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

R

rad - Variable in class ProGAL.geom3d.volumes.Cone

rad - Variable in class ProGAL.geom3d.volumes.LSS

radius - Variable in class ProGAL.geom3d.volumes.RSS

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

RamachandranDistribution - Class in ProGAL.proteins.dunbrack

An aminoacid dependent distribution of Ramachandran angles based on the Dunbrack TCBIG dataset.

randBetween(int, int) - Static method in class ProGAL.math.Randomization

Return a uniform random number between (including) i1 and (not including) i2.

randBetween(double, double) - Static method in class ProGAL.math.Randomization

Return a uniform random double between (including) d1 and (not including) d2

Randomization - Class in ProGAL.math

A wrapper for static randomization functions.

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

randomizeInPlace(int[]) - Static method in class ProGAL.math.Randomization

Randomize an array.

randomPermutation() - Method in class ProGAL.dataStructures.Set

randomPermutation(int) - Static method in class ProGAL.math.Randomization

Generate a random permutation of integers between (including) 0 and (not including) max

RangeSearchDataStructure - Interface in ProGAL.dataStructures.rangeSearching

RangeTree - Class in ProGAL.dataStructures.rangeSearching.rangeTree

RangeTree(List<Point>) - Constructor for class ProGAL.dataStructures.rangeSearching.rangeTree.RangeTree

Initialize the range tree by presorting according to each dimension.

RangeTreeAssocValue - Class in ProGAL.dataStructures.rangeSearching.rangeTree

RangeTreeAssocValue(Point, int, int) - Constructor for class ProGAL.dataStructures.rangeSearching.rangeTree.RangeTreeAssocValue

Instanciates an value object in a associated structure.

RangeTreeNode - Class in ProGAL.dataStructures.rangeSearching.rangeTree

RangeTreeNode() - Constructor for class ProGAL.dataStructures.rangeSearching.rangeTree.RangeTreeNode

RangeTreeNode1d - Class in ProGAL.dataStructures.rangeSearching.rangeTree

RangeTreeNode1d(List<List<Point>>) - Constructor for class ProGAL.dataStructures.rangeSearching.rangeTree.RangeTreeNode1d

RangeTreeNode2d - Class in ProGAL.dataStructures.rangeSearching.rangeTree

RangeTreeNode2d(List<List<Point>>, int) - Constructor for class ProGAL.dataStructures.rangeSearching.rangeTree.RangeTreeNode2d

Initialize the RangeTreeNode for 2 dimensions.

RangeTreeNodeNd - Class in ProGAL.dataStructures.rangeSearching.rangeTree

RangeTreeNodeNd(List<List<Point>>, int) - Constructor for class ProGAL.dataStructures.rangeSearching.rangeTree.RangeTreeNodeNd

Initialize the RangeTreeNode for N dimensions.

rank() - Method in class ProGAL.math.SingularValueDecomposition

Effective numerical matrix rank

readFasta(String) - Static method in class ProGAL.proteins.PDBWebReader

readFromFile(String) - Static method in class ProGAL.io.IOToolbox

Read the contents of the specified file and return it in a string.

readFromInternalFile(String) - Static method in class ProGAL.io.IOToolbox

Read the contents of the specified file and return it in a string.

readSerializedFile(String) - Static method in class ProGAL.io.IOToolbox

Reads a serialized object from the specified file-name.

rebuildACO() - Method in class ProGAL.proteins.beltaStructure.ChainTreeLoop

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

rebuildAnalytically() - Method in class ProGAL.proteins.beltaStructure.ChainTreeLoop

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

rebuildCCD() - Method in class ProGAL.proteins.beltaStructure.ChainTreeLoop

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

rebuildJacobian() - Method in class ProGAL.proteins.beltaStructure.ChainTreeLoop

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

recordString - Variable in class ProGAL.proteins.PDBFile.AnisouRecord

recordString - Variable in class ProGAL.proteins.PDBFile.OtherRecord

recordString - Variable in class ProGAL.proteins.PDBFile.ParentRecord

Rectangle - Class in ProGAL.geom3d

A planar rectangle in 3d.

Rectangle(Point, Vector[]) - Constructor for class ProGAL.geom3d.Rectangle

rectangle - Variable in class ProGAL.geom3d.volumes.RSS

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

Reduce this matrix to row canonical form (reduced row echelon form).

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

Reduce this matrix to row canonical form (reduced row echelon form).

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

Reflects this point through origo.

RegularComplex - Class in ProGAL.geom3d.complex.delaunayComplex

TODO: Fix

RegularComplex(List<Point>) - Constructor for class ProGAL.geom3d.complex.delaunayComplex.RegularComplex

RegularComplexVisualTest - Class in ProGAL.geom3d.complex.delaunayComplex.tests

RegularComplexVisualTest() - Constructor for class ProGAL.geom3d.complex.delaunayComplex.tests.RegularComplexVisualTest

RegularTessellation - Class in ProGAL.geom3d.tessellation.BowyerWatson

RegularTessellation() - Constructor for class ProGAL.geom3d.tessellation.BowyerWatson.RegularTessellation

RegularTessellation(List<PointWeighted>) - Constructor for class ProGAL.geom3d.tessellation.BowyerWatson.RegularTessellation

regularTetrahedron() - Static method in class ProGAL.geom3d.volumes.Tetrahedron

remark - Variable in class ProGAL.proteins.PDBFile.RemarkRecord

remove() - Method in class ProGAL.dataStructures.SetIterator

REMOVE_ONE - Static variable in class ProGAL.geom3d.superposition.GDT

REMOVE_TEN_PERCENT - Static variable in class ProGAL.geom3d.superposition.GDT

removeAllShapes() - Method in class ProGAL.geom2d.viewer.J2DScene

Remove all shapes from the scene

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

Remove all volumes from the scene.

removeShape(Shape) - Method in class ProGAL.geom2d.viewer.J2DScene

Remove the specified shape from the scene

removeShape(Shape) - Method in class ProGAL.geom3d.viewer.J3DScene

Removes one volume from the scene.

repaint() - Method in class ProGAL.geom2d.viewer.J2DScene

Repaint the scene

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

Repaint the canvas.

repaintRepeatedly(long) - Method in class ProGAL.geom3d.viewer.J3DScene

Repaint the canvas repeatedly every millisecondDelay milliseconds.

reshape(J2DScene, boolean) - Method in class ProGAL.geom2d.TriangulationFace

residueNumber - Variable in class ProGAL.proteins.PDBFile.AtomRecord

residueNumber - Variable in class ProGAL.proteins.PDBFile.TerRecord

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

Determine if this beta-topology respects some other topology.

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

Determine if this secondary structure respects ss.

reverse() - Method in class ProGAL.dataStructures.Set

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

swaps the end-points of this segment

right() - Method in interface ProGAL.dataStructures.viewer.InteractiveBinaryTree

right - Variable in class ProGAL.geom3d.complex.alphaComplex.Node

right() - Method in class ProGAL.geom3d.complex.alphaComplex.Node

rightExtremePointIndx() - Method in class ProGAL.geom2d.Polygon

returns the index of the rightmost point (in case of ties, index of the topmost one is returned)

rightindex - Variable in class ProGAL.dataStructures.rangeSearching.rangeTree.RangeTreeAssocValue

rightLegColor() - Method in interface ProGAL.dataStructures.viewer.InteractiveBinaryTree

rightLegColor() - Method in class ProGAL.geom3d.complex.alphaComplex.Node

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

Returns true if points a, b and c make a right turn at b or are colinear

rightTurn(Vector, Vector) - Static method in class ProGAL.geom2d.Vector

RMSD - Class in ProGAL.geom3d.superposition

RMSD() - Constructor for class ProGAL.geom3d.superposition.RMSD

RMSDTest - Class in ProGAL.geom3d.superposition.tests

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

root - Variable in class ProGAL.dataStructures.viewer.BinaryTreePainter

root - Variable in class ProGAL.geom3d.complex.alphaComplex.VoidTree

rotate(Point, List<TriangulationVertex>, double, boolean) - Method in class ProGAL.geom2d.delaunay.Kinetic

rotate(int, double) - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexRotation

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

Return a rotation of p around this line.

rotate90() - Method in class ProGAL.geom2d.Vector

rotate90This() - Method in class ProGAL.geom2d.Vector

rotateAllAtOnce(int, double) - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexRotation

rotateAllAtOnceBySmallAngle(int, double) - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexRotation

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

Rotate point around this line, store the result in point and return the results.

rotateIn(Vector, double) - Method in class ProGAL.geom3d.Vector

Perform a right-handed rotation of v around this vector.

rotateOneAtTime(int, double) - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexRotation

rotateThis(double) - Method in class ProGAL.geom2d.Vector

rotation(double) - Method in class ProGAL.geom2d.Point

rotates the point around the origo (counterclockwise)

rotation(double, double) - Method in class ProGAL.geom2d.Point

rotation(Point, double) - Method in class ProGAL.geom2d.Point

rotates point p around this point by angle

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

rotates (clockwise) the point around the line through the origo with the direction unit vector v.

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

rotates (clockwise) the point around the line through the point p with the direction unit vector v.

rotationClone(double) - Method in class ProGAL.geom2d.Point

roundUpToPowerOf2(int) - Static method in class ProGAL.math.Functions

returns the smallest power of 2 above n, see http://en.wikipedia.org/wiki/Power_of_two

RSS - Class in ProGAL.geom3d.volumes

Implementation of a Rectangular Swept Sphere that supports overlap check and construction from a point-set and two RSS'.

RSS(Point, Vector[], double) - Constructor for class ProGAL.geom3d.volumes.RSS

run() - Method in class ProGAL.proteins.beltaStructure.bnb.BnBSolver

runBenchmark() - Method in class ProGAL.Benchmark