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Package Hierarchies:
ProGAL
,
ProGAL.dataStructures
,
ProGAL.dataStructures.rangeSearching
,
ProGAL.dataStructures.rangeSearching.rangeTree
,
ProGAL.dataStructures.viewer
,
ProGAL.geom2d
,
ProGAL.geom2d.convexHull
,
ProGAL.geom2d.delaunay
,
ProGAL.geom2d.viewer
,
ProGAL.geom3d
,
ProGAL.geom3d.complex
,
ProGAL.geom3d.complex.alphaComplex
,
ProGAL.geom3d.complex.alphaComplex.tests
,
ProGAL.geom3d.complex.delaunayComplex
,
ProGAL.geom3d.complex.delaunayComplex.tests
,
ProGAL.geom3d.complex.tessellation
,
ProGAL.geom3d.predicates
,
ProGAL.geom3d.predicates.tests
,
ProGAL.geom3d.superposition
,
ProGAL.geom3d.superposition.tests
,
ProGAL.geom3d.surface
,
ProGAL.geom3d.tess
,
ProGAL.geom3d.tessellation.BowyerWatson
,
ProGAL.geom3d.tests
,
ProGAL.geom3d.viewer
,
ProGAL.geom3d.volumes
,
ProGAL.geom3d.volumes.tests
,
ProGAL.geomNd
,
ProGAL.geomNd.complex
,
ProGAL.geomNd.complex.delaunayComplex
,
ProGAL.geomNd.complex.delaunayComplex.tests
,
ProGAL.geomNd.tests
,
ProGAL.io
,
ProGAL.math
,
ProGAL.math.test
,
ProGAL.proteins
,
ProGAL.proteins.belta
,
ProGAL.proteins.belta.tests
,
ProGAL.proteins.beltaStructure
,
ProGAL.proteins.beltaStructure.bnb
,
ProGAL.proteins.beltaStructure.bnb.lowerBounds
,
ProGAL.proteins.beltaStructure.loop
,
ProGAL.proteins.beltaStructure.sheet
,
ProGAL.proteins.beltaStructure.sheetLoop
,
ProGAL.proteins.chainTree
,
ProGAL.proteins.dunbrack
,
ProGAL.proteins.structure
,
ProGAL.proteins.structure.generators
,
ProGAL.proteins.viewer
,
ProGAL.statistics
,
ProGAL.statistics.tests
Class Hierarchy
java.lang.Object
java.util.AbstractCollection<E> (implements java.util.Collection<E>)
java.util.AbstractList<E> (implements java.util.List<E>)
java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
ProGAL.geomNd.
PointList
ProGAL.geom3d.
PointList
ProGAL.geom3d.complex.alphaComplex.
EiffelPointList
ProGAL.geom2d.
Polygon
(implements ProGAL.geom2d.
Shape
)
ProGAL.geom2d.
ConvexPolygon
ProGAL.proteins.structure.generators.
AllAtomAminoAcidGenerator
(implements ProGAL.proteins.structure.generators.
AtomGenerator
)
ProGAL.
AllTests
ProGAL.geom3d.complex.alphaComplex.tests.
AlphaComplexDebugger
ProGAL.geom3d.complex.alphaComplex.
AlphaFiltration
ProGAL.geom3d.complex.alphaComplex.
AlphaComplex
(implements ProGAL.geom3d.complex.
SimplicialComplex
)
ProGAL.proteins.
ProteinComplex
ProGAL.proteins.structure.
AminoAcid
ProGAL.proteins.structure.
AminoAcidChain
ProGAL.proteins.beltaStructure.sheetLoop.
SheetLoopStructure
(implements ProGAL.proteins.beltaStructure.sheetLoop.
PartialStructure
)
ProGAL.geom2d.
ApolloniusSolver
ProGAL.geomNd.
ApolloniusSolver
ProGAL.geom3d.
ApolloniusSolver
ProGAL.dataStructures.rangeSearching.
Benchmark
ProGAL.
Benchmark
ProGAL.proteins.belta.
BetaTopology
ProGAL.proteins.belta.tests.
BetaTopologyTest
ProGAL.geom3d.complex.alphaComplex.tests.
BettiDebugger
ProGAL.geom3d.tessellation.BowyerWatson.
BigDecimalPredicates
ProGAL.dataStructures.viewer.
BinaryTreePainter.PNode
ProGAL.proteins.beltaStructure.bnb.
BnBNode
(implements java.lang.Comparable<T>)
ProGAL.proteins.beltaStructure.bnb.
BnBSolver
ProGAL.proteins.beltaStructure.bnb.
BnBTreeExplorer
ProGAL.geomNd.complex.delaunayComplex.
BowyerWatson
ProGAL.geomNd.complex.delaunayComplex.tests.
BowyerWatsonTest
ProGAL.geomNd.complex.delaunayComplex.
BWViewer
ProGAL.proteins.structure.generators.
CABAminoAcidGenerator
(implements ProGAL.proteins.structure.generators.
AtomGenerator
)
ProGAL.proteins.beltaStructure.loop.
CALoopStructure
(implements ProGAL.proteins.beltaStructure.sheetLoop.
PartialStructure
)
ProGAL.proteins.beltaStructure.loop.
CALoopStructure.SegmentStructure
(implements ProGAL.proteins.beltaStructure.sheetLoop.
PartialStructure
)
ProGAL.geom3d.viewer.
Camera
(implements java.awt.event.KeyListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.MouseWheelListener)
ProGAL.proteins.beltaStructure.
CanonicalSheet
ProGAL.proteins.structure.
CBond
ProGAL.proteins.chainTree.
ChainTree
ProGAL.proteins.beltaStructure.
ChainTreeLoop
ProGAL.geom2d.
Circle
(implements ProGAL.geom2d.
Shape
)
ProGAL.geom3d.
Circle
(implements ProGAL.geom3d.
Shape
)
ProGAL.proteins.beltaStructure.bnb.lowerBounds.
CN_ClashLowerBound
(implements ProGAL.proteins.beltaStructure.bnb.lowerBounds.
LowerBound
)
ProGAL.proteins.beltaStructure.loop.
CoilDatabase
ProGAL.math.
Combinatorics
ProGAL.math.test.
CombinatoricsTest
java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
java.awt.Container
java.awt.Window (implements javax.accessibility.Accessible)
java.awt.Frame (implements java.awt.MenuContainer)
javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
ProGAL.dataStructures.viewer.
BinaryTreePainter
ProGAL.geom3d.volumes.
Cone
(implements ProGAL.geom3d.volumes.
Volume
)
ProGAL.math.
Constants
ProGAL.geom3d.tessellation.BowyerWatson.
Corner
ProGAL.geom3d.volumes.
Cylinder
(implements ProGAL.geom3d.volumes.
Volume
)
ProGAL.geom3d.complex.delaunayComplex.
DelaunayComplex
(implements ProGAL.geom3d.complex.
SimplicialComplex
)
ProGAL.geom3d.complex.delaunayComplex.
RegularComplex
(implements ProGAL.geom3d.complex.
SimplicialComplex
)
ProGAL.geom3d.complex.delaunayComplex.
DelaunayComplexKinetic
ProGAL.geom3d.complex.delaunayComplex.
DelaunayComplexRotation
ProGAL.geom3d.complex.delaunayComplex.
DelaunayComplexRotation_Stavefejl
ProGAL.geom3d.complex.delaunayComplex.
DelaunayComplexRotation.HeapItemComp
(implements ProGAL.dataStructures.
SortTool
)
ProGAL.geom3d.complex.delaunayComplex.tests.
DelaunayComplexTest
ProGAL.geom3d.complex.tessellation.
DelaunayTessellation
ProGAL.proteins.beltaStructure.bnb.lowerBounds.
Diameter_Clash_LowerBound
(implements ProGAL.proteins.beltaStructure.bnb.lowerBounds.
LowerBound
)
ProGAL.dataStructures.
DisjointSet
ProGAL.geom3d.complex.alphaComplex.
DisjointSet
ProGAL.dataStructures.
DisjointSet.DSNode
ProGAL.geom3d.complex.alphaComplex.
DisjointSet.Set
ProGAL.geom2d.convexHull.
DivideAndConquer
ProGAL.dataStructures.
DLCyclicList
<T> (implements java.lang.Iterable<T>)
ProGAL.dataStructures.
DLCyclicList.DLNode
<T>
ProGAL.dataStructures.
DLList
ProGAL.geom2d.delaunay.
DTNoBigPoints
ProGAL.geom2d.delaunay.
DTWithBigPoints
ProGAL.geom3d.complex.alphaComplex.
EdgeAlphaProperties
(implements ProGAL.geom3d.complex.alphaComplex.
SimplexAlphaProperties
)
ProGAL.geom3d.predicates.tests.
ExactJavaPredicatesTest
ProGAL.geom3d.superposition.
FastRMSD
java.io.File (implements java.lang.Comparable<T>, java.io.Serializable)
ProGAL.proteins.
PDBFile
ProGAL.proteins.belta.
PDBFile
ProGAL.math.
Functions
ProGAL.geom3d.superposition.
GDT
ProGAL.geom2d.convexHull.
GrahamScan
ProGAL.dataStructures.rangeSearching.
GridMap
(implements ProGAL.dataStructures.rangeSearching.
RangeSearchDataStructure
)
ProGAL.dataStructures.
Heap
ProGAL.proteins.structure.generators.
HeavyAtomAminoAcidGenerator
(implements ProGAL.proteins.structure.generators.
AtomGenerator
)
ProGAL.statistics.
Histogram
ProGAL.statistics.tests.
HistogramTest
ProGAL.geomNd.
HyperSphere
ProGAL.geom3d.predicates.tests.
InexactJavaPredicatesTest
ProGAL.geom3d.volumes.
InfCylinder
ProGAL.geom3d.complex.alphaComplex.
Interval
ProGAL.io.
IOToolbox
ProGAL.geom2d.viewer.
J2DScene
ProGAL.geom3d.viewer.
J3DImageFileWriter
ProGAL.geom3d.viewer.
J3DScene
ProGAL.geom2d.delaunay.
Kinetic
ProGAL.geom3d.volumes.
Lens
(implements ProGAL.geom3d.volumes.
Volume
)
ProGAL.geom3d.volumes.tests.
LensTest
ProGAL.geom2d.
Line
(implements ProGAL.geom2d.
Shape
)
ProGAL.geom3d.
Line
ProGAL.dataStructures.rangeSearching.
LinearRangeSearch
(implements ProGAL.dataStructures.rangeSearching.
RangeSearchDataStructure
)
ProGAL.geom2d.
LineSegment
(implements ProGAL.geom2d.
Shape
)
ProGAL.geom3d.
LineSegment
(implements ProGAL.geom3d.
Simplex
)
ProGAL.geom3d.complex.
CEdge
ProGAL.geom3d.tests.
LineTest
ProGAL.proteins.beltaStructure.loop.
LoopStructure
(implements ProGAL.proteins.beltaStructure.sheetLoop.
PartialStructure
)
ProGAL.geom2d.
LSC
(implements ProGAL.geom2d.
Shape
)
ProGAL.geom3d.volumes.
LSS
(implements ProGAL.geom3d.volumes.
Volume
)
ProGAL.math.
LUDecomposition
(implements java.io.Serializable)
ProGAL.math.
Matrix
ProGAL.math.
Matrix.ImmutableMatrix
ProGAL.math.
Matrix3x3
ProGAL.math.
Matrix.EigenvalueDecomposition
ProGAL.math.test.
MatrixTest
ProGAL.geom3d.complex.alphaComplex.
Node
(implements ProGAL.dataStructures.viewer.
InteractiveBinaryTree
)
ProGAL.geom3d.volumes.
OBB
(implements ProGAL.geom3d.volumes.
Volume
)
ProGAL.geom3d.tess.
OldTESS
ProGAL.geom3d.
ParametricPlane
ProGAL.geom3d.surface.
ParametricSurface
(implements ProGAL.geom3d.
Shape
)
ProGAL.proteins.viewer.
CoilSurface
ProGAL.proteins.viewer.
HelixSurface
ProGAL.geom3d.surface.
ParametricParaboloid
ProGAL.geom3d.surface.
ParametricPlane
ProGAL.proteins.viewer.
StrandSurface
ProGAL.proteins.beltaStructure.sheet.
ParametricSurface
ProGAL.proteins.
PDBFile.AnisouRecord
(implements ProGAL.proteins.
PDBFile.PDBRecord
)
ProGAL.proteins.
PDBFile.AtomRecord
(implements ProGAL.proteins.
PDBFile.PDBRecord
)
ProGAL.proteins.
PDBFile.HetatmRecord
ProGAL.proteins.
PDBFile.EndModelRecord
(implements ProGAL.proteins.
PDBFile.PDBRecord
)
ProGAL.proteins.
PDBFile.HelixRecord
(implements ProGAL.proteins.
PDBFile.PDBRecord
)
ProGAL.proteins.
PDBFile.ModelRecord
(implements ProGAL.proteins.
PDBFile.PDBRecord
)
ProGAL.proteins.
PDBFile.OtherRecord
(implements ProGAL.proteins.
PDBFile.PDBRecord
)
ProGAL.proteins.
PDBFile.ParentRecord
(implements ProGAL.proteins.
PDBFile.PDBRecord
)
ProGAL.proteins.
PDBFile.PDBChain
ProGAL.proteins.
PDBFile.PDBModel
ProGAL.proteins.
PDBFile.RemarkRecord
(implements ProGAL.proteins.
PDBFile.PDBRecord
)
ProGAL.proteins.
PDBFile.SheetRecord
(implements ProGAL.proteins.
PDBFile.PDBRecord
)
ProGAL.proteins.
PDBFile.TerRecord
(implements ProGAL.proteins.
PDBFile.PDBRecord
)
ProGAL.proteins.viewer.
PDBFileViewer
ProGAL.proteins.
PDBWebReader
ProGAL.geom3d.
Plane
(implements ProGAL.geom3d.
Shape
)
ProGAL.geom3d.tests.
PlaneTest
ProGAL.geomNd.
Point
(implements java.io.Serializable)
ProGAL.geom2d.
Point
ProGAL.geom2d.
TriangulationVertex
ProGAL.geom2d.delaunay.
Vertex
ProGAL.geom3d.
Point
(implements ProGAL.geom3d.
Simplex
)
ProGAL.proteins.structure.
Atom
ProGAL.geom3d.complex.
CVertex
ProGAL.geom3d.
PointWeighted
ProGAL.geomNd.complex.
Vertex
ProGAL.dataStructures.rangeSearching.rangeTree.
PointDimensionComparator
(implements java.util.Comparator<T>)
ProGAL.geomNd.tests.
PointTest
ProGAL.geom3d.tests.
PointTest
ProGAL.math.
Polynomial
ProGAL.math.test.
PolynomialTest
ProGAL.geom3d.predicates.
Predicates
ProGAL.geom3d.predicates.
ExactJavaPredicates
ProGAL.geom3d.predicates.
ExactNativePredicates
ProGAL.geom3d.predicates.
InexactJavaPredicates
ProGAL.geom3d.predicates.
InexactRegularJavaPredicates
ProGAL.proteins.belta.
PrimaryStructure
ProGAL.proteins.
ProteinComplex.Cavity
ProGAL.proteins.
ProteinComplex.Hole
ProGAL.proteins.dunbrack.
RamachandranDistribution
ProGAL.math.
Randomization
ProGAL.dataStructures.rangeSearching.rangeTree.
RangeTree
(implements ProGAL.dataStructures.rangeSearching.
RangeSearchDataStructure
)
ProGAL.dataStructures.rangeSearching.rangeTree.
RangeTreeAssocValue
ProGAL.dataStructures.rangeSearching.rangeTree.
RangeTreeNode
ProGAL.dataStructures.rangeSearching.rangeTree.
RangeTreeNode1d
ProGAL.dataStructures.rangeSearching.rangeTree.
RangeTreeNode2d
ProGAL.dataStructures.rangeSearching.rangeTree.
RangeTreeNodeNd
ProGAL.geom3d.
Rectangle
ProGAL.geom3d.complex.delaunayComplex.tests.
RegularComplexVisualTest
ProGAL.geom3d.tessellation.BowyerWatson.
RegularTessellation
ProGAL.geom3d.superposition.
RMSD
ProGAL.geom3d.superposition.tests.
RMSDTest
ProGAL.geom3d.volumes.
RSS
(implements ProGAL.geom3d.volumes.
Volume
)
ProGAL.proteins.belta.
SecondaryStructure
ProGAL.proteins.belta.
SecondaryStructure.SSSegment
ProGAL.proteins.belta.tests.
SecondaryStructureTest
ProGAL.proteins.beltaStructure.bnb.
SegmentStructure
(implements ProGAL.proteins.beltaStructure.bnb.
Branchable
)
ProGAL.dataStructures.
Set
<T> (implements java.lang.Iterable<T>)
ProGAL.geom2d.
PointSet
ProGAL.dataStructures.
SetIterator
(implements java.util.Iterator<E>)
ProGAL.proteins.beltaStructure.sheet.
SheetAlignment
ProGAL.proteins.beltaStructure.sheetLoop.
SheetLoopGUI
(implements ProGAL.geom3d.viewer.
ClickListener
)
ProGAL.proteins.beltaStructure.bnb.
SheetStructure
(implements ProGAL.proteins.beltaStructure.bnb.
Branchable
)
ProGAL.proteins.belta.
SheetTopology
ProGAL.proteins.belta.
SheetTopology.StrandPair
ProGAL.proteins.belta.tests.
SheetTopologyTest
ProGAL.geom3d.tessellation.BowyerWatson.
ShewchuckPredicates
ProGAL.math.
SingularValueDecomposition
ProGAL.dataStructures.
Sorter
ProGAL.dataStructures.
SorterQuick
ProGAL.dataStructures.
SortToolDouble
(implements ProGAL.dataStructures.
SortTool
)
ProGAL.dataStructures.
SortToolInteger
(implements ProGAL.dataStructures.
SortTool
)
ProGAL.dataStructures.
SortToolLineSegment2dAroundCommonPoint
(implements ProGAL.dataStructures.
SortTool
)
ProGAL.dataStructures.
SortToolLineSegment2dByLength
(implements ProGAL.dataStructures.
SortTool
)
ProGAL.dataStructures.
SortToolPoint2dAroundOrigo
(implements ProGAL.dataStructures.
SortTool
)
ProGAL.dataStructures.
SortToolPoint2dAroundPoint
(implements ProGAL.dataStructures.
SortTool
)
ProGAL.dataStructures.
SortToolPoint2dDistance
(implements ProGAL.dataStructures.
SortTool
)
ProGAL.dataStructures.
SortToolPoint2dXY
(implements ProGAL.dataStructures.
SortTool
)
ProGAL.dataStructures.
SortToolString
(implements ProGAL.dataStructures.
SortTool
)
ProGAL.geom3d.volumes.
Sphere
(implements ProGAL.geom3d.volumes.
Volume
)
ProGAL.geom3d.superposition.
Superposition
ProGAL.proteins.beltaStructure.sheet.
SurfaceSheetStructure
(implements ProGAL.proteins.beltaStructure.sheetLoop.
PartialStructure
)
ProGAL.geom3d.tess.
TCorner
ProGAL.geom3d.tess.
TESS
ProGAL.geomNd.complex.
Tessel
ProGAL.geom3d.tessellation.BowyerWatson.
Tet
ProGAL.geom3d.volumes.
Tetrahedron
(implements ProGAL.geom3d.
Simplex
, ProGAL.geom3d.volumes.
Volume
)
ProGAL.geom3d.complex.
CTetrahedron
ProGAL.geom3d.tessellation.BowyerWatson.
Tetr
ProGAL.geom3d.complex.alphaComplex.
TetrahedronAlphaProperties
(implements ProGAL.geom3d.complex.alphaComplex.
SimplexAlphaProperties
)
ProGAL.geom3d.viewer.
TextShape
(implements ProGAL.geom3d.
Shape
)
ProGAL.geom2d.viewer.
TextShape
(implements ProGAL.geom2d.
Shape
)
ProGAL.geom3d.tess.
TPoint
ProGAL.geom3d.superposition.
Transform
ProGAL.geom3d.superposition.tests.
TransformTest
ProGAL.geom2d.
Triangle
(implements ProGAL.geom2d.
Shape
)
ProGAL.geom2d.delaunay.
Triangle
ProGAL.geom3d.
Triangle
(implements ProGAL.geom3d.
Simplex
)
ProGAL.geom3d.complex.
CTriangle
ProGAL.geom3d.complex.alphaComplex.
TriangleAlphaProperties
(implements ProGAL.geom3d.complex.alphaComplex.
SimplexAlphaProperties
)
ProGAL.geom3d.tests.
TriangleTest
ProGAL.geom2d.
Triangulation
ProGAL.geom2d.
TriangulationFace
ProGAL.math.
Trigonometry
ProGAL.geom3d.tess.
TSphere
ProGAL.geom3d.complex.alphaComplex.
UnionFind
<E> (implements java.io.Serializable)
ProGAL.geomNd.
Vector
ProGAL.geom2d.
Vector
ProGAL.geom3d.
Vector
ProGAL.geom3d.
Vector.ImmutableVector3d
ProGAL.geom3d.complex.alphaComplex.
VertexAlphaProperties
(implements ProGAL.geom3d.complex.alphaComplex.
SimplexAlphaProperties
)
ProGAL.geom3d.complex.alphaComplex.
VoidTree
ProGAL.io.
WebIOToolbox
Interface Hierarchy
ProGAL.proteins.structure.generators.
AtomGenerator
ProGAL.proteins.beltaStructure.bnb.
Branchable
ProGAL.geom3d.viewer.
ClickListener
ProGAL.proteins.beltaStructure.bnb.
Constraint
ProGAL.dataStructures.viewer.
InteractiveBinaryTree
ProGAL.proteins.beltaStructure.bnb.lowerBounds.
LowerBound
ProGAL.proteins.beltaStructure.sheetLoop.
PartialStructure
ProGAL.proteins.
PDBFile.PDBRecord
ProGAL.dataStructures.rangeSearching.
RangeSearchDataStructure
ProGAL.geom2d.
Shape
ProGAL.geom3d.
Shape
ProGAL.geom3d.
Simplex
ProGAL.geom3d.volumes.
Volume
ProGAL.geom3d.complex.alphaComplex.
SimplexAlphaProperties
ProGAL.geom3d.complex.
SimplicialComplex
ProGAL.dataStructures.
SortTool
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
ProGAL.geom2d.
TriangulationVertex.VertexType
ProGAL.geom2d.
Triangulation.TriangulationAlgorithm
ProGAL.geom2d.
ConvexPolygon.ConvexHullAlgorithm
ProGAL.geom3d.complex.
CVertex.DegenerateCase
ProGAL.geomNd.complex.
Vertex.DegenerateCase
ProGAL.geom3d.predicates.
Predicates.SphereConfig
ProGAL.geom3d.predicates.
Predicates.PlaneConfig
ProGAL.proteins.belta.
SSType
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