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

A

a1 - Variable in class ProGAL.proteins.structure.CBond

a2 - Variable in class ProGAL.proteins.structure.CBond

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

The type of amino acid in a three-letter code, for example: TYR, ALA or ARG

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

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

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

add(Object) - Method in class ProGAL.dataStructures.DLList

add(Vector) - Method in class ProGAL.geom2d.Point

Add the vector v to this point and return the result

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

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

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

Returns p added to this (without changing this object).

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

Add v to this vector and return the result (without changing this object).

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

Add p to this vector and return the result (without changing this object).

add(Point) - Method in class ProGAL.geomNd.PointList

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

Add v to this vector and return the result (without changing this object).

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

Add the components of two matrices.

addAdjacentEdge(CEdge) - Method in class ProGAL.geom3d.complex.CVertex

addClickListener(ClickListener) - Method in class ProGAL.geom3d.viewer.J3DScene

Add a click-listener that gets called every time an object or the background is clicked

addPoint(Point) - Method in class ProGAL.dataStructures.rangeSearching.GridMap

addPoint(Point) - Method in class ProGAL.dataStructures.rangeSearching.LinearRangeSearch

addPoint(Point) - Method in class ProGAL.geom2d.delaunay.DTWithBigPoints

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

Add a shape to this scene.

addShape(Shape, Color) - Method in class ProGAL.geom2d.viewer.J2DScene

Add a shape to this scene with the specified color.

addShape(Shape, Color, double) - Method in class ProGAL.geom2d.viewer.J2DScene

addShape(Shape, Color, double, boolean) - Method in class ProGAL.geom2d.viewer.J2DScene

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

Add a volume object.

addShape(Shape, Color) - Method in class ProGAL.geom3d.viewer.J3DScene

Add a volume object with a specified color

addShape(Shape, Color, int) - Method in class ProGAL.geom3d.viewer.J3DScene

Add a volume object with a specified color and detail-level

addSurface(ParametricSurface) - Method in class ProGAL.geom3d.viewer.J3DScene

addSurface(ParametricSurface, Color) - Method in class ProGAL.geom3d.viewer.J3DScene

addSurface(ParametricSurface, Color, double, double, int, double, double, int) - Method in class ProGAL.geom3d.viewer.J3DScene

addText(String, Point) - Method in class ProGAL.geom3d.viewer.J3DScene

Add a text-object at the specified position.

addText(String, Point, double) - Method in class ProGAL.geom3d.viewer.J3DScene

addText(String, Point, double, Color) - Method in class ProGAL.geom3d.viewer.J3DScene

addThis(Vector) - Method in class ProGAL.geom2d.Point

Add the vector v to this point and return the result (changes this object)

addThis(Point) - Method in class ProGAL.geom2d.Point

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

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

addThis(Point) - Method in class ProGAL.geom2d.Vector

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

Returns p added to this (changing this object).

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

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

Add v to this vector and return the result (changing this object).

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

Add p to this vector and return the result (changing this object).

addThis(Vector) - Method in class ProGAL.geom3d.Vector.ImmutableVector3d

addThis(Vector) - Method in class ProGAL.geomNd.Point

Add the specified vector to this point.

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

Add v to this vector and return the result (changing this object).

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

Add the components of two matrices.

addThis(Matrix) - Method in class ProGAL.math.Matrix.ImmutableMatrix

addToHeap(CTetrahedron, CVertex, double, Circle) - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexRotation

addTriangle(CTriangle) - Method in class ProGAL.geom3d.complex.CEdge

addValue(double) - Method in class ProGAL.statistics.Histogram

addValues(List<Double>) - Method in class ProGAL.statistics.Histogram

alignmentPairs - Variable in class ProGAL.proteins.beltaStructure.sheet.SheetAlignment

The entire alignment is specified by sTop.strandPairs.size() residue indices.

AllAtomAminoAcidGenerator - Class in ProGAL.proteins.structure.generators

AllAtomAminoAcidGenerator() - Constructor for class ProGAL.proteins.structure.generators.AllAtomAminoAcidGenerator

allKnownElements() - Method in class ProGAL.geom3d.complex.alphaComplex.UnionFind

Returns an unmodifiable set containing all elements that this UnionFind structure has knowledge about.

AllTests - Class in ProGAL

AllTests() - Constructor for class ProGAL.AllTests

AlphaComplex - Class in ProGAL.geom3d.complex.alphaComplex

An alpha complex for a set of d-dimensional points and a real number alpha is a subset of the Delaunay complex where all simplices that can be enclosed by an alpha-probe (a hypersphere of radius alpha), without the probe enclosing any points, are removed.

AlphaComplex(List<Point>, double) - Constructor for class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

Build the alpha-complex of the specified point-list.

AlphaComplex(RegularComplex, double) - Constructor for class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

Build the alpha-complex of the specified Delaunay complex.

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

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

AlphaFiltration - Class in ProGAL.geom3d.complex.alphaComplex

An alpha complex for a set of d-dimensional points and a real number alpha is a subset of the Delaunay complex where all simplices that can be enclosed by an alpha-probe (a hypersphere of radius alpha), without the probe enclosing any points, are removed.

AlphaFiltration(List<Point>) - Constructor for class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

Build the alpha-filtration of the specified point-list.

AlphaFiltration(DelaunayComplex) - Constructor for class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

Build the alpha-filtration of the specified Delaunay complex.

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

AminoAcid - Class in ProGAL.proteins.structure

An amino acid containing the following properties: Pointers to all atoms within this amino acid a pointer to the AminoAcidChain that contains this amino acid the type of the amino acid (Alanine, arginine etc.) an index specifying this amino acids placement in the aminoAcidChain().aminoAcids()-array (for convenience)

AminoAcid(char, Atom[]) - Constructor for class ProGAL.proteins.structure.AminoAcid

aminoAcid(int) - Method in class ProGAL.proteins.structure.AminoAcidChain

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

aminoAcidChain() - Method in class ProGAL.proteins.structure.AminoAcid

AminoAcidChain - Class in ProGAL.proteins.structure

A chain of amino acids.

AminoAcidChain(String) - Constructor for class ProGAL.proteins.structure.AminoAcidChain

AminoAcidChain(String, AtomGenerator) - Constructor for class ProGAL.proteins.structure.AminoAcidChain

aminoAcids() - Method in class ProGAL.proteins.structure.AminoAcidChain

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

Get the angle between this vector and v.

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

Get the angle between this vector and v.

apexid(int) - Method in class ProGAL.geom3d.complex.CTetrahedron

apexid(int) - Method in class ProGAL.geomNd.complex.Tessel

ApolloniusSolver - Class in ProGAL.geom2d

ApolloniusSolver() - Constructor for class ProGAL.geom2d.ApolloniusSolver

ApolloniusSolver - Class in ProGAL.geom3d

ApolloniusSolver() - Constructor for class ProGAL.geom3d.ApolloniusSolver

ApolloniusSolver - Class in ProGAL.geomNd

ApolloniusSolver() - Constructor for class ProGAL.geomNd.ApolloniusSolver

append(Set<T>) - Method in class ProGAL.dataStructures.Set

append(T[]) - Method in class ProGAL.dataStructures.Set

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

Returns the signed area of the triangle defined by the three points a, b and c (positive if counterclockwise)

areParallel(Line, Line) - Static method in class ProGAL.geom2d.Line

areUnified(E, E) - Method in class ProGAL.geom3d.complex.alphaComplex.UnionFind

Checks whether the elements e1 and e2 are unified in this union-find structure.

atom(String) - Method in class ProGAL.proteins.structure.AminoAcid

atom(int) - Method in class ProGAL.proteins.structure.AminoAcid

atom(int, String) - Method in class ProGAL.proteins.structure.AminoAcidChain

atom(int, int) - Method in class ProGAL.proteins.structure.AminoAcidChain

Atom - Class in ProGAL.proteins.structure

A class to represent the following properties of an atom: Position Van der waals radius covalent bonds name an id unique to this atom among all the atoms within the same amino acid a pointer to the residue that the atom belongs to The position is maintained in the super-class Point.

Atom(String) - Constructor for class ProGAL.proteins.structure.Atom

Atom(String, char, double) - Constructor for class ProGAL.proteins.structure.Atom

AtomGenerator - Interface in ProGAL.proteins.structure.generators

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

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

atoms() - Method in class ProGAL.proteins.structure.AminoAcid

atoms() - Method in class ProGAL.proteins.structure.AminoAcidChain

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

The type of atom.

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

Zoom the view to enclose all the objects in the scene.

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

Zooms such that the maximal distance between two objects is within the view

averageDepth() - Method in class ProGAL.proteins.ProteinComplex.Hole