the [N B T] equivalent to the quaternion.
Quaternion	Quaternion.multiply(Quaternion quat) Creates a clone of the calling Quaternion and multiplies it by the Quaternion given as an argument.
void	Quaternion.multiplyMe(Quaternion quat) Multiplies the calling Quaternion by the argument Quaternion and stores the result in the calling Quaternion.
void	QuaternionDemo.printInterpolation(Quaternion start, Quaternion end, double[] t) For each value in the array t, the slerp() method of class Quaternion will be used to calculate and print an interpolated Quaternion between the start and end Quaternions.
void	LocalFrame.setRotation(Quaternion rotation) Holds on to the Quaternion given as an argument so that it can be used as the rotation of the local coordinate frame.
void	Quaternion.setXYZW(Quaternion quat) Sets the xyzw-values of the quaternion to the xyzw-values of the quaternion given as an argument.
Quaternion	Quaternion.slerp(Quaternion end, double t) Uses SLERP (Spherical Linear intERPolation) to calculate a Quaternion (a rotation) at any point t between the calling Quaternion and the argument Quaternion.

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

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

Uses of Quaternion in org.proteinshader.structure

Methods in org.proteinshader.structure that return Quaternion

Quaternion	Segment.getEndRotation() Returns a clone of the Quaternion for the end rotation of this Segment.
Quaternion	Segment.getMiddleRotation() Returns a clone of the Quaternion for the middle rotation of this Segment.
Quaternion	AminoAcid.getRotation() Returns the rotation (the equivalent of a Frenet Frame) that will be needed for creating a Segment object based on this AminoAcid.
Quaternion	Segment.getStartRotation() Returns a clone of the Quaternion for the start rotation of this Segment.

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

void	AminoAcid.setRotation(Quaternion rotation) Sets the rotation (the equivalent of a Frenet Frame) that will be needed for creating a Segment object based on this AminoAcid.

Constructors in org.proteinshader.structure with parameters of type Quaternion

Segment(AminoAcid aminoAcid, Hermite hermite1, Hermite hermite2, Quaternion startRotation, Quaternion middleRotation, Quaternion endRotation, boolean alwaysCapStart, boolean alwaysCapEnd)
Creates a Segment.

Uses of Quaternion in org.proteinshader.structure.visitor

Methods in org.proteinshader.structure.visitor that return Quaternion

Quaternion

FrenetFrameGeneratorVisitor.calculateRotation(Atom atom1, Atom atom2, Atom atom3) Calculates a rotation matrix [N B T] based on the xyz-centers of the three Atoms given as arguments, and then converts the rotation matrix into a Quaternion that is returned.