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

targetAtoms - Variable in class ProGAL.proteins.beltaStructure.loop.LoopStructure

TAU - Static variable in class ProGAL.math.Constants

TCorner - Class in ProGAL.geom3d.tess

TCorner() - Constructor for class ProGAL.geom3d.tess.TCorner

TESS - Class in ProGAL.geom3d.tess

TESS() - Constructor for class ProGAL.geom3d.tess.TESS

Tessel - Class in ProGAL.geomNd.complex

Tessel(Vertex[]) - Constructor for class ProGAL.geomNd.complex.Tessel

testAbove() - Method in class ProGAL.geom3d.tests.PlaneTest

testAdd() - Method in class ProGAL.geom3d.tests.PointTest

testAdd() - Method in class ProGAL.math.test.MatrixTest

testAddThis() - Method in class ProGAL.geom3d.tests.PointTest

testAddThis() - Method in class ProGAL.math.test.MatrixTest

testApplyToInPoint() - Method in class ProGAL.math.test.MatrixTest

testApplyToMatrix() - Method in class ProGAL.math.test.MatrixTest

testApplyToThis() - Method in class ProGAL.math.test.MatrixTest

testApplyToVector() - Method in class ProGAL.math.test.MatrixTest

testBelow() - Method in class ProGAL.geom3d.tests.PlaneTest

testBetaTopology() - Method in class ProGAL.proteins.belta.tests.BetaTopologyTest

testBinCenters() - Method in class ProGAL.statistics.tests.HistogramTest

testBinom() - Method in class ProGAL.math.test.CombinatoricsTest

testCalcRootsDoubleDoubleDouble() - Method in class ProGAL.math.test.PolynomialTest

testCalcRootsDoubleDoubleDoubleDouble() - Method in class ProGAL.math.test.PolynomialTest

testCircumradiusPointPointPoint() - Method in class ProGAL.geom3d.predicates.tests.ExactJavaPredicatesTest

testCircumradiusPointPointPoint() - Method in class ProGAL.geom3d.predicates.tests.InexactJavaPredicatesTest

testCircumradiusPointPointPointPoint() - Method in class ProGAL.geom3d.predicates.tests.ExactJavaPredicatesTest

testCircumradiusPointPointPointPoint() - Method in class ProGAL.geom3d.predicates.tests.InexactJavaPredicatesTest

testClone() - Method in class ProGAL.geom3d.tests.PointTest

testCollinear() - Method in class ProGAL.geom3d.tests.PointTest

testContainsStrand() - Method in class ProGAL.proteins.belta.tests.SheetTopologyTest

testCoplanar() - Method in class ProGAL.geom3d.tests.PointTest

testCreate4x4ColumnMatrix() - Method in class ProGAL.math.test.MatrixTest

testCreateBalancedHistogram() - Method in class ProGAL.statistics.tests.HistogramTest

testCreateColumnMatrix() - Method in class ProGAL.math.test.MatrixTest

testCreateIdentityMatrix() - Method in class ProGAL.math.test.MatrixTest

testCreateRotationMatrix() - Method in class ProGAL.math.test.MatrixTest

testCreateRowMatrix() - Method in class ProGAL.math.test.MatrixTest

testDelaunayComplex() - Method in class ProGAL.geom3d.complex.delaunayComplex.tests.DelaunayComplexTest

testDeterminant() - Method in class ProGAL.math.test.MatrixTest

testDiffsides() - Method in class ProGAL.geom3d.predicates.tests.ExactJavaPredicatesTest

testDiffsides() - Method in class ProGAL.geom3d.predicates.tests.InexactJavaPredicatesTest

testDistance() - Method in class ProGAL.geom3d.volumes.tests.LensTest

testDominatesPoint3d() - Method in class ProGAL.geom3d.tests.PointTest

testDominatesPoint3dIntIntInt() - Method in class ProGAL.geom3d.tests.PointTest

testEdgecircumradius() - Method in class ProGAL.geom3d.predicates.tests.ExactJavaPredicatesTest

testEdgecircumradius() - Method in class ProGAL.geom3d.predicates.tests.InexactJavaPredicatesTest

testEdgeinsphere() - Method in class ProGAL.geom3d.predicates.tests.ExactJavaPredicatesTest

testEdgeinsphere() - Method in class ProGAL.geom3d.predicates.tests.InexactJavaPredicatesTest

testEqualsPoint3d() - Method in class ProGAL.geom3d.tests.PointTest

testGet() - Method in class ProGAL.geom3d.tests.PointTest

testGet() - Method in class ProGAL.geomNd.tests.PointTest

testGetAllPermutations() - Method in class ProGAL.math.test.CombinatoricsTest

testGetAngle() - Method in class ProGAL.geom3d.tests.PointTest

testGetAngle() - Method in class ProGAL.geomNd.tests.PointTest

testGetArea() - Method in class ProGAL.geom3d.tests.TriangleTest

testGetBin() - Method in class ProGAL.statistics.tests.HistogramTest

testGetBisector() - Method in class ProGAL.geom3d.tests.PointTest

testGetCenter() - Method in class ProGAL.geom3d.tests.TriangleTest

testGetCenter() - Method in class ProGAL.geom3d.volumes.tests.LensTest

testGetCoils() - Method in class ProGAL.proteins.belta.tests.SecondaryStructureTest

testGetColumn() - Method in class ProGAL.math.test.MatrixTest

testGetCoord() - Method in class ProGAL.geom3d.tests.PointTest

testGetCoord() - Method in class ProGAL.geomNd.tests.PointTest

testGetCorner() - Method in class ProGAL.geom3d.tests.TriangleTest

testGetDihedralAngle() - Method in class ProGAL.geom3d.tests.PointTest

testGetDir() - Method in class ProGAL.geom3d.tests.LineTest

testGetDistance() - Method in class ProGAL.geom3d.tests.LineTest

testGetDistance() - Method in class ProGAL.geom3d.tests.PlaneTest

testGetDistance() - Method in class ProGAL.geom3d.tests.PointTest

testGetDistance() - Method in class ProGAL.geomNd.tests.PointTest

testGetDistanceSquared() - Method in class ProGAL.geom3d.tests.LineTest

testGetDistanceSquared() - Method in class ProGAL.geom3d.tests.PointTest

testGetDistanceSquared() - Method in class ProGAL.geomNd.tests.PointTest

testGetEigenvalueDecomposition() - Method in class ProGAL.math.test.MatrixTest

testGetFocalDistance() - Method in class ProGAL.geom3d.volumes.tests.LensTest

testGetHelices() - Method in class ProGAL.proteins.belta.tests.SecondaryStructureTest

testGetIntersectionLine() - Method in class ProGAL.geom3d.tests.PlaneTest

testGetIntersectionLineSegment() - Method in class ProGAL.geom3d.tests.PlaneTest

testGetIntersectionParameter() - Method in class ProGAL.geom3d.tests.PlaneTest

testGetMaxDistance() - Method in class ProGAL.geom3d.tests.LineTest

testGetMaxDistanceSquared() - Method in class ProGAL.geom3d.tests.LineTest

testGetMidpoint() - Method in class ProGAL.geomNd.tests.PointTest

testGetNormal() - Method in class ProGAL.geom3d.tests.PlaneTest

testGetNormal() - Method in class ProGAL.geom3d.tests.TriangleTest

testGetNormalizedStrandOrder() - Method in class ProGAL.proteins.belta.tests.SheetTopologyTest

testGetP() - Method in class ProGAL.geom3d.tests.LineTest

testGetP1() - Method in class ProGAL.geom3d.tests.TriangleTest

testGetP2() - Method in class ProGAL.geom3d.tests.TriangleTest

testGetP3() - Method in class ProGAL.geom3d.tests.TriangleTest

testGetParTopology() - Method in class ProGAL.proteins.belta.tests.SheetTopologyTest

testGetPoint() - Method in class ProGAL.geom3d.tests.LineTest

testGetPoint() - Method in class ProGAL.geom3d.tests.PlaneTest

testGetRadius() - Method in class ProGAL.geom3d.volumes.tests.LensTest

testGetRMSD() - Method in class ProGAL.geom3d.superposition.tests.RMSDTest

testGetRow() - Method in class ProGAL.math.test.MatrixTest

testGetSheets() - Method in class ProGAL.proteins.belta.tests.BetaTopologyTest

testGetSquaredDistance() - Method in class ProGAL.geom3d.tests.LineTest

testGetStrandOrder() - Method in class ProGAL.proteins.belta.tests.SheetTopologyTest

testGetStrands() - Method in class ProGAL.proteins.belta.tests.SecondaryStructureTest

testgetUnsignedDihedralAngle() - Method in class ProGAL.geom3d.tests.PlaneTest

testGetVolume() - Method in class ProGAL.geom3d.volumes.tests.LensTest

testGetX() - Method in class ProGAL.geom3d.tests.PointTest

testGetY() - Method in class ProGAL.geom3d.tests.PointTest

testGetZ() - Method in class ProGAL.geom3d.tests.PointTest

testHistogramArray() - Method in class ProGAL.statistics.tests.HistogramTest

testHistogramNormalizedArray() - Method in class ProGAL.statistics.tests.HistogramTest

testInplane() - Method in class ProGAL.geom3d.predicates.tests.ExactJavaPredicatesTest

testInplane() - Method in class ProGAL.geom3d.predicates.tests.InexactJavaPredicatesTest

testInspherePointPointPointPoint() - Method in class ProGAL.geom3d.predicates.tests.ExactJavaPredicatesTest

testInspherePointPointPointPoint() - Method in class ProGAL.geom3d.predicates.tests.InexactJavaPredicatesTest

testInspherePointPointPointPointPoint() - Method in class ProGAL.geom3d.predicates.tests.ExactJavaPredicatesTest

testInspherePointPointPointPointPoint() - Method in class ProGAL.geom3d.predicates.tests.InexactJavaPredicatesTest

testInSphereTesselPointInt() - Method in class ProGAL.geomNd.complex.delaunayComplex.tests.BowyerWatsonTest

testInvert() - Method in class ProGAL.math.test.MatrixTest

testInvertThis() - Method in class ProGAL.math.test.MatrixTest

testIsValid() - Method in class ProGAL.proteins.belta.tests.BetaTopologyTest

testLens() - Method in class ProGAL.geom3d.volumes.tests.LensTest

testLinePointVector() - Method in class ProGAL.geom3d.tests.LineTest

testLineSegment() - Method in class ProGAL.geom3d.tests.LineTest

testLineVector() - Method in class ProGAL.geom3d.tests.LineTest

testMatches() - Method in class ProGAL.proteins.belta.tests.BetaTopologyTest

testMatches() - Method in class ProGAL.proteins.belta.tests.SecondaryStructureTest

testMatrixDoubleArrayArray() - Method in class ProGAL.math.test.MatrixTest

testMatrixIntInt() - Method in class ProGAL.math.test.MatrixTest

testMidpoint() - Method in class ProGAL.geom3d.tests.PointTest

testMinor() - Method in class ProGAL.math.test.MatrixTest

testMultiply() - Method in class ProGAL.math.test.MatrixTest

testMultiplyInVector() - Method in class ProGAL.math.test.MatrixTest

testMultiplyPoint() - Method in class ProGAL.math.test.MatrixTest

testMultiplyThis() - Method in class ProGAL.math.test.MatrixTest

testOptimalSuperpositionListOfPointListOfPoint() - Method in class ProGAL.geom3d.superposition.tests.RMSDTest

testOptimalSuperpositionListOfPointListOfPointListOfInteger() - Method in class ProGAL.geom3d.superposition.tests.RMSDTest

testOrient() - Method in class ProGAL.geom3d.predicates.tests.ExactJavaPredicatesTest

testOrient() - Method in class ProGAL.geom3d.predicates.tests.InexactJavaPredicatesTest

testOrthogonalProjectionParameter() - Method in class ProGAL.geom3d.tests.LineTest

testOrthogonalProjectionParameters() - Method in class ProGAL.geom3d.tests.LineTest

testOrthogonalProjectionPoint() - Method in class ProGAL.geom3d.tests.LineTest

testOrthogonalProjectionPointList() - Method in class ProGAL.geom3d.tests.LineTest

testPlanePointPointPoint() - Method in class ProGAL.geom3d.tests.PlaneTest

testPlanePointVector() - Method in class ProGAL.geom3d.tests.PlaneTest

testPlaneVector() - Method in class ProGAL.geom3d.tests.PlaneTest

testPoint3dDoubleDoubleDouble() - Method in class ProGAL.geom3d.tests.PointTest

testPoint3dPoint3d() - Method in class ProGAL.geom3d.tests.PointTest

testPoint3dVector3d() - Method in class ProGAL.geom3d.tests.PointTest

testPointDoubleArray() - Method in class ProGAL.geomNd.tests.PointTest

testPointInt() - Method in class ProGAL.geomNd.tests.PointTest

testProjectPoint() - Method in class ProGAL.geom3d.tests.PlaneTest

testReduce() - Method in class ProGAL.math.test.MatrixTest

testReduceThis() - Method in class ProGAL.math.test.MatrixTest

testReflectThroughOrigoThis() - Method in class ProGAL.geom3d.tests.PointTest

testRespects() - Method in class ProGAL.proteins.belta.tests.BetaTopologyTest

testRespects() - Method in class ProGAL.proteins.belta.tests.SecondaryStructureTest

testRotate() - Method in class ProGAL.geom3d.tests.LineTest

testScale() - Method in class ProGAL.geom3d.tests.PointTest

testSecondaryStructure() - Method in class ProGAL.proteins.belta.tests.SecondaryStructureTest

testSet() - Method in class ProGAL.geom3d.tests.PointTest

testSet() - Method in class ProGAL.geomNd.tests.PointTest

testSetCoord() - Method in class ProGAL.geom3d.tests.PointTest

testSetNormal() - Method in class ProGAL.geom3d.tests.PlaneTest

testSetX() - Method in class ProGAL.geom3d.tests.PointTest

testSetY() - Method in class ProGAL.geom3d.tests.PointTest

testSetZ() - Method in class ProGAL.geom3d.tests.PointTest

testSheetTopology() - Method in class ProGAL.proteins.belta.tests.SheetTopologyTest

testSubtract() - Method in class ProGAL.geom3d.tests.PointTest

testSubtractThis() - Method in class ProGAL.geom3d.tests.PointTest

testToVector() - Method in class ProGAL.geom3d.tests.PointTest

testToVector() - Method in class ProGAL.geomNd.tests.PointTest

testTransformInPoint() - Method in class ProGAL.geom3d.superposition.tests.TransformTest

testTransformPoint() - Method in class ProGAL.geom3d.superposition.tests.TransformTest

testTranslate() - Method in class ProGAL.geom3d.tests.PointTest

testTranspose() - Method in class ProGAL.math.test.MatrixTest

testVectorTo() - Method in class ProGAL.geom3d.tests.PointTest

Tet - Class in ProGAL.geom3d.tessellation.BowyerWatson

Tetr - Class in ProGAL.geom3d.tessellation.BowyerWatson

Tetr(PointWeighted, PointWeighted, PointWeighted, PointWeighted) - Constructor for class ProGAL.geom3d.tessellation.BowyerWatson.Tetr

tetrahedra - Variable in class ProGAL.proteins.ProteinComplex.Hole

Tetrahedron - Class in ProGAL.geom3d.volumes

A tetrahedron is a polyhedron with four triangular faces.

Tetrahedron(Point, Point, Point, Point) - Constructor for class ProGAL.geom3d.volumes.Tetrahedron

Tetrahedron(Point[]) - Constructor for class ProGAL.geom3d.volumes.Tetrahedron

TetrahedronAlphaProperties - Class in ProGAL.geom3d.complex.alphaComplex

TetrahedronAlphaProperties(double) - Constructor for class ProGAL.geom3d.complex.alphaComplex.TetrahedronAlphaProperties

tetrahedrons - Variable in class ProGAL.proteins.ProteinComplex.Cavity

text - Variable in class ProGAL.geom3d.viewer.TextShape

TextShape - Class in ProGAL.geom2d.viewer

TextShape(String, Point, double) - Constructor for class ProGAL.geom2d.viewer.TextShape

TextShape - Class in ProGAL.geom3d.viewer

TextShape(String, Point) - Constructor for class ProGAL.geom3d.viewer.TextShape

TextShape(String, Point, double) - Constructor for class ProGAL.geom3d.viewer.TextShape

toChar() - Method in enum ProGAL.proteins.belta.SSType

toConsole() - Method in class ProGAL.geom2d.Circle

toConsole(int) - Method in class ProGAL.geom2d.Circle

toConsole(String) - Method in class ProGAL.geom2d.Line

toConsole() - Method in class ProGAL.geom2d.Line

toConsole() - Method in class ProGAL.geom2d.LineSegment

toConsole(int) - Method in class ProGAL.geom2d.PointSet

prints points on the console

toConsole() - Method in class ProGAL.geom2d.Vector

toConsole(int) - Method in class ProGAL.geom2d.Vector

toConsole() - Method in class ProGAL.geom3d.Circle

Writes this circle to System.out with 2 decimals precision.

toConsole(int) - Method in class ProGAL.geom3d.Circle

Writes this circle to System.out with dec decimals precision.

toConsole() - Method in class ProGAL.geom3d.LineSegment

Writes this segment to System.out.

toConsole(int) - Method in class ProGAL.geom3d.LineSegment

Writes this segment to System.out with dec decimals precision.

toConsole() - Method in class ProGAL.geom3d.Point

Writes this point to System.out.

toConsole(int) - Method in class ProGAL.geom3d.Point

Writes this point to System.out with dec decimals precision.

toConsole() - Method in class ProGAL.geom3d.PointList

Writes this point-list to System.out.

toConsole(int) - Method in class ProGAL.geom3d.PointList

Writes this point-list to System.out.

toConsole(int) - Method in class ProGAL.geom3d.superposition.Transform

toConsole() - Method in class ProGAL.geom3d.superposition.Transform

toConsole() - Method in class ProGAL.geom3d.Triangle

Writes this triangle to System.out with 2 decimals precision.

toConsole(int) - Method in class ProGAL.geom3d.Triangle

Writes this triangle to System.out with dec decimals precision.

toConsole() - Method in class ProGAL.geom3d.Vector

Writes this vector to System.out.

toConsole(int) - Method in class ProGAL.geom3d.Vector

Writes this vector to System.out with dec decimals precision.

toConsole(int) - Method in class ProGAL.geom3d.volumes.Cylinder

toConsole() - Method in class ProGAL.geom3d.volumes.Sphere

Writes this sphere to System.out.

toConsole(int) - Method in class ProGAL.geom3d.volumes.Sphere

Writes this sphere to System.out with dec decimals precision.

toConsole() - Method in class ProGAL.geom3d.volumes.Tetrahedron

Writes this tetrahedron to System.out.

toConsole(int) - Method in class ProGAL.geom3d.volumes.Tetrahedron

Writes this tetrahedron to System.out with dec decimals precision.

toConsole() - Method in class ProGAL.geomNd.Point

toConsole(int) - Method in class ProGAL.geomNd.Point

toConsole() - Method in class ProGAL.geomNd.PointList

Writes this point-list to System.out.

toConsole(int) - Method in class ProGAL.geomNd.PointList

Writes this point-list to System.out.

toConsole() - Method in class ProGAL.geomNd.Vector

Writes this vector to System.out.

toConsole(int) - Method in class ProGAL.geomNd.Vector

Writes this vector to System.out with dec decimals precision.

toConsole() - Method in class ProGAL.math.Matrix

toConsole(int) - Method in class ProGAL.math.Matrix

toDeg(double) - Static method in class ProGAL.math.Functions

toggleRotation() - Method in class ProGAL.geom3d.viewer.J3DScene

Toggles rotation

toGnuplotString(int) - Method in class ProGAL.statistics.Histogram

toGnuplotString() - Method in class ProGAL.statistics.Histogram

toPoint() - Method in class ProGAL.geom2d.Vector

toPoint() - Method in class ProGAL.geom3d.Vector

Convert this vector to a point.

toPoint() - Method in class ProGAL.geomNd.Vector

Convert this vector to a point.

toRad(double) - Static method in class ProGAL.math.Functions

toScene(J2DScene) - Method in class ProGAL.geom2d.Circle

toScene(J2DScene, Color) - Method in class ProGAL.geom2d.Circle

toScene(J2DScene) - Method in class ProGAL.geom2d.LineSegment

toScene(J2DScene, double, Color) - Method in class ProGAL.geom2d.Point

toScene(J3DScene, double, int) - Method in class ProGAL.geom3d.Circle

toScene(J3DScene, double, Color) - Method in class ProGAL.geom3d.complex.CTetrahedron

toScene(J3DScene, double, Color) - Method in class ProGAL.geom3d.complex.CTriangle

toScene(J3DScene, Color) - Method in class ProGAL.geom3d.complex.CTriangle

toScene(J3DScene, double, Color) - Method in class ProGAL.geom3d.Line

toScene(J3DScene, double, Color) - Method in class ProGAL.geom3d.LineSegment

toScene(J3DScene, Color, int) - Method in class ProGAL.geom3d.Plane

toScene(J3DScene, double, Color) - Method in class ProGAL.geom3d.Point

toScene(J3DScene, Color) - Method in class ProGAL.geom3d.Triangle

toScene(J3DScene, Color, double) - Method in class ProGAL.geom3d.Vector

toScene(J3DScene, Color) - Method in class ProGAL.geom3d.volumes.Sphere

toScene(J3DScene) - Method in class ProGAL.geom3d.volumes.Tetrahedron

toString() - Method in class ProGAL.dataStructures.viewer.BinaryTreePainter.PNode

toString() - Method in class ProGAL.geom2d.Circle

toString(int) - Method in class ProGAL.geom2d.Circle

toString() - Method in class ProGAL.geom2d.delaunay.Triangle

toString() - Method in class ProGAL.geom2d.delaunay.Vertex

toString(String) - Method in class ProGAL.geom2d.Line

toString() - Method in class ProGAL.geom2d.Line

toString() - Method in class ProGAL.geom2d.LineSegment

toString() - Method in class ProGAL.geom2d.TriangulationFace

toString() - Method in class ProGAL.geom2d.Vector

toString(int) - Method in class ProGAL.geom2d.Vector

toString() - Method in class ProGAL.geom3d.Circle

Returns a string-representation of this circle formatted with two decimals precision.

toString(int) - Method in class ProGAL.geom3d.Circle

Returns a string-representation of this circle formatted with dec decimals precision.

toString() - Method in class ProGAL.geom3d.complex.alphaComplex.Interval

toString() - Method in class ProGAL.geom3d.complex.CVertex

toString(int) - Method in class ProGAL.geom3d.complex.CVertex

toString() - Method in class ProGAL.geom3d.Line

Returns a string-representation of this line.

toString(int) - Method in class ProGAL.geom3d.Line

Returns a string-representation of this line with dec decimals precision.

toString() - Method in class ProGAL.geom3d.LineSegment

Returns a string representation of this segments.

toString(int) - Method in class ProGAL.geom3d.LineSegment

Returns a string representation of this segments with dec decimals precision.

toString() - Method in class ProGAL.geom3d.Point

Returns a string-representation of this point formatted with two decimals precision.

toString(int) - Method in class ProGAL.geom3d.Point

Returns a string-representation of this point formatted with dec decimals precision.

toString(int) - Method in class ProGAL.geom3d.superposition.Transform

toString() - Method in class ProGAL.geom3d.surface.ParametricParaboloid

toString() - Method in class ProGAL.geom3d.tess.TPoint

toString() - Method in class ProGAL.geom3d.tessellation.BowyerWatson.Tetr

toString() - Method in class ProGAL.geom3d.Triangle

Returns a string-representation of this triangle formatted with two decimals precision.

toString(int) - Method in class ProGAL.geom3d.Triangle

Returns a string-representation of this triangle formatted with dec decimals precision.

toString() - Method in class ProGAL.geom3d.Vector

Returns a string-representation of this vector formatted with two decimals precision.

toString(int) - Method in class ProGAL.geom3d.Vector

Returns a string-representation of this vector formatted with dec decimals precision.

toString() - Method in class ProGAL.geom3d.volumes.Cylinder

toString(int) - Method in class ProGAL.geom3d.volumes.Cylinder

toString() - Method in class ProGAL.geom3d.volumes.InfCylinder

toString() - Method in class ProGAL.geom3d.volumes.LSS

toString() - Method in class ProGAL.geom3d.volumes.OBB

toString() - Method in class ProGAL.geom3d.volumes.RSS

toString() - Method in class ProGAL.geom3d.volumes.Sphere

Return a string representation of this sphere.

toString(int) - Method in class ProGAL.geom3d.volumes.Sphere

Return a string representation of this sphere with dec decimals precision

toString() - Method in class ProGAL.geom3d.volumes.Tetrahedron

Return a string representation of this tetrahedron.

toString(int) - Method in class ProGAL.geom3d.volumes.Tetrahedron

Return a string representation of this tetrahedron with dec decimals precision

toString() - Method in class ProGAL.geomNd.complex.Tessel

toString() - Method in class ProGAL.geomNd.complex.Vertex

toString(int) - Method in class ProGAL.geomNd.complex.Vertex

toString() - Method in class ProGAL.geomNd.HyperSphere

toString(int) - Method in class ProGAL.geomNd.HyperSphere

toString() - Method in class ProGAL.geomNd.Point

toString(int) - Method in class ProGAL.geomNd.Point

toString() - Method in class ProGAL.geomNd.Vector

Returns a string-representation of this vector formatted with two decimals precision.

toString(int) - Method in class ProGAL.geomNd.Vector

Returns a string-representation of this vector formatted with dec decimals precision.

toString() - Method in class ProGAL.math.Matrix

toString(int) - Method in class ProGAL.math.Matrix

toString() - Method in class ProGAL.proteins.belta.BetaTopology

toString() - Method in class ProGAL.proteins.belta.PrimaryStructure

toString() - Method in class ProGAL.proteins.belta.SecondaryStructure.SSSegment

toString() - Method in class ProGAL.proteins.belta.SecondaryStructure

TODO: Comment

toString() - Method in class ProGAL.proteins.belta.SheetTopology

toString() - Method in class ProGAL.proteins.beltaStructure.bnb.BnBNode

toString() - Method in class ProGAL.proteins.beltaStructure.loop.LoopStructure

toString() - Method in class ProGAL.proteins.beltaStructure.sheet.SurfaceSheetStructure

toString() - Method in class ProGAL.proteins.PDBFile.AnisouRecord

toString() - Method in class ProGAL.proteins.PDBFile.AtomRecord

Returns a string representation of this ATOM-record that follows the PDB-file format.

toString() - Method in class ProGAL.proteins.PDBFile.OtherRecord

toString() - Method in class ProGAL.proteins.PDBFile.ParentRecord

toString() - Method in class ProGAL.proteins.PDBFile.RemarkRecord

toString() - Method in class ProGAL.proteins.PDBFile.TerRecord

toString() - Method in class ProGAL.proteins.ProteinComplex.Cavity

toString() - Method in class ProGAL.proteins.ProteinComplex.Hole

toString() - Method in class ProGAL.proteins.structure.Atom

toString() - Method in class ProGAL.statistics.Histogram

toVector() - Method in class ProGAL.geom3d.Point

Returns the vector from origo to this point.

toVector() - Method in class ProGAL.geomNd.Point

TPoint - Class in ProGAL.geom3d.tess

TPoint() - Constructor for class ProGAL.geom3d.tess.TPoint

Transform - Class in ProGAL.geom3d.superposition

Transform(Matrix, Vector, Vector) - Constructor for class ProGAL.geom3d.superposition.Transform

Transform(Matrix, Vector) - Constructor for class ProGAL.geom3d.superposition.Transform

transform(List<Point>) - Method in class ProGAL.geom3d.superposition.Transform

transform(Point) - Method in class ProGAL.geom3d.superposition.Transform

transformIn(List<Point>) - Method in class ProGAL.geom3d.superposition.Transform

transformIn(Point) - Method in class ProGAL.geom3d.superposition.Transform

TransformTest - Class in ProGAL.geom3d.superposition.tests

TransformTest() - Constructor for class ProGAL.geom3d.superposition.tests.TransformTest

translate(Vector) - Method in class ProGAL.geom2d.PointSet

translates all points by the specified vector

translate(Vector) - Method in class ProGAL.geom3d.volumes.Tetrahedron

translate(Point) - Method in class ProGAL.geom3d.volumes.Tetrahedron

translate(double, double, double) - Method in class ProGAL.geom3d.volumes.Tetrahedron

translateThis(double, double, double) - Method in class ProGAL.geom3d.Point

Translates this point by (x,y,z).

transpose() - Method in class ProGAL.math.Matrix

Get the transpose of this matrix

Triangle - Class in ProGAL.geom2d.delaunay

All triangles should be counter-clock-wise (TODO: add an assert)

Triangle(Vertex, Vertex, Vertex) - Constructor for class ProGAL.geom2d.delaunay.Triangle

Triangle - Class in ProGAL.geom2d

Triangle(Point, Point, Point) - Constructor for class ProGAL.geom2d.Triangle

Triangle - Class in ProGAL.geom3d

A triangle in (x,y,z)-space represented by the three corner-points.

Triangle(Point, Point, Point) - Constructor for class ProGAL.geom3d.Triangle

Construct a triangle using the three specified points as corners

Triangle(Point[]) - Constructor for class ProGAL.geom3d.Triangle

TriangleAlphaProperties - Class in ProGAL.geom3d.complex.alphaComplex

TriangleAlphaProperties(Interval, Interval, Interval, boolean, double) - Constructor for class ProGAL.geom3d.complex.alphaComplex.TriangleAlphaProperties

TriangleAlphaProperties(double, double, double, boolean, boolean) - Constructor for class ProGAL.geom3d.complex.alphaComplex.TriangleAlphaProperties

triangles - Variable in class ProGAL.geom2d.delaunay.DTNoBigPoints

TriangleTest - Class in ProGAL.geom3d.tests

TriangleTest() - Constructor for class ProGAL.geom3d.tests.TriangleTest

Triangulation - Class in ProGAL.geom2d

Triangulation(PointSet, Triangulation.TriangulationAlgorithm) - Constructor for class ProGAL.geom2d.Triangulation

creates a triangulation of a set of points Two triangulation algorithms are so far implemented: Greedy, Delaunay

Triangulation.TriangulationAlgorithm - Enum in ProGAL.geom2d

TriangulationFace - Class in ProGAL.geom2d

TriangulationFace(TriangulationVertex, TriangulationVertex, TriangulationVertex) - Constructor for class ProGAL.geom2d.TriangulationFace

TriangulationFace(TriangulationVertex, TriangulationVertex, TriangulationVertex, J2DScene, boolean) - Constructor for class ProGAL.geom2d.TriangulationFace

triangulationFaces - Variable in class ProGAL.geom2d.Triangulation

TriangulationVertex - Class in ProGAL.geom2d

TriangulationVertex(double, double) - Constructor for class ProGAL.geom2d.TriangulationVertex

TriangulationVertex.VertexType - Enum in ProGAL.geom2d

Trigonometry - Class in ProGAL.math

Trigonometry() - Constructor for class ProGAL.math.Trigonometry

TSphere - Class in ProGAL.geom3d.tess

TSphere() - Constructor for class ProGAL.geom3d.tess.TSphere

twozeroMove(Point, Point, Point, Point) - Static method in class ProGAL.geom2d.Circle

type - Variable in class ProGAL.proteins.belta.SecondaryStructure.SSSegment

type() - Method in class ProGAL.proteins.structure.AminoAcid

typeName() - Method in class ProGAL.proteins.structure.AminoAcid

typeThreeLetter() - Method in class ProGAL.proteins.structure.AminoAcid