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

I

incenter() - Method in class ProGAL.geom3d.Triangle

incenter() - Method in class ProGAL.geom3d.volumes.Tetrahedron

Find the center of the inscribed sphere.

inCH(Triangle) - Method in class ProGAL.geom2d.delaunay.DTWithBigPoints

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

Returns a positive double if the point is inside the circle through the 3 specified points (must be in clockwise order).

incircle(double[], double[], double[], double[]) - Method in class ProGAL.geom3d.predicates.ExactJavaPredicates

inCircumCircle(Point) - Method in class ProGAL.geom2d.Triangle

inCylinder(Point) - Method in class ProGAL.geom3d.volumes.Cylinder

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

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

InexactJavaPredicates - Class in ProGAL.geom3d.predicates

InexactJavaPredicates() - Constructor for class ProGAL.geom3d.predicates.InexactJavaPredicates

InexactJavaPredicatesTest - Class in ProGAL.geom3d.predicates.tests

InexactJavaPredicatesTest() - Constructor for class ProGAL.geom3d.predicates.tests.InexactJavaPredicatesTest

InexactRegularJavaPredicates - Class in ProGAL.geom3d.predicates

InexactRegularJavaPredicates() - Constructor for class ProGAL.geom3d.predicates.InexactRegularJavaPredicates

InfCylinder - Class in ProGAL.geom3d.volumes

An infinitely extended cylinder defined using a line and a radius.

InfCylinder(Line, double) - Constructor for class ProGAL.geom3d.volumes.InfCylinder

initChainID - Variable in class ProGAL.proteins.PDBFile.HelixRecord

initChainID - Variable in class ProGAL.proteins.PDBFile.SheetRecord

initSeqNum - Variable in class ProGAL.proteins.PDBFile.HelixRecord

initSeqNum - Variable in class ProGAL.proteins.PDBFile.SheetRecord

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

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

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

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

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

inradius() - Method in class ProGAL.geom3d.Triangle

insert(Object) - Method in class ProGAL.dataStructures.Heap

insert(T) - Method in class ProGAL.dataStructures.Set

insertAfter(Point, int) - Method in class ProGAL.geom2d.Polygon

inserts point p into the polygon after the corner with specified index

inSphere(Point, Point, Point, Point, Point) - Static method in class ProGAL.geom3d.Point

Returns a positive double if point t is inside the sphere through points p, q, r, s.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

inSphere(Tessel, Point) - Static method in class ProGAL.geomNd.complex.delaunayComplex.BowyerWatson

Return true if and only if the point p is inside or on the boundary of the circumsphere of t

InteractiveBinaryTree - Interface in ProGAL.dataStructures.viewer

intersectionParameter(Line) - Method in class ProGAL.geom2d.Line

intersectionParameter(Line) - Method in class ProGAL.geom3d.ParametricPlane

Returns a parameter setting for the line describing the intersection with this plane.

intersectionParameter(Line) - Method in class ProGAL.geom3d.volumes.Cylinder

intersectionParameters(Line) - Method in class ProGAL.geom3d.volumes.Sphere

Returns the two line-parameters that indicate where line intersects this sphere.

intersections(Circle) - Method in class ProGAL.geom2d.Circle

intersections(Line) - Method in class ProGAL.geom2d.Circle

intersects(LineSegment) - Method in class ProGAL.geom2d.LineSegment

returns TRUE if this line segment properly intersects line segment s.

intersects(Interval) - Method in class ProGAL.geom3d.complex.alphaComplex.Interval

Interval - Class in ProGAL.geom3d.complex.alphaComplex

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

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

Return the inverse of this matrix.

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

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

Invert this matrix (overwrites this and returns it).

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

Invert this matrix (overwrites this and returns it).

IOToolbox - Class in ProGAL.io

A wrapper class for static file input/output methods.

IOToolbox() - Constructor for class ProGAL.io.IOToolbox

isAcute() - Method in class ProGAL.geom3d.volumes.Tetrahedron

isAlive() - Method in class ProGAL.geom2d.TriangulationFace

isAttached() - Method in class ProGAL.geom3d.complex.alphaComplex.EdgeAlphaProperties

isAttached() - Method in interface ProGAL.geom3d.complex.alphaComplex.SimplexAlphaProperties

isAttached() - Method in class ProGAL.geom3d.complex.alphaComplex.TetrahedronAlphaProperties

isAttached() - Method in class ProGAL.geom3d.complex.alphaComplex.TriangleAlphaProperties

isAttached() - Method in class ProGAL.geom3d.complex.alphaComplex.VertexAlphaProperties

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

isBigpoint() - Method in class ProGAL.geom3d.complex.CVertex

isBigpoint() - Method in class ProGAL.geomNd.complex.Vertex

isBuried(CVertex) - Method in class ProGAL.proteins.ProteinComplex

isBuried(PDBFile.AtomRecord) - Method in class ProGAL.proteins.ProteinComplex

isClosed() - Method in class ProGAL.proteins.beltaStructure.ChainTreeLoop

isClosed() - Method in class ProGAL.proteins.beltaStructure.loop.LoopStructure

Indicates if the loop is closed, ie.

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

isDegenerate() - Method in class ProGAL.geom3d.complex.CVertex

isDegenerate() - Method in class ProGAL.geomNd.complex.Vertex

isDelaunay() - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplex

TODO: Finish

isEmpty() - Method in class ProGAL.dataStructures.DLCyclicList

Returns true if the list is empty

isEmpty() - Method in class ProGAL.dataStructures.DLList

isEmpty() - Method in class ProGAL.dataStructures.Heap

returns true if the heap is empty.

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

isEmpty(Point[], double) - Method in class ProGAL.geom3d.volumes.Sphere

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

isFlat() - Method in class ProGAL.geom2d.TriangulationFace

isFlat() - Method in class ProGAL.geom3d.complex.CTetrahedron

isHydrogen() - Method in class ProGAL.proteins.PDBFile.AtomRecord

isHydrogenAcceptor() - Method in class ProGAL.proteins.PDBFile.AtomRecord

Returns true if the atom can act as a hydrogen acceptor in a hydrogen bond

isHydrogenDonor() - Method in class ProGAL.proteins.PDBFile.AtomRecord

Returns true if the atom can act as a hydrogen donor in a hydrogen bond

isInside(Point) - Method in class ProGAL.geom3d.volumes.Sphere

Returns true if the point is inside this sphere

isInside(Point, double) - Method in class ProGAL.geom3d.volumes.Sphere

isInside(Point) - Method in class ProGAL.geom3d.volumes.Tetrahedron

Returns true if the point p is inside this tetrahedron.

isIntersected(Sphere) - Method in class ProGAL.geom3d.volumes.Sphere

Returns true if this sphere is intersected or touched by another sphere.

isLocked(int, int) - Method in class ProGAL.proteins.chainTree.ChainTree

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

isModified() - Method in class ProGAL.geom3d.complex.CTetrahedron

isModified() - Method in class ProGAL.geomNd.complex.Tessel

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

Is the matrix nonsingular?

isOnBackbone() - Method in class ProGAL.proteins.PDBFile.AtomRecord

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

isParallelWith(Line) - Method in class ProGAL.geom2d.Line

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

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

isValid() - Method in class ProGAL.proteins.belta.BetaTopology

Checks if this beta-topology is valid.

isVertical() - Method in class ProGAL.geom2d.Line

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

Return true if the length of this vector is 0.

iterator() - Method in class ProGAL.dataStructures.DLCyclicList

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