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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
 

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