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

D

definedResidues() - Method in interface ProGAL.proteins.beltaStructure.bnb.Branchable

definedResidues() - Method in class ProGAL.proteins.beltaStructure.bnb.SegmentStructure

definedResidues() - Method in class ProGAL.proteins.beltaStructure.bnb.SheetStructure

DelaunayComplex - Class in ProGAL.geom3d.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).

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

Builds the Delaunay complex of the specified point-set

DelaunayComplexKinetic - Class in ProGAL.geom3d.complex.delaunayComplex

DelaunayComplexKinetic() - Constructor for class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexKinetic

DelaunayComplexRotation - Class in ProGAL.geom3d.complex.delaunayComplex

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

DelaunayComplexRotation.HeapItemComp - Class in ProGAL.geom3d.complex.delaunayComplex

DelaunayComplexRotation.HeapItemComp() - Constructor for class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexRotation.HeapItemComp

DelaunayComplexRotation_Stavefejl - Class in ProGAL.geom3d.complex.delaunayComplex

DelaunayComplexRotation_Stavefejl() - Constructor for class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexRotation_Stavefejl

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

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

DelaunayTessellation - Class in ProGAL.geom3d.complex.tessellation

A Delaunay tessellation 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).

DelaunayTessellation(List<Point>) - Constructor for class ProGAL.geom3d.complex.tessellation.DelaunayTessellation

Builds the Delaunay complex of the specified point-set

delete(DLCyclicList.DLNode<T>) - Method in class ProGAL.dataStructures.DLCyclicList

Deletes a node from the list and returns its object.

delete(DLList.DLNode) - Method in class ProGAL.dataStructures.DLList

delete(Object) - Method in class ProGAL.dataStructures.Set

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

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

deleteIndex(int) - Method in class ProGAL.dataStructures.Set

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

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

deletes last corner of the polygon

det() - Method in class ProGAL.math.LUDecomposition

Determinant

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

Get the determinant of this matrix.

determinant() - Method in class ProGAL.math.Matrix3x3

Get the determinant of this matrix.

Diameter_Clash_LowerBound - Class in ProGAL.proteins.beltaStructure.bnb.lowerBounds

A lower bound that seeks to minimize the diameter of the structure while not allowing any clashes.

Diameter_Clash_LowerBound() - Constructor for class ProGAL.proteins.beltaStructure.bnb.lowerBounds.Diameter_Clash_LowerBound

diameterSqrt3Approx() - Method in class ProGAL.geom3d.PointList

Get a segment seg between two points in the set such that diameter/sqrt(3) <= seg.

diffsides(Point, Point, Point, Point, Point) - Method in class ProGAL.geom3d.predicates.ExactJavaPredicates

diffsides(Point, Point, Point, Point, Point) - Method in class ProGAL.geom3d.predicates.ExactNativePredicates

diffsides(Point, Point, Point, Point, Point) - Method in class ProGAL.geom3d.predicates.InexactJavaPredicates

diffsides(Point, Point, Point, Point, Point) - Method in class ProGAL.geom3d.predicates.InexactRegularJavaPredicates

diffsides(Point, Point, Point, Point, Point) - Method in class ProGAL.geom3d.predicates.Predicates

DisjointSet - Class in ProGAL.dataStructures

DisjointSet() - Constructor for class ProGAL.dataStructures.DisjointSet

DisjointSet - Class in ProGAL.geom3d.complex.alphaComplex

A class for maintaining disjoint sets using union-by-rank and path-compression.

DisjointSet() - Constructor for class ProGAL.geom3d.complex.alphaComplex.DisjointSet

DisjointSet.DSNode - Class in ProGAL.dataStructures

DisjointSet.DSNode(Object) - Constructor for class ProGAL.dataStructures.DisjointSet.DSNode

DisjointSet.Set - Class in ProGAL.geom3d.complex.alphaComplex

A class representing a set.

DisjointSet.Set() - Constructor for class ProGAL.geom3d.complex.alphaComplex.DisjointSet.Set

display2D(BowyerWatson) - Static method in class ProGAL.geomNd.complex.delaunayComplex.BWViewer

display3D(BowyerWatson) - Static method in class ProGAL.geomNd.complex.delaunayComplex.BWViewer

displayStructure(PDBFile) - Method in class ProGAL.proteins.viewer.PDBFileViewer

displayTessel(BowyerWatson) - Static method in class ProGAL.geomNd.complex.delaunayComplex.BWViewer

distance(Point) - Method in class ProGAL.geom2d.LineSegment

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

Get the distance from this point to point q

distance(Rectangle) - Method in class ProGAL.geom3d.Rectangle

distance(Point) - Method in class ProGAL.geom3d.volumes.Lens

distance(Lens) - Method in class ProGAL.geom3d.volumes.Lens

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

Returns distance to the point p

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

Returns distance to the origo

distance_Gottschalk(Rectangle) - Method in class ProGAL.geom3d.Rectangle

distance_nonoptimized(Rectangle) - Method in class ProGAL.geom3d.Rectangle

670HOps

distance_optimized(Rectangle) - Method in class ProGAL.geom3d.Rectangle

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

Get the squared distance from this point to point q.

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

Returns squared distance to the point p

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

Returns squared distance to the origo

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

Returns the squared distance to the origo of this point projected onto xy plane

distanceToPoint(Point) - Method in class ProGAL.geom3d.volumes.LSS

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

Returns the distance to the origo of this point projected onto xy plane

divide(double) - Method in class ProGAL.geom3d.Vector

Divide this vector by s and return the result (without changing this object).

divide(double) - Method in class ProGAL.geomNd.Vector

Divide this vector by s and return the result (without changing this object).

DivideAndConquer - Class in ProGAL.geom2d.convexHull

DivideAndConquer() - Constructor for class ProGAL.geom2d.convexHull.DivideAndConquer

divideThis(double) - Method in class ProGAL.geom3d.Vector

Divide this vector by s and return the result (changing this object).

divideThis(double) - Method in class ProGAL.geomNd.Vector

Divide this vector by s and return the result (changing this object).

DLCyclicList<T> - Class in ProGAL.dataStructures

DLCyclicList() - Constructor for class ProGAL.dataStructures.DLCyclicList

DLCyclicList.DLNode<T> - Class in ProGAL.dataStructures

DLCyclicList.DLNode(T) - Constructor for class ProGAL.dataStructures.DLCyclicList.DLNode

DLCyclicList.DLNode(T, DLCyclicList.DLNode<T>, DLCyclicList.DLNode<T>) - Constructor for class ProGAL.dataStructures.DLCyclicList.DLNode

DLList - Class in ProGAL.dataStructures

DLList() - Constructor for class ProGAL.dataStructures.DLList

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

Returns true if this point dominates point q.

dominates(Point, int, int, int) - Method in class ProGAL.geom3d.Point

Returns true if this point dominates point q (i=0,1,2 is the most important coordinate, j=0,1,2 is the second most important coordinate and k=0,1,2 is the least important coordinate).

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

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

dot(Vector) - Method in class ProGAL.geom3d.Point

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

Get the dot-product of this vector and v.

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

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

Get the dot-product of this vector and v.

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

downloadFile(String) - Static method in class ProGAL.io.WebIOToolbox

Downloads an online document to a temporary file and returns its path.

downloadPDBFile(String) - Static method in class ProGAL.proteins.PDBFile

Read a PDB-file from www.pdb.org.

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

downloadPDBFile(String, boolean) - Static method in class ProGAL.proteins.PDBWebReader

Downloads a PDB-file to a temporary file and returns the path

draw(J2DScene, Color) - Method in class ProGAL.geom2d.Polygon

draws the polygon

draw(J2DScene) - Method in class ProGAL.geom2d.Polygon

draw(J2DScene) - Method in class ProGAL.geom2d.Triangulation

draw(J2DScene, Color) - Method in class ProGAL.geom2d.TriangulationFace

draw(J2DScene) - Method in class ProGAL.geom2d.TriangulationFace

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

drawCircumCircle(J2DScene, Color) - Method in class ProGAL.geom2d.TriangulationFace

drawRotatedCircumCircle(J2DScene, Color, double, List<Integer>) - Method in class ProGAL.geom2d.TriangulationFace

drawScene(J3DScene, CVertex, Circle) - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexRotation

DTNoBigPoints - Class in ProGAL.geom2d.delaunay

Constructs a delaunay triangulation from a point-set without using big points.

DTNoBigPoints(List<Point>) - Constructor for class ProGAL.geom2d.delaunay.DTNoBigPoints

Constructs the Delaunay triangulation

DTWithBigPoints - Class in ProGAL.geom2d.delaunay

Constructs a Delaunay triangulation using 3 big points.

DTWithBigPoints(List<Point>) - Constructor for class ProGAL.geom2d.delaunay.DTWithBigPoints