A B C D E F G H I J L M N O P Q R S T U V W X Y Z

S

scale(float) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3

performs multiplication of vector by number (scaling) (doesn't alter any existing vectors)

scaleMe(float) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3

multiplies current vector by a number (and alters it!)

scalingfactor - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.StructureRenderer

ScreenShot - Class in pl.krakow.cmuj.bioinformatics.jellipse

ScreenShot(jEllipse, GLEventListener) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.ScreenShot

Creates a new instance of ScreenShoot

Screenshottable - Interface in pl.krakow.cmuj.bioinformatics.jellipse

SCREENSHOTTING - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.PlotRenderer

SCREENSHOTTING - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.StructureRenderer

screenshotting_plot - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse

screenshotting_structure - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse

Sd - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Methionine

selectedchainid - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.ChainChooser

One-letter id of the chain that the user has choosen.

selectedchainid - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse

Serine - Class in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids

A serine molecule.

Serine(String, Map) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Serine

Creates a new instance of the Serine aminoacid.

set(float, float, float) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3

set(int, float) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3

set(float[]) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3

set(Vector3) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3

setAbsDeviation(float) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid

setAntiAlias(boolean) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

setAvgDihedralAngle(float) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid

sets average dihedral angle between two consecutive bond planes and between the pair of planes just one aacid next to

setBackboneComplete() - Method in class pl.krakow.cmuj.bioinformatics.jellipse.StructureRenderer

setBackboneVirtual() - Method in class pl.krakow.cmuj.bioinformatics.jellipse.StructureRenderer

setBounds(float, float, float, float, float, float) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Peptide

setComposite(boolean) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

setDescription(String) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.FFilter

Sets the human readable description of this filter.

setDeviation(float) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid

setExtensionListInDescription(boolean) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.FFilter

Determines whether the extension list (.pdb, .mmCIF, etc) should show up in the human readable description.

setId(char) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Peptide

setImageType(int) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

setLnRadiusOfCurvature(float) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid

sets radius of curvature of the pentapeptide in which current aminoacid is the central one

setMonitor(boolean) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

setPdbId(String) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.PdbFetcher

Sets PdbFetcher's PDB ID in uppercase.

setPhiAngle(Atom) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid

Calls calcTorsionalAngle with appropriate atoms.

setPsiAngle(Atom) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid

Calls calcTorsionalAngle with appropriate atoms.

setRendering(boolean) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

setScreenshotting(DataBufferInt) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.PlotRenderer

setScreenshotting(DataBufferInt) - Method in interface pl.krakow.cmuj.bioinformatics.jellipse.Screenshottable

setScreenshotting(DataBufferInt) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.StructureRenderer

setSleepAmount(long) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

setTexture(Object) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

setValue(Object) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.SwingWorker

Set the value produced by worker thread

setW(float) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Quaternion

Sets the scalar value of the quaternion.

setX(float) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Quaternion

Sets the first vector value of the quaternion.

setY(float) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Quaternion

Sets the second vector value of the quaternion.

setZ(float) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Quaternion

Sets the third vector value of the quaternion.

Sg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Cysteine

shottable - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.ScreenShot

shouldStop - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse.NotSoGreedyAnimator

shouldStop - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse.QuiteLazyAnimator

showPropertyName() - Method in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse

sleepAmount - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

start() - Method in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse.NotSoGreedyAnimator

Starts this animator as Thread

start() - Method in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse.QuiteLazyAnimator

Starts this animator as Thread

start - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

start() - Method in class pl.krakow.cmuj.bioinformatics.jellipse.SwingWorker

Start the worker thread.

stop() - Method in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse.NotSoGreedyAnimator

Stops this animator, blocking until the animation thread has finished.

stop() - Method in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse.QuiteLazyAnimator

Stops this animator, blocking until the animation thread has finished.

StructureRenderer - Class in pl.krakow.cmuj.bioinformatics.jellipse

StructureRenderer(jEllipse, Peptide) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.StructureRenderer

StructureRenderer(jEllipse, Peptide, float[]) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.StructureRenderer

StructureRenderer.wl - Class in pl.krakow.cmuj.bioinformatics.jellipse

StructureRenderer.wl() - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.StructureRenderer.wl

StructureRer - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse

StVec - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.StructureRenderer

subject - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.ScreenShot

subtr(Vector3) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3

subtracts a given vector from the current one (doesn't alter any existing vectors) current vector is minuend

subtrFromMe(Vector3) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3

subtracts a given vector from the current one (and alters it!)

Surface - Class in pl.krakow.cmuj.bioinformatics.jellipse

General-purpose drawing (plotting area).

Surface() - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.Surface

SwingWorker - Class in pl.krakow.cmuj.bioinformatics.jellipse

This is the 3rd version of SwingWorker, an abstract class that yousubclass to perform GUI-related work in a dedicated thread.

SwingWorker() - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.SwingWorker

Start a thread that will call the construct method and then exit.

SwingWorker.ThreadVar - Class in pl.krakow.cmuj.bioinformatics.jellipse

Class to maintain reference to current worker thread under separate synchronization control.

SwingWorker.ThreadVar(Thread) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.SwingWorker.ThreadVar