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

B

bases - Variable in class ProGAL.geom3d.Rectangle

beamDetector() - Method in class ProGAL.geom2d.ConvexPolygon

below(Point) - Method in class ProGAL.geom3d.Plane

Returns 1/0/-1 if point p is below/on/above this plane

Benchmark - Class in ProGAL

Benchmark - Class in ProGAL.dataStructures.rangeSearching

Benchmark() - Constructor for class ProGAL.dataStructures.rangeSearching.Benchmark

BetaTopology - Class in ProGAL.proteins.belta

Representation of a beta-topology.

BetaTopology(SecondaryStructure) - Constructor for class ProGAL.proteins.belta.BetaTopology

Constructs a beta-topology associated with the specified secondary structure but with no pairings.

BetaTopology(SecondaryStructure, boolean[][]) - Constructor for class ProGAL.proteins.belta.BetaTopology

Constructs a beta-topology associated with the specified secondary structure and pairings.

betaTopology - Variable in class ProGAL.proteins.beltaStructure.sheetLoop.SheetLoopStructure

BetaTopologyTest - Class in ProGAL.proteins.belta.tests

BetaTopologyTest() - Constructor for class ProGAL.proteins.belta.tests.BetaTopologyTest

BettiDebugger - Class in ProGAL.geom3d.complex.alphaComplex.tests

BettiDebugger() - Constructor for class ProGAL.geom3d.complex.alphaComplex.tests.BettiDebugger

BigDecimalPredicates - Class in ProGAL.geom3d.tessellation.BowyerWatson

bigDouble - Static variable in class ProGAL.math.Constants

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

binarySearch(SortTool, Object) - Method in class ProGAL.dataStructures.Set

BinaryTreePainter - Class in ProGAL.dataStructures.viewer

BinaryTreePainter(InteractiveBinaryTree) - Constructor for class ProGAL.dataStructures.viewer.BinaryTreePainter

BinaryTreePainter.PNode - Class in ProGAL.dataStructures.viewer

BinaryTreePainter.PNode(InteractiveBinaryTree, int) - Constructor for class ProGAL.dataStructures.viewer.BinaryTreePainter.PNode

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

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

binom(int, int) - Static method in class ProGAL.math.Combinatorics

Calculate the binomial coefficient.

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

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

BnBNode - Class in ProGAL.proteins.beltaStructure.bnb

A node in a branch and bound tree corresponding to a partial protein structure.

BnBSolver - Class in ProGAL.proteins.beltaStructure.bnb

BnBSolver(BetaTopology, LowerBound) - Constructor for class ProGAL.proteins.beltaStructure.bnb.BnBSolver

BnBTreeExplorer - Class in ProGAL.proteins.beltaStructure.bnb

BnBTreeExplorer(BetaTopology) - Constructor for class ProGAL.proteins.beltaStructure.bnb.BnBTreeExplorer

boundaryFlipIn(TriangulationVertex, TriangulationVertex, TriangulationVertex) - Method in class ProGAL.geom2d.Triangulation

boundaryFlipIn(TriangulationVertex, TriangulationVertex, TriangulationVertex, J2DScene, boolean) - Method in class ProGAL.geom2d.Triangulation

boundaryFlipOut(TriangulationVertex, TriangulationFace, J2DScene, boolean) - Method in class ProGAL.geom2d.Triangulation

BowyerWatson - Class in ProGAL.geomNd.complex.delaunayComplex

A Delaunay complex for a set of d-dimensional points is a tesselation of the points such that no point is inside the circumscribing hypersphere of the d-simplices (for the 3D case: Tetrahedra).

BowyerWatson(List<Point>) - Constructor for class ProGAL.geomNd.complex.delaunayComplex.BowyerWatson

Builds the Delaunay complex of the specified point-set using Bowyer-Watson algorithm

BowyerWatsonTest - Class in ProGAL.geomNd.complex.delaunayComplex.tests

BowyerWatsonTest() - Constructor for class ProGAL.geomNd.complex.delaunayComplex.tests.BowyerWatsonTest

Branchable - Interface in ProGAL.proteins.beltaStructure.bnb

A part of a protein chain.

BWViewer - Class in ProGAL.geomNd.complex.delaunayComplex

BWViewer() - Constructor for class ProGAL.geomNd.complex.delaunayComplex.BWViewer