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

S

samplePhiPsi(int) - Method in class ProGAL.proteins.dunbrack.RamachandranDistribution

scale(double) - Method in class ProGAL.geom2d.Vector

scaleThis(double) - Method in class ProGAL.geom3d.Point

Scale this point by a factor s

scaleToLength(double) - Method in class ProGAL.geom2d.Vector

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

Scale this vector to a certain length (returns new object and does not change this object).

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

Scale this vector to a certain length (returns new object and does not change this object).

scaleToLengthThis(double) - Method in class ProGAL.geom3d.Vector.ImmutableVector3d

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

Scale this vector to a certain length (changes this object).

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

Scale this vector to a certain length (changes this object).

scene - Variable in class ProGAL.proteins.viewer.PDBFileViewer

secondaryStructure - Variable in class ProGAL.proteins.belta.BetaTopology

The secondary structure that the beta-topology is related to

SecondaryStructure - Class in ProGAL.proteins.belta

Representation of a secondary structure assignment.

SecondaryStructure(PrimaryStructure, String) - Constructor for class ProGAL.proteins.belta.SecondaryStructure

Construct a secondary structure object from a string representation.

SecondaryStructure(String) - Constructor for class ProGAL.proteins.belta.SecondaryStructure

Construct a secondary structure object from a string representation.

secondaryStructure - Variable in class ProGAL.proteins.belta.SheetTopology

The secondary structure that the sheet-topology is related to

secondaryStructure - Variable in class ProGAL.proteins.beltaStructure.ChainTreeLoop

secondaryStructure - Variable in class ProGAL.proteins.beltaStructure.loop.CALoopStructure

secondaryStructure - Variable in class ProGAL.proteins.beltaStructure.loop.LoopStructure

secondaryStructure - Variable in class ProGAL.proteins.beltaStructure.sheetLoop.SheetLoopStructure

SecondaryStructure.SSSegment - Class in ProGAL.proteins.belta

A secondary structure segment of either helix, coil or strand.

SecondaryStructureTest - Class in ProGAL.proteins.belta.tests

SecondaryStructureTest() - Constructor for class ProGAL.proteins.belta.tests.SecondaryStructureTest

seed(long) - Static method in class ProGAL.math.Randomization

Seeds the random generater used by this class.

seg - Variable in class ProGAL.proteins.beltaStructure.bnb.SegmentStructure

segment - Variable in class ProGAL.geom3d.volumes.LSS

segment1 - Variable in class ProGAL.proteins.beltaStructure.ChainTreeLoop

segment1 - Variable in class ProGAL.proteins.beltaStructure.loop.CALoopStructure

segment1 - Variable in class ProGAL.proteins.beltaStructure.loop.LoopStructure

segment2 - Variable in class ProGAL.proteins.beltaStructure.ChainTreeLoop

segment2 - Variable in class ProGAL.proteins.beltaStructure.loop.CALoopStructure

segment2 - Variable in class ProGAL.proteins.beltaStructure.loop.LoopStructure

segmentIndex - Variable in class ProGAL.proteins.belta.SecondaryStructure.SSSegment

segments - Variable in class ProGAL.proteins.belta.SecondaryStructure

Secondary structure segments (helix, coil or strand)

segments - Variable in class ProGAL.proteins.beltaStructure.loop.CALoopStructure

SegmentStructure - Class in ProGAL.proteins.beltaStructure.bnb

SegmentStructure(int, int, SecondaryStructure, SecondaryStructure.SSSegment, AminoAcidChain) - Constructor for class ProGAL.proteins.beltaStructure.bnb.SegmentStructure

Construct a segment structure for the specified segment with dirs directions, rots rotations

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

sequence - Variable in class ProGAL.proteins.belta.PrimaryStructure

The sequence of a protein chain

Set<T> - Class in ProGAL.dataStructures

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

Set(int) - Constructor for class ProGAL.dataStructures.Set

Set(Object) - Constructor for class ProGAL.dataStructures.Set

Set(Object[]) - Constructor for class ProGAL.dataStructures.Set

Set(Set<T>) - Constructor for class ProGAL.dataStructures.Set

set(int, Object) - Method in class ProGAL.dataStructures.Set

set(int, double) - Method in class ProGAL.geom3d.Vector.ImmutableVector3d

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

Set all coordinates of this vector equal to those of v

set(int, double) - Method in class ProGAL.geomNd.Point

Set the d'th coordinate.

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

Set the coordinates to be identical to those in the specified point.

set(int, double) - Method in class ProGAL.geomNd.Vector

Set the i'th coordinate to v

set(int, int, double) - Method in class ProGAL.math.Matrix.ImmutableMatrix

set(int, int, double) - Method in class ProGAL.math.Matrix

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

setA(Point) - Method in class ProGAL.geom3d.LineSegment

Change the first point spanning the segment.

setA(double) - Method in class ProGAL.geom3d.surface.ParametricParaboloid

setAligned(int, int) - Method in class ProGAL.proteins.beltaStructure.sheet.SheetAlignment

Aligns the strand with residue res1 with another strand containing res2 such that res1 and res2 are aligned.

setAlive(boolean) - Method in class ProGAL.geom2d.TriangulationFace

setAlpha(double) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

setAnchor(Point) - Method in class ProGAL.geom3d.volumes.OBB

setAntialiasing(boolean) - Method in class ProGAL.geom3d.viewer.J3DScene

setAxisEnabled(boolean) - Method in class ProGAL.geom3d.viewer.J3DScene

Enables or disables xyz-axis from the origo

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

setB(Point) - Method in class ProGAL.geom3d.LineSegment

Change the second point spanning the segment.

setB(double) - Method in class ProGAL.geom3d.surface.ParametricParaboloid

setBackClip(double) - Method in class ProGAL.geom3d.viewer.Camera

setBackFog(double) - Method in class ProGAL.geom3d.viewer.Camera

setBackgroundColor(Color) - Method in class ProGAL.geom3d.viewer.J3DScene

Set color of background.

setC(double) - Method in class ProGAL.geom3d.surface.ParametricParaboloid

setCenter(Point) - Method in class ProGAL.geom2d.Circle

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

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

setCenter(Point) - Method in class ProGAL.geomNd.HyperSphere

setChild(Node, int) - Method in class ProGAL.geom3d.complex.alphaComplex.Node

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

setCircumCircle(Circle) - Method in class ProGAL.geom2d.TriangulationFace

setCircumCircleCenterX(double) - Method in class ProGAL.geom2d.TriangulationFace

setCircumCircleCenterY(double) - Method in class ProGAL.geom2d.TriangulationFace

setCircumCircleRadius(double) - Method in class ProGAL.geom2d.TriangulationFace

setColumn(int, Vector) - Method in class ProGAL.math.Matrix

setCoord(int, double) - Method in class ProGAL.geom3d.Vector.ImmutableVector3d

setCoord(int, double) - Method in class ProGAL.geomNd.Point

Set the d'th coordinate.

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

Set the coordinates to be identical to those in the specified point.

setCoord(int, double) - Method in class ProGAL.geomNd.Vector

Set the i'th coordinate to v

setCoords(double[]) - Method in class ProGAL.geomNd.Vector

Set the coordinates

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

setCorner(Point, int) - Method in class ProGAL.geom2d.Triangle

setCosAngle(double) - Method in class ProGAL.geom2d.TriangulationVertex

setCovalentBonds(CBond[]) - Method in class ProGAL.proteins.structure.Atom

setDegCase(CVertex.DegenerateCase) - Method in class ProGAL.geom3d.complex.CVertex

setDegenerate(boolean) - Method in class ProGAL.geom3d.complex.CVertex

setDegenerate(boolean) - Method in class ProGAL.geomNd.complex.Vertex

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

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

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

setDisplacement(Vector) - Method in class ProGAL.geom3d.surface.ParametricParaboloid

setEdge(int, CEdge) - Method in class ProGAL.geom3d.complex.CTriangle

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

setFace(TriangulationFace) - Method in class ProGAL.geom2d.TriangulationVertex

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

setFirstTransformation(Matrix) - Method in class ProGAL.proteins.chainTree.ChainTree

Change the orientation and translation of the entire chain.

setFlat(boolean) - Method in class ProGAL.geom3d.complex.CTetrahedron

setFrontClip(double) - Method in class ProGAL.geom3d.viewer.Camera

setFrontFog(double) - Method in class ProGAL.geom3d.viewer.Camera

setId(int) - Method in class ProGAL.geom2d.TriangulationFace

setId(int) - Method in class ProGAL.geom2d.TriangulationVertex

setIncludeHetatms(boolean) - Method in class ProGAL.proteins.PDBFile

setIncludeHydrogens(boolean) - Method in class ProGAL.proteins.PDBFile

setItem(int, Object) - Method in class ProGAL.dataStructures.Heap

SetIterator - Class in ProGAL.dataStructures

SetIterator(Set) - Constructor for class ProGAL.dataStructures.SetIterator

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

setLocation(Point) - Method in class ProGAL.geom3d.viewer.Camera

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

setLookingAt(Point) - Method in class ProGAL.geom3d.viewer.Camera

setModified(boolean) - Method in class ProGAL.geom3d.complex.CTetrahedron

setModified(boolean) - Method in class ProGAL.geomNd.complex.Tessel

setNeighbor(int, TriangulationFace) - Method in class ProGAL.geom2d.TriangulationFace

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

setNeighbour(int, CTetrahedron) - Method in class ProGAL.geom3d.complex.CTriangle

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

setNormal(Vector) - Method in class ProGAL.geom3d.Plane

Set the normal to n.

setNotPaired(int, int) - Method in class ProGAL.proteins.belta.BetaTopology

Set strands i and j to be unpaired.

setOmega(int, double) - Method in class ProGAL.proteins.beltaStructure.ChainTreeLoop

setPaired(int, int) - Method in class ProGAL.proteins.belta.BetaTopology

Set strands i and j to be paired.

setParallelProjection(boolean) - Method in class ProGAL.geom3d.viewer.J3DScene

Enables and disables parallel projection (as opposed to perspective projection).

setPhi(int, double) - Method in class ProGAL.proteins.beltaStructure.ChainTreeLoop

setPoint(CVertex, int) - Method in class ProGAL.geom3d.complex.CTetrahedron

setPoint(int, Point) - Method in class ProGAL.geom3d.volumes.Tetrahedron

TODO: Comment

setPolarAngle(double) - Method in class ProGAL.geom2d.TriangulationVertex

setPolarRadius(double) - Method in class ProGAL.geom2d.TriangulationVertex

setPsi(int, double) - Method in class ProGAL.proteins.beltaStructure.ChainTreeLoop

setRadius(double) - Method in class ProGAL.geom2d.Circle

setRadius(double) - Method in class ProGAL.geom2d.LSC

setRadius(double) - Method in class ProGAL.geom3d.volumes.Sphere

setRadius(double) - Method in class ProGAL.geomNd.HyperSphere

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

setRoot(InteractiveBinaryTree) - Method in class ProGAL.dataStructures.viewer.BinaryTreePainter

setRoot() - Method in class ProGAL.geom3d.complex.alphaComplex.VoidTree

setRotation(Matrix) - Method in class ProGAL.geom3d.surface.ParametricParaboloid

setRow(int, Vector) - Method in class ProGAL.math.Matrix

setSegment(LineSegment) - Method in class ProGAL.geom3d.volumes.Cylinder

setSinAngle(double) - Method in class ProGAL.geom2d.TriangulationVertex

setSquaredPolarRadius(double) - Method in class ProGAL.geom2d.TriangulationVertex

setStandardChain(int) - Method in class ProGAL.proteins.PDBFile

setStandardChain(char) - Method in class ProGAL.proteins.PDBFile

setStandardModel(int) - Method in class ProGAL.proteins.PDBFile

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

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

Sets the structure of this segment.

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

setSubmatrix(int, int, Matrix) - Method in class ProGAL.math.Matrix

setTorsion(int, int, double) - Method in class ProGAL.proteins.beltaStructure.ChainTreeLoop

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

Changes the torsion angle of the specified residue and bond.

setTriangle(int, CTriangle) - Method in class ProGAL.geom3d.complex.CTetrahedron

setType(TriangulationVertex.VertexType) - Method in class ProGAL.geom2d.TriangulationVertex

setUp() - Method in class ProGAL.geom3d.predicates.tests.ExactJavaPredicatesTest

setUp() - Method in class ProGAL.geom3d.predicates.tests.InexactJavaPredicatesTest

setUp(Vector) - Method in class ProGAL.geom3d.viewer.Camera

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

setViewAngle(double) - Method in class ProGAL.geom3d.viewer.Camera

setX(double) - Method in class ProGAL.geom3d.Point

Set the first coordinate

setX(double) - Method in class ProGAL.geom3d.Vector.ImmutableVector3d

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

Set the first coordinate

setY(double) - Method in class ProGAL.geom3d.Point

Set the second coordinate

setY(double) - Method in class ProGAL.geom3d.Vector.ImmutableVector3d

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

Set the second coordinate

setZ(double) - Method in class ProGAL.geom3d.Point

Set the third coordinate

setZ(double) - Method in class ProGAL.geom3d.Vector.ImmutableVector3d

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

Set the third coordinate

Shape - Interface in ProGAL.geom2d

An interface for 2d shapes such as circles, rectangles and text.

Shape - Interface in ProGAL.geom3d

An interface for 3d shapes such as spheres, but also flat objects such as rectangles and text.

shapeClicked(Shape, MouseEvent) - Method in interface ProGAL.geom3d.viewer.ClickListener

shapeClicked(Shape, MouseEvent) - Method in class ProGAL.proteins.beltaStructure.sheetLoop.SheetLoopGUI

SheetAlignment - Class in ProGAL.proteins.beltaStructure.sheet

SheetAlignment(SheetTopology) - Constructor for class ProGAL.proteins.beltaStructure.sheet.SheetAlignment

Construct an alignment of strands in the given topology.

SheetAlignment(SheetTopology, PDBFile) - Constructor for class ProGAL.proteins.beltaStructure.sheet.SheetAlignment

sheetAlignment - Variable in class ProGAL.proteins.beltaStructure.sheet.SurfaceSheetStructure

The sheet alignment of this structure.

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

SheetLoopGUI - Class in ProGAL.proteins.beltaStructure.sheetLoop

A viewer and editor of SheetLoopStructures.

SheetLoopGUI(SheetLoopStructure) - Constructor for class ProGAL.proteins.beltaStructure.sheetLoop.SheetLoopGUI

SheetLoopStructure - Class in ProGAL.proteins.beltaStructure.sheetLoop

SheetLoopStructure(BetaTopology) - Constructor for class ProGAL.proteins.beltaStructure.sheetLoop.SheetLoopStructure

SheetStructure - Class in ProGAL.proteins.beltaStructure.bnb

SheetStructure(int, SheetTopology, AminoAcidChain) - Constructor for class ProGAL.proteins.beltaStructure.bnb.SheetStructure

SheetTopology - Class in ProGAL.proteins.belta

Representation of the topology of a single sheet.

SheetTopology(BetaTopology, int) - Constructor for class ProGAL.proteins.belta.SheetTopology

Construct the sheet containing the specified strand.

sheetTopology - Variable in class ProGAL.proteins.beltaStructure.CanonicalSheet

SheetTopology.StrandPair - Class in ProGAL.proteins.belta

A pair of strands specified by two strand-indices (i.e.

SheetTopologyTest - Class in ProGAL.proteins.belta.tests

SheetTopologyTest() - Constructor for class ProGAL.proteins.belta.tests.SheetTopologyTest

ShewchuckPredicates - Class in ProGAL.geom3d.tessellation.BowyerWatson

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

shift(int) - Method in class ProGAL.geom2d.Polygon

first corner of the polygon is moved by shiftStep positions

shift(int) - Method in class ProGAL.proteins.belta.PDBFile

shuffle(Object[]) - Static method in class ProGAL.math.Randomization

siftDown(int) - Method in class ProGAL.dataStructures.Heap

siftUp(int) - Method in class ProGAL.dataStructures.Heap

Simplex - Interface in ProGAL.geom3d

TODO: Comment

SimplexAlphaProperties - Interface in ProGAL.geom3d.complex.alphaComplex

SimplicialComplex - Interface in ProGAL.geom3d.complex

SingularValueDecomposition - Class in ProGAL.math

A class for calculating and representing the singular value decomposition.

SingularValueDecomposition(Matrix) - Constructor for class ProGAL.math.SingularValueDecomposition

Construct the singular value decomposition

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

Return number of elements

solve(Matrix) - Method in class ProGAL.math.LUDecomposition

Solve A*X = B

solveApollonius(Circle, Circle, Circle, int, int, int) - Static method in class ProGAL.geom2d.ApolloniusSolver

Solves the Apollonius problem of finding a circle tangent to three other circles in the plane.

solveApollonius(Sphere, Sphere, Sphere, Sphere, int, int, int, int) - Static method in class ProGAL.geom3d.ApolloniusSolver

Solves the Apollonius problem of finding a circle tangent to three other circles in the plane.

solveApollonius(Point[], double[], int[]) - Static method in class ProGAL.geom3d.ApolloniusSolver

solveApollonius(HyperSphere[], int[]) - Static method in class ProGAL.geomNd.ApolloniusSolver

Solves the Apollonius problem of finding a circle tangent to three other circles in the plane.

solveAsinXPlusBcosXplusC(double, double, double) - Static method in class ProGAL.math.Trigonometry

solves equation AsinX + BCosX + C = 0

solveBDAsinXPlusBcosXplusC(double, double, double) - Static method in class ProGAL.math.Trigonometry

solves equation AsinX + BCosX + C = 0

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

Sort(Set, SortTool) - Method in class ProGAL.dataStructures.Sorter

Sort(Set, SortTool, boolean) - Method in class ProGAL.dataStructures.Sorter

Sort(Set, SortTool, boolean) - Method in class ProGAL.dataStructures.SorterQuick

Sorter - Class in ProGAL.dataStructures

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

SorterQuick - Class in ProGAL.dataStructures

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

SortTool - Interface in ProGAL.dataStructures

SortToolDouble - Class in ProGAL.dataStructures

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

SortToolInteger - Class in ProGAL.dataStructures

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

SortToolLineSegment2dAroundCommonPoint - Class in ProGAL.dataStructures

SortToolLineSegment2dAroundCommonPoint(Point) - Constructor for class ProGAL.dataStructures.SortToolLineSegment2dAroundCommonPoint

SortToolLineSegment2dByLength - Class in ProGAL.dataStructures

SortToolLineSegment2dByLength() - Constructor for class ProGAL.dataStructures.SortToolLineSegment2dByLength

SortToolPoint2dAroundOrigo - Class in ProGAL.dataStructures

SortToolPoint2dAroundOrigo() - Constructor for class ProGAL.dataStructures.SortToolPoint2dAroundOrigo

SortToolPoint2dAroundPoint - Class in ProGAL.dataStructures

SortToolPoint2dAroundPoint(Point) - Constructor for class ProGAL.dataStructures.SortToolPoint2dAroundPoint

SortToolPoint2dDistance - Class in ProGAL.dataStructures

SortToolPoint2dDistance() - Constructor for class ProGAL.dataStructures.SortToolPoint2dDistance

SortToolPoint2dXY - Class in ProGAL.dataStructures

SortToolPoint2dXY() - Constructor for class ProGAL.dataStructures.SortToolPoint2dXY

SortToolString - Class in ProGAL.dataStructures

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

Sphere - Class in ProGAL.geom3d.volumes

A sphere represented by a center-point and a radius.

Sphere(Point, double) - Constructor for class ProGAL.geom3d.volumes.Sphere

Constructs a sphere with the specified center and the specified radius.

Sphere(Point[]) - Constructor for class ProGAL.geom3d.volumes.Sphere

Sphere(Point, Point, Point, Point) - Constructor for class ProGAL.geom3d.volumes.Sphere

Sphere(CTetrahedron) - Constructor for class ProGAL.geom3d.volumes.Sphere

Sphere(PointWeighted) - Constructor for class ProGAL.geom3d.volumes.Sphere

Constructs a sphere with the weighted point as center and a radius with the square root of the points weight.

Sphere(Circle) - Constructor for class ProGAL.geom3d.volumes.Sphere

creates a sphere with the specified circle as equator

SPHERES - Static variable in class ProGAL.proteins.viewer.PDBFileViewer

SQRT2 - Static variable in class ProGAL.math.Constants

SQRT3 - Static variable in class ProGAL.math.Constants

SSType - Enum in ProGAL.proteins.belta

Types of secondary structure

start - Variable in class ProGAL.proteins.belta.SecondaryStructure.SSSegment

The residue-index of the first amino acid in this segment

STICKS - Static variable in class ProGAL.proteins.viewer.PDBFileViewer

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

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

strand1 - Variable in class ProGAL.proteins.belta.SheetTopology.StrandPair

strand2 - Variable in class ProGAL.proteins.belta.SheetTopology.StrandPair

strandCenter(int) - Method in class ProGAL.proteins.beltaStructure.CanonicalSheet

strandOrientation(int) - Method in class ProGAL.proteins.beltaStructure.CanonicalSheet

strandPairs - Variable in class ProGAL.proteins.belta.SheetTopology

An ordered list of strand-pairs.

strands - Variable in class ProGAL.proteins.belta.SheetTopology

A sorted list of strand-indices.

StrandSurface - Class in ProGAL.proteins.viewer

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

Subtract the vector v from this point and return the result

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

Returns p subtracted from this (without changing this object).

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

Subtract v from this vector and return the result (without changing this object).

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

Subtract v from this vector and return the result (without changing this object).

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

Subtract the components of two matrices.

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

Subtract the vector v from this point and return the result (changes this object)

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

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

Returns p subtracted from this (changing this object).

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

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

Subract v from this vector and return the result (changing this object).

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

Subtract v from this vector and return the result (changing this object).

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

Subtract the components of two matrices.

superposeOnto(PDBFile) - Method in class ProGAL.proteins.PDBFile

Superposition - Class in ProGAL.geom3d.superposition

A wrapper-class for doing 3D point-superpositions.

Superposition() - Constructor for class ProGAL.geom3d.superposition.Superposition

SurfaceSheetStructure - Class in ProGAL.proteins.beltaStructure.sheet

A representation of the backbone-structure of a beta-sheet based on an arbitrary parametric surface.

SurfaceSheetStructure(SheetAlignment) - Constructor for class ProGAL.proteins.beltaStructure.sheet.SurfaceSheetStructure

Constructs a sheet structure using the specified sheet alignment and a hyperbolic paraboloid as the surface.

swap(int, int) - Method in class ProGAL.dataStructures.Set