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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
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