A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

T

tan() - Method in class org.simtk.geometry3d.Angle

TAN - Static variable in class org.simtk.util.ColorName

TAN1 - Static variable in class org.simtk.util.ColorName

TAN2 - Static variable in class org.simtk.util.ColorName

TAN3 - Static variable in class org.simtk.util.ColorName

TAN4 - Static variable in class org.simtk.util.ColorName

taperLength - Variable in class org.simtk.moleculargraphics.cartoon.vtkTaperedWidthFilter

TEAL - Static variable in class org.simtk.util.ColorName

temporarilySelectedResidues - Variable in class org.simtk.moleculargraphics.TornadoSequenceCanvas

TensorGlyphCartoon - Class in org.simtk.moleculargraphics.cartoon

TestArrowRibbon - Class in org.simtk.moleculargraphics

TestArrowRibbon() - Constructor for class org.simtk.moleculargraphics.TestArrowRibbon

testArrowRibbon() - Static method in class org.simtk.moleculargraphics.TestArrowRibbon

testCentroidCollectionOfVector3D() - Method in class org.simtk.geometry3d.TestVector3DClass

testCentroidVector3DArrayDoubleArray() - Method in class org.simtk.geometry3d.TestVector3DClass

testCopy() - Method in class org.simtk.geometry3d.TestVector3DClass

testCross() - Method in class org.simtk.geometry3d.TestVector3DClass

testDistance() - Method in class org.simtk.geometry3d.TestVector3DClass

testDistanceSquared() - Method in class org.simtk.geometry3d.TestVector3DClass

testDot() - Method in class org.simtk.geometry3d.TestVector3DClass

testEqualsObject() - Method in class org.simtk.geometry3d.TestVector3DClass

testFullScreen() - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

testGet() - Method in class org.simtk.geometry3d.TestVector3DClass

testGetDimension() - Method in class org.simtk.geometry3d.TestVector3DClass

testGetElement() - Method in class org.simtk.geometry3d.TestVector3DClass

testGetX() - Method in class org.simtk.geometry3d.TestVector3DClass

testGetY() - Method in class org.simtk.geometry3d.TestVector3DClass

testGetZ() - Method in class org.simtk.geometry3d.TestVector3DClass

testHashCode() - Method in class org.simtk.geometry3d.TestVector3DClass

testIterator() - Method in class org.simtk.geometry3d.TestVector3DClass

testKabsch78() - Method in class org.simtk.geometry3d.TestKabschSuperposition

TestKabschSuperposition - Class in org.simtk.geometry3d

TestKabschSuperposition() - Constructor for class org.simtk.geometry3d.TestKabschSuperposition

testLength() - Method in class org.simtk.geometry3d.TestVector3DClass

testLengthSquared() - Method in class org.simtk.geometry3d.TestVector3DClass

testLoadSStructViewFile() - Method in class org.simtk.toon.secstruct.TestSecondaryStructureCanvas

testMathVectorClass() - Method in class org.simtk.geometry3d.TestVector3DClass

TestMatrix - Class in Jama.test

TestMatrix tests the functionality of the Jama Matrix class and associated decompositions.

TestMatrix() - Constructor for class Jama.test.TestMatrix

TestMenu - Class in org.simtk.moleculargraphics

testMinusEquals() - Method in class org.simtk.geometry3d.TestVector3DClass

testMinusMathVector() - Method in class org.simtk.geometry3d.TestVector3DClass

testMinusMathVector1() - Method in class org.simtk.geometry3d.TestVector3DClass

testNussinovDiagram() - Static method in class org.simtk.toon.secstruct.TestSecondaryStructureCanvas

testPlusEquals() - Method in class org.simtk.geometry3d.TestVector3DClass

testPlusMathVector() - Method in class org.simtk.geometry3d.TestVector3DClass

testPlusMathVector1() - Method in class org.simtk.geometry3d.TestVector3DClass

testRotate() - Method in class org.simtk.geometry3d.TestVector3DClass

TestSecondaryStructureCanvas - Class in org.simtk.toon.secstruct

TestSecondaryStructureCanvas() - Constructor for class org.simtk.toon.secstruct.TestSecondaryStructureCanvas

testSelfUnit() - Method in class org.simtk.geometry3d.TestVector3DClass

testSet() - Method in class org.simtk.geometry3d.TestVector3DClass

testSetX() - Method in class org.simtk.geometry3d.TestVector3DClass

testSetY() - Method in class org.simtk.geometry3d.TestVector3DClass

testSetZ() - Method in class org.simtk.geometry3d.TestVector3DClass

TestSuperposition - Class in org.simtk.geometry3d

TestSuperposition() - Constructor for class org.simtk.geometry3d.TestSuperposition

testTimesDouble() - Method in class org.simtk.geometry3d.TestVector3DClass

testTimesDouble1() - Method in class org.simtk.geometry3d.TestVector3DClass

testTimesEquals() - Method in class org.simtk.geometry3d.TestVector3DClass

testToString() - Method in class org.simtk.geometry3d.TestVector3DClass

testUnit() - Method in class org.simtk.geometry3d.TestVector3DClass

testUnit1() - Method in class org.simtk.geometry3d.TestVector3DClass

TestVector3DClass - Class in org.simtk.geometry3d

TestVector3DClass() - Constructor for class org.simtk.geometry3d.TestVector3DClass

testVector3DClass() - Method in class org.simtk.geometry3d.TestVector3DClass

testX() - Method in class org.simtk.geometry3d.TestVector3DClass

testY() - Method in class org.simtk.geometry3d.TestVector3DClass

testZ() - Method in class org.simtk.geometry3d.TestVector3DClass

thickness - Variable in class org.simtk.moleculargraphics.cartoon.vtkArrowWidthFilter

thickness - Variable in class org.simtk.moleculargraphics.cartoon.vtkPreExtrusionCenteringFilter

thickness - Variable in class org.simtk.moleculargraphics.cartoon.vtkTaperedWidthFilter

THISTLE - Static variable in class org.simtk.util.ColorName

THISTLE1 - Static variable in class org.simtk.util.ColorName

THISTLE2 - Static variable in class org.simtk.util.ColorName

THISTLE3 - Static variable in class org.simtk.util.ColorName

THISTLE4 - Static variable in class org.simtk.util.ColorName

threeLetterCode - Variable in class org.simtk.molecularstructure.ResidueTypeClass

Threonine - Class in org.simtk.molecularstructure.protein

Threonine() - Constructor for class org.simtk.molecularstructure.protein.Threonine

Throbber - Class in org.simtk.gui

Throbber(Icon[]) - Constructor for class org.simtk.gui.Throbber

Thymidylate - Class in org.simtk.molecularstructure.nucleicacid

Thymidylate() - Constructor for class org.simtk.molecularstructure.nucleicacid.Thymidylate

times(double) - Method in class Jama.Matrix

Multiply a matrix by a scalar, C = s*A

times(Matrix) - Method in class Jama.Matrix

Linear algebraic matrix multiplication, A * B

times(Vector3D) - Method in interface org.simtk.geometry3d.HomogeneousTransform

times(HomogeneousTransform) - Method in interface org.simtk.geometry3d.HomogeneousTransform

times(Vector3D) - Method in class org.simtk.geometry3d.HomogeneousTransformClass

times(HomogeneousTransform) - Method in class org.simtk.geometry3d.HomogeneousTransformClass

times(double) - Method in interface org.simtk.geometry3d.MathMatrix

times(MathVector) - Method in interface org.simtk.geometry3d.MathMatrix

times(MathMatrix) - Method in interface org.simtk.geometry3d.MathMatrix

times(MathMatrix) - Method in class org.simtk.geometry3d.MathMatrixClass

times(MathVector) - Method in class org.simtk.geometry3d.MathMatrixClass

times(double) - Method in class org.simtk.geometry3d.MathMatrixClass

times(double) - Method in interface org.simtk.geometry3d.MathVector

times(double) - Method in class org.simtk.geometry3d.MathVectorClass

times(double) - Method in interface org.simtk.geometry3d.Matrix3D

times(MathVector) - Method in interface org.simtk.geometry3d.Matrix3D

times(MathMatrix) - Method in interface org.simtk.geometry3d.Matrix3D

times(MathVector) - Method in class org.simtk.geometry3d.Matrix3DClass

times(MathMatrix) - Method in class org.simtk.geometry3d.Matrix3DClass

times(double) - Method in class org.simtk.geometry3d.Matrix3DClass

times(double) - Method in interface org.simtk.geometry3d.Vector2D

times(double) - Method in class org.simtk.geometry3d.Vector2DClass

times(double) - Method in interface org.simtk.geometry3d.Vector3D

times(double) - Method in class org.simtk.geometry3d.Vector3DClass

timesEquals(double) - Method in class Jama.Matrix

Multiply a matrix by a scalar in place, A = s*A

timesEquals(double) - Method in class org.simtk.geometry3d.MathMatrixClass

timesEquals(MathMatrix) - Method in class org.simtk.geometry3d.MathMatrixClass

timesEquals(double) - Method in class org.simtk.geometry3d.MathVectorClass

timesEquals(double) - Method in interface org.simtk.geometry3d.MutableMathMatrix

timesEquals(MathMatrix) - Method in interface org.simtk.geometry3d.MutableMathMatrix

timesEquals(double) - Method in interface org.simtk.geometry3d.MutableMathVector

tipWidth - Variable in class org.simtk.moleculargraphics.cartoon.vtkArrowWidthFilter

tipWidth - Variable in class org.simtk.moleculargraphics.cartoon.vtkTaperedWidthFilter

toArray() - Method in interface org.simtk.geometry3d.Matrix3D

toArray() - Method in class org.simtk.geometry3d.Matrix3DClass

toArray() - Method in interface org.simtk.geometry3d.Vector2D

toArray() - Method in class org.simtk.geometry3d.Vector2DClass

toArray() - Method in interface org.simtk.geometry3d.Vector3D

toArray() - Method in class org.simtk.geometry3d.Vector3DClass

TOMATO - Static variable in class org.simtk.util.ColorName

TOMATO1 - Static variable in class org.simtk.util.ColorName

TOMATO2 - Static variable in class org.simtk.util.ColorName

TOMATO3 - Static variable in class org.simtk.util.ColorName

TOMATO4 - Static variable in class org.simtk.util.ColorName

toonColors - Variable in class org.simtk.moleculargraphics.cartoon.MoleculeCartoonClass

ToonColors - Class in org.simtk.moleculargraphics.cartoon

toonRange - Variable in class org.simtk.moleculargraphics.Tornado

Tornado - Class in org.simtk.moleculargraphics

Tornado3DCanvas - Class in org.simtk.moleculargraphics

Tornado3DCanvas() - Constructor for class org.simtk.moleculargraphics.Tornado3DCanvas

TornadoSequenceCanvas - Class in org.simtk.moleculargraphics

TornadoSequenceCanvas(String, SequencePane, ResidueHighlightBroadcaster, ResidueCenterBroadcaster) - Constructor for class org.simtk.moleculargraphics.TornadoSequenceCanvas

TornadoSplasher - Class in org.simtk.splashscreen

TornadoSplasher() - Constructor for class org.simtk.splashscreen.TornadoSplasher

toString() - Method in class org.simtk.geometry3d.Angle

toString() - Method in class org.simtk.geometry3d.MathMatrixClass

toString() - Method in class org.simtk.geometry3d.MathVectorClass

toString() - Method in class org.simtk.geometry3d.Vector2DClass

toString() - Method in class org.simtk.geometry3d.Vector3DClass

toString() - Method in class org.simtk.molecularstructure.nucleicacid.BasePair

trace() - Method in class Jama.Matrix

Matrix trace.

trace() - Method in interface org.simtk.geometry3d.MathMatrix

trace() - Method in class org.simtk.geometry3d.MathMatrixClass

trace() - Method in interface org.simtk.geometry3d.Matrix3D

transform - Variable in class org.simtk.toon.secstruct.SecondaryStructureCanvas

transformToBoundingBox(BoundingBox) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

translate(double, double) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

transpose() - Method in class Jama.Matrix

Matrix transpose.

transpose() - Method in interface org.simtk.geometry3d.MathMatrix

transpose() - Method in class org.simtk.geometry3d.MathMatrixClass

transpose() - Method in interface org.simtk.geometry3d.Matrix3D

transpose() - Method in class org.simtk.geometry3d.Matrix3DClass

Tryptophan - Class in org.simtk.molecularstructure.protein

Tryptophan() - Constructor for class org.simtk.molecularstructure.protein.Tryptophan

TubeAndStickTrace - Class in org.simtk.moleculargraphics.cartoon

TubeAndStickTrace() - Constructor for class org.simtk.moleculargraphics.cartoon.TubeAndStickTrace

TubeAndStickTrace(double, double) - Constructor for class org.simtk.moleculargraphics.cartoon.TubeAndStickTrace

TURQUOISE - Static variable in class org.simtk.util.ColorName

TURQUOISE1 - Static variable in class org.simtk.util.ColorName

TURQUOISE2 - Static variable in class org.simtk.util.ColorName

TURQUOISE3 - Static variable in class org.simtk.util.ColorName

TURQUOISE4 - Static variable in class org.simtk.util.ColorName

TWO_PI - Static variable in class org.simtk.geometry3d.Angle

Tyrosine - Class in org.simtk.molecularstructure.protein

Tyrosine() - Constructor for class org.simtk.molecularstructure.protein.Tyrosine