Serialized Form

Package ProGAL.dataStructures.viewer

Class ProGAL.dataStructures.viewer.BinaryTreePainter extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

root

BinaryTreePainter.PNode root

pp

ProGAL.dataStructures.viewer.BinaryTreePainter.PaintPane pp

Package ProGAL.geom2d

Class ProGAL.geom2d.ConvexPolygon extends Polygon implements Serializable

serialVersionUID: 1L

Class ProGAL.geom2d.Point extends Point implements Serializable

serialVersionUID: 8095991200265432551L

Class ProGAL.geom2d.Polygon extends java.util.ArrayList<Point> implements Serializable

serialVersionUID: 1L

Class ProGAL.geom2d.TriangulationVertex extends Point implements Serializable

serialVersionUID: 1L

Serialized Fields

id

int id

face

TriangulationFace face

orbit

Circle orbit

polarAngle

double polarAngle

cosAngle

double cosAngle

sinAngle

double sinAngle

polarRadius

double polarRadius

squaredPolarRadius

double squaredPolarRadius

type

TriangulationVertex.VertexType type

Package ProGAL.geom2d.delaunay

Class ProGAL.geom2d.delaunay.Vertex extends Point implements Serializable

serialVersionUID: 1L

Serialized Fields

id

int id

first

Triangle first

last

Triangle last

Package ProGAL.geom3d

Class ProGAL.geom3d.Point extends Point implements Serializable

serialVersionUID: -2120468832687547475L

Class ProGAL.geom3d.PointList extends java.util.ArrayList<Point> implements Serializable

serialVersionUID: -4824374877674925546L

Class ProGAL.geom3d.PointWeighted extends Point implements Serializable

serialVersionUID: 1L

Serialized Fields

w

double w

Package ProGAL.geom3d.complex

Class ProGAL.geom3d.complex.CVertex extends Point implements Serializable

serialVersionUID: 1L

Serialized Fields

degenerate

boolean degenerate

degCase

CVertex.DegenerateCase degCase

degPointOpposite

CVertex degPointOpposite

degPointA

CVertex degPointA

degPointB

CVertex degPointB

bigPoint

boolean bigPoint

adjacentEdges

java.util.List<E> adjacentEdges

Package ProGAL.geom3d.complex.alphaComplex

Class ProGAL.geom3d.complex.alphaComplex.EiffelPointList extends PointList implements Serializable

serialVersionUID: 1L

Serialized Fields

points

Point[] points

Class ProGAL.geom3d.complex.alphaComplex.UnionFind extends java.lang.Object implements Serializable

serialVersionUID: -9141049716473285037L

Serialized Fields

elmap

java.util.Map<K,V> elmap

Package ProGAL.geomNd

Class ProGAL.geomNd.Point extends java.lang.Object implements Serializable

serialVersionUID: -6776647998875885511L

Serialized Fields

coords

double[] coords

The double-array that holds the value of this point

dim

int dim

The dimension of this point.

Class ProGAL.geomNd.PointList extends java.util.ArrayList<Point> implements Serializable

serialVersionUID: -2860146038113339241L

Serialized Fields

dim

int dim

Package ProGAL.geomNd.complex

Class ProGAL.geomNd.complex.Vertex extends Point implements Serializable

serialVersionUID: 1L

Serialized Fields

degenerate

boolean degenerate

bigPoint

boolean bigPoint

Package ProGAL.math

Class ProGAL.math.LUDecomposition extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

LU

double[][] LU

Array for internal storage of decomposition.

internal array storage.

m

int m

Row and column dimensions, and pivot sign.

column dimension.

n

int n

Row and column dimensions, and pivot sign.

column dimension.

pivsign

int pivsign

Row and column dimensions, and pivot sign.

column dimension.

piv

int[] piv

Internal storage of pivot vector.

pivot vector.

Package ProGAL.proteins

Class ProGAL.proteins.PDBFile extends java.io.File implements Serializable

serialVersionUID: 1791445213018199901L

Serialized Fields

includeHydrogens

boolean includeHydrogens

includeHetAtms

boolean includeHetAtms

standardModel

int standardModel

standardChain

int standardChain

records

java.util.List<E> records

models

java.util.List<E> models

name

java.lang.String name

The name of this PDB-file. Typically the PDB-id.

Package ProGAL.proteins.belta

Class ProGAL.proteins.belta.PDBFile extends PDBFile implements Serializable

serialVersionUID: -8750143450211694975L

Serialized Fields

helixRecords

java.util.List<E> helixRecords

sheetRecords

java.util.List<E> sheetRecords

shiftMap

java.util.Map<K,V> shiftMap

Package ProGAL.proteins.structure

Class ProGAL.proteins.structure.Atom extends Point implements Serializable

serialVersionUID: -6262882698432071090L

Serialized Fields

radius

double radius

element

char element

name

java.lang.String name

id

int id

covalentBonds

CBond[] covalentBonds

aminoAcid

AminoAcid aminoAcid

index

int index