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A

absoluteGridToCartesian(double, double, double, Point3d) - Method in class astex.Map
Convert grid coordiantes to cartesian.
accept - Variable in class astex.ColorChooser
 
accept(File, String) - Method in class astex.UniversalFilenameFilter
Tell whether we want to accept this file.
ACTINIUM - Static variable in class astex.PeriodicTable
 
actionPerformed(ActionEvent) - Method in class astex.ColorChooser
 
actionPerformed(JCActionEvent) - Method in class astex.ColorChooser
 
actionPerformed(ActionEvent) - Method in class astex.MoleculeViewer
Implementation of ActionListener.
actionPerformed(JCActionEvent) - Method in class astex.ObjectControl
Handle actions.
actionPerformed(JCActionEvent) - Method in class astex.ObjectPropertyDialog
Handle actions on the user interface.
actionPerformed(JCActionEvent) - Method in class astex.UserInterface
Handle actions on the user interface.
ACTIVE - Static variable in class astex.sym
 
ACTIVE_SITE - Static variable in class astex.sym
 
add(int, int) - Static method in class astex.Color32
 
add(double) - Method in class astex.DoubleArray
Add an entry to the CLASSNAME.
add(Object) - Method in class astex.DynamicArray
Add an entry to the CLASSNAME.
add(float) - Method in class astex.FloatArray
Add an entry to the CLASSNAME.
add(int) - Method in class astex.IntArray
Add an entry to the CLASSNAME.
add(int, double, double, double) - Method in class astex.Lattice
Add an object reference to the lattice.
add(int, double, double, double) - Method in class astex.NeighbourGrid
Add an object to the appropriate cell.
add(int, double, double) - Method in class astex.NeighbourGrid2D
Add an object to the appropriate cell.
add(Point3d) - Method in class astex.Point3d
Add the x, y and z coordinates from another Point3d to the coordinates of this point.
add(String) - Method in class astex.StringArray
Add an entry to the CLASSNAME.
add(Object) - Static method in class astex.UI
 
add(Object, int) - Static method in class astex.UI
 
add(Object, int, int) - Static method in class astex.UI
 
add(Object, int, int, int) - Static method in class astex.UI
 
addActionListener(ActionListener) - Method in class astex.ImageButton
 
addAngle(Atom, Atom, Atom) - Method in class astex.MoleculeRenderer
Add a set of atoms to the angle list.
addAtom() - Method in class astex.Molecule
Add an atom to the molecule and return the reference to it.
addAtom(Residue) - Method in class astex.Molecule
Add an atom to the chain, residue set.
addAtom(Atom) - Method in class astex.Residue
Add an atom to the list.
addAtom(Atom) - Method in class astex.Ring
Add an atom to the ring.
addBond(Bond) - Method in class astex.Atom
Add a bond to the atom.
addBond(Atom, Atom, int) - Method in class astex.Molecule
Add a bond to the molecule and return a reference to it.
addBond(Atom, Atom, int, boolean) - Method in class astex.Molecule
Add a bond to the molecule and return a reference to it.
addBond(Atom, Atom) - Method in class astex.Molecule
Add a bond between two atoms with default bond order.
addBond(int, int, int) - Method in class astex.Molecule
Add a bond to the molecule and return a reference to it.
addBond(int, int) - Method in class astex.Molecule
Add a bond to the molecule and return a reference to it.
addBond(Bond) - Method in class astex.Ring
Add a bond to the ring.
addBondFromIds(int, int, int) - Method in class astex.Molecule
Add a bond to the molecule and return a reference to it.
addBumpPair(Atom, Atom) - Method in class astex.MoleculeRenderer
Add a pair of bump atoms.
addChain() - Method in class astex.Molecule
Add a chain to the molecule.
addChild(GenericInterface) - Method in class astex.Atom
Add a child.
addChild(GenericInterface) - Method in class astex.generic.Generic
 
addChild(GenericInterface) - Method in interface astex.generic.GenericInterface
Add a child.
addContourLevel(double, int, boolean, int) - Method in class astex.MoleculeRenderer
Add a contour level.
addCylinder(double, double, double, double, double, double, double, int, int) - Method in class astex.Tmesh
Add a cylinder to this tmesh.
addCylinderToCacheList(double, double, double, double, double, double, double) - Static method in class astex.ShadowCache
Add a cylinder to the cache list.
addDash(String) - Static method in class astex.Arguments
Add a dash to the argument if it doesn't exist.
addDistance(Distance) - Method in class astex.MoleculeRenderer
Add a distance monitor to the list.
addDistance(Atom, Atom) - Method in class astex.MoleculeRenderer
Add a pair of atoms to the distance list.
addDistance2(Atom, Atom) - Method in class astex.MoleculeRenderer
Add a pair of atoms to the distance list.
addDistanceBetweenSelectedAtoms() - Method in class astex.MoleculeRenderer
Add a distance monitor between the selected atoms.
addGraphicalObject(Tmesh) - Method in class astex.MoleculeRenderer
 
addGraphicalObject(Tmesh) - Method in class astex.Renderer
Add a graphical object.
addImproper(Atom, Atom, Atom, Atom) - Method in class astex.Molecule
Create a improper for the 4 specified atoms.
addLabelledAtom(Atom) - Method in class astex.MoleculeRenderer
Add a labelled atom.
addLight(boolean, double, double, double, int, int, double) - Method in class astex.Renderer
Add a light.
addLine(int, int, int) - Method in class astex.Tmesh
Add a line to the object.
addLine(double, double, double, double, double, double, int, int) - Method in class astex.Tmesh
Add a line to this mesh.
addListener(GenericEventInterface) - Method in class astex.Atom
Add a listener.
addListener(GenericEventInterface) - Method in class astex.generic.Generic
 
addListener(GenericEventInterface) - Method in interface astex.generic.GenericInterface
Add a listener.
addMap(Map) - Method in class astex.MoleculeRenderer
Add a map to the scene.
addMap(Map) - Method in class astex.MoleculeViewer
Add a map to the renderer.
addMolecule(Molecule) - Method in class astex.MoleculeRenderer
Add a molecule to the scene.
addMolecule(String, String) - Method in class astex.MoleculeRenderer
Add a molecule to the scene.
addMolecule(Molecule) - Method in class astex.MoleculeViewer
Set the molecule that the renderer will use.
addMoleculeRendererListener(MoleculeRendererListener) - Method in class astex.MoleculeRenderer
Add a MoleculeRendererListener.
addNotify() - Method in class astex.MoleculeViewer
 
addParent(GenericInterface) - Method in class astex.Atom
Add a parent.
addParent(GenericInterface) - Method in class astex.generic.Generic
 
addParent(GenericInterface) - Method in interface astex.generic.GenericInterface
Add a parent.
addPoint(Point3d, Point3d, double, double) - Method in class astex.Tmesh
Add a point to the object.
addPoint(double[], double[], double, double) - Method in class astex.Tmesh
Add a point to the object.
addPoint(double, double, double, double, double, double, double, double) - Method in class astex.Tmesh
Add a point to the object.
addPoint(double, double, double, int) - Method in class astex.Tmesh
 
addRendererEventListener(RendererEventListener) - Method in class astex.Renderer
Add a listener for renderer events.
addRepaintListener(Component) - Method in class astex.MoleculeViewer
 
addResidue() - Method in class astex.Chain
Add a residue to the chain.
addResidue() - Method in class astex.Molecule
Add a residue to the current chain.
addRing() - Method in class astex.Molecule
Add a new ring to the molecule.
addSelectedAtom(Atom) - Method in class astex.MoleculeRenderer
Add a selected atom.
addSphere(double, double, double, double, int) - Method in class astex.Tmesh
Add a sphere to this tmesh.
addSphereToCacheList(double, double, double, double) - Static method in class astex.ShadowCache
Add a sphere to the cache list.
addSymmetryAtoms(Molecule, Point3d, double, Matrix, Molecule) - Method in class astex.MoleculeRenderer
Add the symmetry atoms that overlap.
addTmesh(Tmesh) - Method in class astex.Renderer
Add a tmesh to the renderer.
addTorsion(Atom, Atom, Atom, Atom) - Method in class astex.MoleculeRenderer
Add a set of atoms to the angle list.
addTriangle(int, int, int) - Method in class astex.Tmesh
 
addTriangle(int, int, int, int) - Method in class astex.Tmesh
 
addTriangleToCacheList(double, double, double, double, double, double, double, double, double, int) - Static method in class astex.ShadowCache
Add a cylinder to the cache list.
adjoint(Matrix, Matrix) - Static method in class astex.Matrix
adjoint( original_matrix, inverse_matrix ) calculate the adjoint of a 4x4 matrix Let a denote the minor determinant of matrix A obtained by ij deleting the ith row and jth column from A.
adjustmentValueChanged(AdjustmentEvent) - Method in class astex.MoleculeViewer
AdjustmentListener to listen to contour levels being created.
adjustmentValueChanged(JCAdjustmentEvent) - Method in class astex.ObjectControl
Adjustment changed on slider for instance.
adjustmentValueChanged(JCAdjustmentEvent) - Method in class astex.UserInterface
 
affectedAtoms - Variable in class astex.EnergyTerm
The list of atoms that are affected by this energy term.
ALL - Static variable in class astex.match
All possible matching features.
all(MoleculeRenderer) - Static method in class astex.Selection
Select all the atoms.
ALL - Static variable in class astex.sym
 
Alpha - Static variable in class astex.Color32
Alpha bits.
ALUMINUM - Static variable in class astex.PeriodicTable
 
AMERICIUM - Static variable in class astex.PeriodicTable
 
AmideBond - Static variable in class astex.Bond
Constant that defines an aromatic bond.
aminoacid(MoleculeRenderer) - Static method in class astex.Selection
Aminoacid expression.
AMINOACID - Static variable in class astex.sym
 
aminoacidNames - Static variable in class astex.Selection
Residue names for aminoacids.
analyticalSpheres - Variable in class astex.Renderer
Do we do analytical spheres?
ANASURFACE - Static variable in class astex.sym
 
and(byte[], byte[]) - Static method in class astex.Selection
And two selection masks together.
AND - Static variable in class astex.sym
 
Angle - Class in astex
A class for storing information about a bond angle.
angle(Point3d, Point3d, Point3d) - Static method in class astex.Point3d
Calculate the angle between the 3 points.
ANGLE - Static variable in class astex.sym
 
ANGLE_PICK - Static variable in class astex.MoleculeRenderer
Angle picking mode.
angleDegrees(Point3d, Point3d, Point3d) - Static method in class astex.Point3d
Calcluate the angle in degrees.
Animate - Class in astex
 
Animate() - Constructor for class astex.Animate
 
animate() - Method in class astex.AnimationObject
Do the step.
ANIMATE - Static variable in class astex.sym
 
animating() - Method in class astex.MoleculeViewer
Are we animating?
AnimationObject - Class in astex
 
AnimationObject() - Constructor for class astex.AnimationObject
 
announce - Variable in class astex.MoleculeViewer
Are we announcing the origin of AstexViewer.
antialias - Variable in class astex.Renderer
Are we antialiasing.
ANTIMONY - Static variable in class astex.PeriodicTable
 
AnyBond - Static variable in class astex.Bond
Constant that defines any bond.
Apollo - Class in astex
 
Apollo() - Constructor for class astex.Apollo
 
APPEND - Static variable in class astex.sym
 
applyTexture(String, String) - Method in class astex.Renderer
Apply texture to the specified objects.
applyTransform(double, double, double, double[]) - Method in class astex.Renderer
Apply a transform to a point.
applyTransform2(double, double, double, int[]) - Method in class astex.Renderer
Apply a transform to a point.
applyZoom(double) - Method in class astex.Renderer
Change the zoom for the molecule.
aquamarine - Static variable in class astex.Color32
 
ARG - Static variable in class astex.sym
 
ARGON - Static variable in class astex.PeriodicTable
 
Arguments - Class in astex
 
Arguments() - Constructor for class astex.Arguments
 
Aromatic - Static variable in class astex.Atom
 
AromaticBond - Static variable in class astex.Bond
Constant that defines an aromatic bond.
AROUND - Static variable in class astex.sym
 
arrayToMask(MoleculeRenderer, DynamicArray) - Static method in class astex.Selection
Return a mask from a DynamicArray.
arrow(Arguments, Tmesh) - Static method in class astex.Schematic
Add an arrow to the object.
ARSENIC - Static variable in class astex.PeriodicTable
 
ASSERT - Static variable in class astex.Log
 
assign(DynamicArray) - Static method in class astex.SecondaryStructure
Assign secondary structure to residues in a protein molecule.
assignAtomNumbers() - Method in class astex.Molecule
Assign atom numbers.
assignInitialType(Residue) - Static method in class astex.SecondaryStructure
Assign initial type on basis of phi/psi.
assignMolecule(Molecule) - Static method in class astex.SecondaryStructure
Assign secondary structure for this molecule.
assignSymmetryAtomColors(Molecule) - Method in class astex.MoleculeRenderer
Assign atom colors.
ASTATINE - Static variable in class astex.PeriodicTable
 
ASTERISK - Static variable in class astex.match
This flag represents the asterisk (`*') wildcard character.
astex - package astex
 
astex.generic - package astex.generic
 
ASTEX_ASCII - Static variable in class astex.Map
 
AstexLogo - Class in astex
 
AstexLogo() - Constructor for class astex.AstexLogo
 
atof(String) - Static method in class astex.Format
Converts a string of digits to an double
atoi(String) - Static method in class astex.Format
Converts a string of digits (decimal, octal or hex) to an integer
atol(String) - Static method in class astex.Format
Converts a string of digits (decimal, octal or hex) to a long integer
Atom - Class in astex
A class for holding information about an atom.
atom(MoleculeRenderer, Vector) - Static method in class astex.Selection
Select a set of atoms on the basis of atom ids.
ATOM - Static variable in class astex.sym
 
AtomAdded - Static variable in class astex.MoleculeEvent
 
AtomChanged - Static variable in class astex.MoleculeEvent
 
AtomEventMask - Static variable in class astex.MoleculeEvent
 
AtomicElement - Class in astex
 
AtomicElement(int, String, double, int, int, int, int, int, int) - Constructor for class astex.AtomicElement
 
atomicNumber - Variable in class astex.AtomicElement
 
AtomIterator - Class in astex
 
AtomIterator(MoleculeRenderer) - Constructor for class astex.AtomIterator
The only public constructor.
atomNeedsImproper(Atom) - Method in class astex.Molecule
Does this atom need a improper restraint.
AtomRemoved - Static variable in class astex.MoleculeEvent
 
atoms - Variable in class astex.Molecule
Dynmamic array of atoms.
atoms - Variable in class astex.Residue
Dynmamic array of atoms.
atomsCached - Static variable in class astex.Atom
 
atomsCreated - Static variable in class astex.Atom
 
AtomSelected - Static variable in class astex.MoleculeEvent
 
atomSelected(MoleculeRenderer, Atom) - Method in interface astex.MoleculeRendererListener
An atom was selected.
atomSelected(MoleculeRenderer, Atom) - Method in class astex.MoleculeViewer
Respond to an atom click event.
atomSelected(MoleculeRenderer, Atom) - Method in class astex.UserInterface
An atom was selected.
atomType - Variable in class astex.Atom
The (usually sybyl) atom type of the atom.
attachmentLabels - Static variable in class astex.PeriodicTable
Symbols used for displaying attachment points.
attribute(MoleculeRenderer, int, int, double) - Static method in class astex.Selection
Select on the basis of an attribute.
ATTRIBUTE - Static variable in class astex.sym
 
attributes - Variable in class astex.Atom
An integer for storing various attributes.
attributes - Variable in class astex.Bond
The integer that stores the attributes.
axis - Variable in class astex.Map
 
azure - Static variable in class astex.Color32
 

B

B - Static variable in class astex.Atom
The B coordinate attribute.
back - Variable in class astex.Renderer
The distance behind the center of the back clip plane.
backClip - Variable in class astex.Renderer
The integer back plane.
BackClipMoved - Static variable in class astex.RendererEvent
 
BACKFACE - Static variable in class astex.sym
 
BACKGROUND - Static variable in class astex.sym
 
backlit - Variable in class astex.Renderer
Are we backlighting back facing triangles.
BACKSLASH - Static variable in class astex.match
This flag represents escaping feature, using backslash (`\').
BALL_RADIUS - Static variable in class astex.sym
 
BallAndStick - Static variable in class astex.Atom
The property set flag.
ballRadius - Variable in class astex.Atom
The stick radius of the atom.
BARIUM - Static variable in class astex.PeriodicTable
 
BAttribute - Static variable in class astex.Atom
 
beige - Static variable in class astex.Color32
 
BERKELIUM - Static variable in class astex.PeriodicTable
 
BERYLLIUM - Static variable in class astex.PeriodicTable
 
BISMUTH - Static variable in class astex.PeriodicTable
 
bisque - Static variable in class astex.Color32
 
black - Static variable in class astex.Color32
 
blend(int, int, int) - Static method in class astex.Color32
 
blend(int, int, double) - Static method in class astex.Color32
Interpolate two colors.
Blue - Static variable in class astex.Color32
Blue bits.
blue - Static variable in class astex.Color32
 
Bond - Class in astex
 
BOND_WIDTH - Static variable in class astex.sym
 
bonded(MoleculeRenderer, byte[]) - Static method in class astex.Selection
Select a set of atoms on the basis of residue names.
BondIterator - Class in astex
 
BondIterator(MoleculeRenderer) - Constructor for class astex.BondIterator
The only public constructor.
BondOrder - Static variable in class astex.Bond
 
bonds - Variable in class astex.Molecule
Dynamic array of bonds.
bondScale - Static variable in class astex.Bond
 
BORON - Static variable in class astex.PeriodicTable
 
BOTH - Static variable in class astex.UI
 
boundingSphereCylinder(double, double, double, double, double, double, double, double[]) - Static method in class astex.ShadowCache
Prepare bounding sphere that encloses cylinder.
boundingSphereTriangle(double, double, double, double, double, double, double, double, double, double[]) - Static method in class astex. ShadowCache
Prepare bounding sphere that encloses cylinder.
BOX(double) - Method in class astex.Lattice
Return the cell box id along one axis.
BRACKETS - Static variable in class astex.match
This flag represents the bracket (`[..]') matching feature.
BROMINE - Static variable in class astex.PeriodicTable
 
brown - Static variable in class astex.Color32
 
buildContourLevelDialog() - Method in class astex.MoleculeViewer
Actually build the contour level.
buildOverallMatrix() - Method in class astex.Renderer
Build the overall transformation matrix.
buildSelectionCommand(Selectable, int) - Method in class astex.UserInterface
Build a string that will perform a selection operation.
builtin(MoleculeRenderer, DynamicArray) - Static method in class astex.Selection
Evaluate a builtin expression against residue names.
builtin2(MoleculeRenderer, DynamicArray) - Static method in class astex.Selection
Evaluate a builtin expression atom names.
builtin3(MoleculeRenderer, DynamicArray) - Static method in class astex.Selection
Evaluate a builtin expression atom names.
builtinColors - Variable in class astex.MoleculeViewer
 
burlywood - Static variable in class astex.Color32
 
button(String, String, JCActionListener) - Static method in class astex.UI
Create a button.
byresidue(MoleculeRenderer, byte[]) - Static method in class astex.Selection
Select a set of atoms on the basis of residue names.
BYRESIDUE - Static variable in class astex.sym
 

C

c2lx(int) - Method in class astex.LightCanvas
 
c2ly(int) - Method in class astex.LightCanvas
 
CADMIUM - Static variable in class astex.PeriodicTable
 
calc(double, double, double) - Method in class astex.ColorSpace
 
CALCIUM - Static variable in class astex.PeriodicTable
 
calculateHbonds(DynamicArray, Arguments) - Method in class astex.MoleculeRenderer
Calculate hydrogen bonds.
CALIFORNIUM - Static variable in class astex.PeriodicTable
 
call(MoleculeViewer, Arguments) - Method in interface astex.UserCommand
 
CARBON - Static variable in class astex.PeriodicTable
 
cartesianToFractional - Variable in class astex.Symmetry
The matrix that converts cartesian to fractional coordinates.
CartoonLightingModel - Static variable in class astex.Renderer
The cartoon style.
ccacher - Static variable in class astex.ShadowCache
 
ccachex0 - Static variable in class astex.ShadowCache
Cylinder cache for shadows.
ccachex1 - Static variable in class astex.ShadowCache
 
ccachey0 - Static variable in class astex.ShadowCache
 
ccachey1 - Static variable in class astex.ShadowCache
 
ccachez0 - Static variable in class astex.ShadowCache
 
ccachez1 - Static variable in class astex.ShadowCache
 
CCP4_BINARY - Static variable in class astex.Map
Various definitions of map types.
CENTER - Static variable in class astex.sym
 
centerGrid - Variable in class astex.Map
The center grid point for the current stored map data.
Centroids - Static variable in class astex.Distance
The centroid distance mode.
CERIUM - Static variable in class astex.PeriodicTable
 
CESIUM - Static variable in class astex.PeriodicTable
 
Chain - Class in astex
A class for storing a group of atoms that form part of a protein chain.
chain(MoleculeRenderer, Vector) - Static method in class astex.Selection
Select a set of atoms on the basis of residue names.
CHAIN - Static variable in class astex.sym
 
chainSchematic(Arguments, Tmesh, Chain) - Static method in class astex.Schematic
Add schematic objects for this chain.
CHARGE - Static variable in class astex.sym
 
chartreuse - Static variable in class astex.Color32
 
check(boolean, String) - Static method in class astex.Log
 
check(boolean, String, double) - Static method in class astex.Log
 
check(boolean, String, long) - Static method in class astex.Log
 
checkbox(String, String, JCItemListener) - Static method in class astex.UI
Create a checkBox.
checkExtension(Molecule, String) - Method in class astex.MoleculeViewer
Check the file extension on a save file name.
Child - Static variable in class astex.generic.GenericEvent
 
ChildAdded - Static variable in class astex.generic.GenericEvent
 
ChildRemoved - Static variable in class astex.generic.GenericEvent
 
CHLORINE - Static variable in class astex.PeriodicTable
 
chocolate - Static variable in class astex.Color32
 
CHROMIUM - Static variable in class astex.PeriodicTable
 
clamp(int) - Static method in class astex.Color32
Clamp number to range specified.
Class - Static variable in class astex.generic.GenericEvent
 
ClassName - Static variable in class astex.generic.Generic
 
CLEAR - Static variable in class astex.sym
 
clearShadowCaches() - Static method in class astex.ShadowCache
Clear out the shadow data structures.
clearVisitFlags() - Method in class astex.Molecule
Clear the visit flags on all of the atoms.
CLIP - Static variable in class astex.sym
 
clip(int) - Method in class astex.Tmesh
Clip Tmesh to those triangles and points that have visible texture coordinates.
clipContour(Tmesh, double) - Method in class astex.MoleculeRenderer
Clip the contour object to the molecule.
clipIncrement - Variable in class astex.Renderer
The clip increment.
clipMap(Map, DynamicArray, boolean) - Method in class astex.MoleculeRenderer
Clip this map.
clipMaps() - Method in class astex.MoleculeRenderer
Clip around center point.
clipMaps(String, DynamicArray, boolean) - Method in class astex.MoleculeRenderer
Clip any maps we are displaying to show only unoccupied density.
clipped(Point3d, DynamicArray) - Method in class astex.MoleculeRenderer
Is this point inside an atom in the molecule.
clipping - Variable in class astex.Renderer
Is clipping enabled?
clipSurface(Tmesh, boolean) - Static method in class astex.Surface
 
clipTriangle - Variable in class astex.Renderer
Does this triangle need clipping?
clone() - Method in class astex.Point3d
Clone method
close() - Method in class astex.FILE
Close a file object.
cnxSpaceGroupNameToNumber(String) - Method in class astex.Symmetry
 
COBALT - Static variable in class astex.PeriodicTable
 
Coil - Static variable in class astex.Residue
Sheet secondary structure type.
COLON - Static variable in class astex.sym
 
Color - Static variable in class astex.Atom
 
Color - Static variable in class astex.Distance
 
COLOR - Static variable in class astex.sym
 
Color32 - Class in astex
 
Color32() - Constructor for class astex.Color32
 
COLOR_BY_ATOM - Static variable in class astex.sym
 
COLOR_BY_BVALUE - Static variable in class astex.sym
 
COLOR_BY_BVALUE_RANGE - Static variable in class astex.sym
 
COLOR_BY_CHAIN - Static variable in class astex.sym
 
COLOR_BY_ENERGY - Static variable in class astex.sym
 
COLOR_BY_RAINBOW - Static variable in class astex.sym
 
ColorButton - Class in astex
 
ColorButton() - Constructor for class astex.ColorButton
Default constructor.
ColorButton(Color, int) - Constructor for class astex.ColorButton
Create a color button.
colorByAtom() - Method in class astex.MoleculeRenderer
Color by atom type.
colorByBFactor() - Method in class astex.MoleculeRenderer
Color by bFactor.
colorByChain() - Method in class astex.MoleculeRenderer
Color by chain.
colorByPropertyRange(int) - Method in class astex.MoleculeRenderer
Color by b-factor but bin the colors according to range.
colorByRainbow(DynamicArray) - Method in class astex.MoleculeRenderer
Color a set of atoms with rainbow hue.
colorBySpecifiedColor(int) - Method in class astex.MoleculeRenderer
Color by bFactor.
ColorChooser - Class in astex
 
ColorChooser(Dialog) - Constructor for class astex.ColorChooser
 
colorInitialised - Variable in class astex.Renderer
Have we initialised the single color lookup table?
ColorSpace - Class in astex
 
ColorSpace() - Constructor for class astex.ColorSpace
 
colorStyle - Variable in class astex.Tmesh
Color style.
colorTriangle - Variable in class astex.Renderer
Are we doing triangle debugging color style.
COMMA - Static variable in class astex.sym
 
Command - Static variable in class astex.AnimationObject
Constant to indicate that we are recentering.
composite(MoleculeRenderer, Vector) - Static method in class astex.Selection
Select a set of atoms on the basis of ids.
COMPOSITE - Static variable in class astex.sym
 
compositeSelection(MoleculeRenderer, Vector, Vector, Vector, Vector) - Static method in class astex.Selection
Composite specification.
connect() - Method in class astex.Molecule
Connect the atoms in a molecule using standard bonding radii.
connect2() - Method in class astex.Molecule
Connect the atoms using a neighbour grid.
connected121314(Atom) - Method in class astex.Atom
Are these atoms connected 1,2, 1,3 or 1,4.
connected13(Atom) - Method in class astex.Atom
Is this atom connected by two bonds to the specified atom.
connected14(Atom) - Method in class astex.Atom
Is this atom connected by three bonds to the specified atom.
connectResidue(Residue) - Method in class astex.Molecule
Connect all of the atoms in a single residue.
connectResidues(Residue, Residue) - Method in class astex.Molecule
Connect all of the atoms in a single residue.
connolly(DynamicArray, double, boolean) - Static method in class astex.Surface
Create a soft object surface.
constrain(Container, Component, int, int, int, int, int, int, double, double) - Static method in class astex.Layout
 
constrained - Variable in class astex.EnergyTerm
Is this torsion constrained e.g.
contact(MoleculeRenderer, double, byte[]) - Static method in class astex.Selection
Return a set of atoms withinin a tolerance of sum of vdw radii.
CONTACT - Static variable in class astex.sym
 
contains(double) - Method in class astex.DoubleArray
Does the array contain the specified object.
contains(Object) - Method in class astex.DynamicArray
Does the array contain the specified object.
contains(float) - Method in class astex.FloatArray
Does the array contain the specified object.
contains(int) - Method in class astex.IntArray
Does the array contain the specified object.
contains(Atom) - Method in class astex.Ring
Does this ring contain the specified atom?
contains(Bond) - Method in class astex.Ring
Does this ring contain the specified bond?
contains(String) - Method in class astex.StringArray
Does the array contain the specified object.
CONTEXT - Static variable in class astex.sym
 
Contour - Class in astex
A class for contouring numeric grids in 3-dimensions.
Contour() - Constructor for class astex.Contour
 
contour(float[], int, int, int, double, Tmesh) - Static method in class astex.Contour
Main entry point for contouring methods.
CONTOUR - Static variable in class astex.sym
 
contourMap(Map, int) - Method in class astex.MoleculeRenderer
Generate one specific contour level for the map.
contourMaps() - Method in class astex.MoleculeRenderer
Contour the maps that we are displaying.
contourRegion(Map, int, int) - Method in class astex.MoleculeRenderer
Contour the data that is in stored in the map.
ContourScrollbar - Class in astex
Class that extends Scrollbar so that we can force it to occupy a particular size.
ContourScrollbar(int) - Constructor for class astex.ContourScrollbar
 
contourSize - Variable in class astex.MoleculeRenderer
The current contour grid size.
convertBigToLittle(int) - Static method in class astex.Map
Convert from big to little endian byte ordering.
COPPER - Static variable in class astex.PeriodicTable
 
copy(Matrix) - Method in class astex.Matrix
Copy m into this matrix.
copy(DynamicArray) - Static method in class astex.Tmesh
Copy the specified objects into a new object.
coral - Static variable in class astex.Color32
 
cornsilk - Static variable in class astex.Color32
 
cosWrapAngle - Variable in class astex.Renderer
 
countAngles() - Method in class astex.Molecule
Count how many bond angles this molecule has.
CRC32 - Class in astex
Calculates the CRC32 - 32 bit Cyclical Redundancy Check
crc32(String) - Static method in class astex.CRC32
Convenience mithod for generating a CRC from a single String.
crc32(byte[]) - Static method in class astex.CRC32
Convenience method for generating a CRC from a byte array.
crc32(String, int) - Static method in class astex.CRC32
Convenience method for generating a CRC from a series of String's.
crc32(byte[], int) - Static method in class astex.CRC32
Convenience method for generating a CRC from a series of byte arrays.
crc32(byte[], int, int, int) - Static method in class astex.CRC32
General CRC generation function.
crc32(int[], int, int, int) - Static method in class astex.CRC32
General CRC generation function.
create() - Static method in class astex.Angle
A method that will create a new Bond.
create() - Static method in class astex.Atom
Create an atom.
create() - Static method in class astex.Bond
A method that will create a new Bond.
create() - Static method in class astex.Chain
Public interface for creating chains.
create() - Static method in class astex.Improper
A method that will create a new Improper.
create() - Static method in class astex.Map
Public interface to map creation.
create() - Static method in class astex.Residue
Public interface for creating residues.
create() - Static method in class astex.Ring
Create a ring.
create(Arguments, MoleculeRenderer, DynamicArray) - Static method in class astex.Schematic
Create a schematic.
createBMPMenu() - Method in class astex.MoleculeViewer
 
createCheckboxMenuItem(String, boolean) - Method in class astex.MoleculeViewer
Create a single checkbox menu item.
createCloseMoleculeMenu() - Method in class astex.MoleculeViewer
Create the menu that lets us close molecules.
createColorMenu() - Method in class astex.MoleculeViewer
Create the color menu.
createControls() - Method in class astex.ObjectPropertyDialog
Create the controls for this property editor.
createDisplayMenu() - Method in class astex.MoleculeViewer
Create the display menu.
createDistanceMonitor(Atom, Atom) - Static method in class astex.Distance
Get the distance mode.
createFileMenu() - Method in class astex.MoleculeViewer
Create the file menu.
createLigandMenu() - Method in class astex.MoleculeViewer
Create the menu that lets us choose ligand groups.
createMeasureMenu() - Method in class astex.MoleculeViewer
Create the menu that picks measurement options.
createMenuBar() - Method in class astex.MoleculeViewer
Create the menu bar that we will use.
createMenuItem(String) - Method in class astex.MoleculeViewer
Create a single menu item.
createOptionsMenu() - Method in class astex.MoleculeViewer
Create the option menu.
createPopup(MouseEvent) - Method in class astex.MoleculeViewer
Create a popup menu.
createSaveMoleculeMenu() - Method in class astex.MoleculeViewer
Create the menu that lets us save molecules.
createSelectMenu() - Method in class astex.MoleculeViewer
Create the select menu.
createSimpleMap() - Static method in class astex.Map
Create a simple map for internal use.
createViewMenu() - Method in class astex.MoleculeViewer
Create the view menu.
cross(double[], double[], double[]) - Static method in class astex.Geometry
Form cross product of two vectors(a = b x c).
cross(Point3d) - Method in class astex.Point3d
Return cross product with c.
cross(Point3d, Point3d, Point3d) - Static method in class astex.Point3d
Set a to cross product of b and c.
cross(double[], double[], double[]) - Static method in class astex.Point3d
Generate cross product for double[] vectors.
crossNoNormalise(Point3d, Point3d, Point3d) - Static method in class astex.Point3d
Set a to cross product of b and c.
CURIUM - Static variable in class astex.PeriodicTable
 
current(MoleculeRenderer) - Static method in class astex.Selection
Return the current selection.
CURRENT - Static variable in class astex.sym
 
currentLineContains(String, int) - Method in class astex.FILE
Does the current line contain the specified string at the specified location.
CURVATURE - Static variable in class astex.sym
 
curvature(Tmesh, DynamicArray, int, double) - Static method in class astex.Texgen
Calculate pseudo curvature.
CustomLabelled - Static variable in class astex.Atom
The property set flag.
cyan - Static variable in class astex.Color32
 
Cylinder - Static variable in class astex.Atom
The property set flag.
CYLINDER_RADIUS - Static variable in class astex.sym
 
CYLINDERS - Static variable in class astex.sym
 
cylinders - Variable in class astex.Tmesh
Cylinder graphical object.
CYLINDERS - Static variable in class astex.Tmesh
Types for style.
cylinderShadowCacheList - Static variable in class astex.ShadowCache
 

D

DASH - Static variable in class astex.sym
 
data - Variable in class astex.Map
 
dcol - Variable in class astex.AtomicElement
 
debug - Static variable in class astex.Fit
Should we output debugging info.
DEBUG - Static variable in class astex.Log
The hard wired log level settings.
debug(String, double) - Static method in class astex.Log
 
debug(String, long) - Static method in class astex.Log
 
debug(String) - Static method in class astex.Log
 
debug - Variable in class astex.Molecule
Is debugging on.
debug - Variable in class astex.MoleculeRenderer
Are we debugging.
debug - Variable in class astex.Renderer
Is debugging information enabled?
debug - Static variable in class astex.SecondaryStructure
 
debug(String) - Static method in class astex.Surface
Print a debuggin message.
debug - Variable in class astex.Tmesh
Debugging on?
DEBUG1 - Static variable in class astex.Log
 
debug1(String, double) - Static method in class astex.Log
 
debug1(String, long) - Static method in class astex.Log
 
debug1(String) - Static method in class astex.Log
 
DEBUG2 - Static variable in class astex.Log
 
debug2(String, double) - Static method in class astex.Log
 
debug2(String, long) - Static method in class astex.Log
 
debug2(String) - Static method in class astex.Log
 
DEBUG3 - Static variable in class astex.Log
 
debug3(String, double) - Static method in class astex.Log
 
debug3(String, long) - Static method in class astex.Log
 
debug3(String) - Static method in class astex.Log
 
debugColor - Variable in class astex.Renderer
Contrasting colors for debugging renderer performance.
debugOff() - Method in class MoleculeViewerApplet
Turn on debugging.
debugOn() - Method in class MoleculeViewerApplet
Turn on debugging.
decodeSymmetryToken(String, double[]) - Static method in class astex.Symmetry
Decode the symmetry token in the String.
DECREASE - Static variable in class astex.sym
 
decrementClip() - Method in class astex.Renderer
Decrement the clip plane distance.
decrementFrontClip() - Method in class astex.Renderer
Decrement the clip plane distance.
DEFAULT - Static variable in class astex.match
The default matching constructs (ASTERISK, QUESTION_MARK, and BRACKETS).
DEFAULT - Static variable in class astex.sym
 
DefaultLightingModel - Static variable in class astex.Renderer
The default lighting model.
defaultSelection(MoleculeRenderer) - Static method in class astex.Selection
Return the default selection.
DEFINE - Static variable in class astex.sym
 
defined(String) - Method in class astex.Arguments
Is this argument defined.
delete() - Method in class astex.Atom
Remove an atom.
delete() - Method in class astex.Bond
Delete this bond.
delete() - Method in class astex.Residue
Remove this residue.
deleteAtom(Atom) - Method in class astex.MoleculeRenderer
Actually delete an atom.
depthcue - Variable in class astex.Renderer
Do depth cueing of the final image.
destroy() - Method in class MoleculeViewerApplet
Destroy the applet.
determineRegion(Map) - Method in class astex.MoleculeRenderer
Figure out the region of the map we will contour.
determineSymmetry() - Method in class astex.MoleculeRenderer
Determine the set of symmetry operators.
diffuse - Variable in class astex.Light
Packed diffuse colour.
dirty - Variable in class astex.MoleculeRenderer
Has something changed the scene.
dirtyRepaint() - Method in class astex.MoleculeViewer
Mark the renderer dirty and ask for repaint().
DISPLAY - Static variable in class astex.sym
 
displayAsCylinders - Variable in class astex.MoleculeRenderer
 
DisplayBondDetails - Static variable in class astex.Molecule
 
displayBondTypes(boolean) - Method in class astex.MoleculeRenderer
Set whether or not we display bond types.
Displayed - Static variable in class astex.Atom
The atom display flag.
Displayed - Static variable in class astex.Molecule
 
displayed(MoleculeRenderer) - Static method in class astex.Selection
Return the atoms that are actively displayed.
DISPLAYED - Static variable in class astex.sym
 
DisplayedMask - Static variable in class astex.Atom
 
DisplayHydrogens - Static variable in class astex.Molecule
 
dispose() - Method in class astex.MoleculeViewer
 
Distance - Class in astex
 
Distance() - Constructor for class astex.Distance
 
distance(Point3d) - Method in class astex.Point3d
Return the distance to the specified point.
distance(Point3d, Point3d) - Static method in class astex.Point3d
Static distance method.
distance(double, double, double, double, double, double) - Static method in class astex.Surface
Calculate the distance between two points.
DISTANCE - Static variable in class astex.sym
 
distance(Tmesh, DynamicArray, int) - Static method in class astex.Texgen
Measure distance to nearest point in point list.
distance(int, int) - Method in class astex.Tmesh
Distance between two points.
distance(int, double[]) - Method in class astex.Tmesh
Distance between vertex and point.
distance2(double, double, double, double, double, double) - Static method in class astex.Surface
Calucate the sqaured distance between two points.
DISTANCE_PICK - Static variable in class astex.MoleculeRenderer
Distance picking mode.
distanceSq(Point3d) - Method in class astex.Point3d
Return the square of the distance to the specified point.
distanceSq(Point3d, Point3d) - Static method in class astex.Point3d
Static distance squared method.
divide(double) - Method in class astex.Point3d
Scale a vector by the amount specified for each coordinate.
dna(MoleculeRenderer) - Static method in class astex.Selection
DNA expression.
DNA - Static variable in class astex.sym
 
dnaNames - Static variable in class astex.Selection
Residue names for dna.
doAntialias(int[], int, int, int) - Static method in class astex.ViewCommand
 
DOLLAR - Static variable in class astex.sym
 
dot(double[], double[]) - Static method in class astex.Geometry
Generate the dot product.
dot(Point3d) - Method in class astex.Point3d
Return the dot product of this vector with another one.
DOTS - Static variable in class astex.Tmesh
Types for style.
dotSurface(DynamicArray, int) - Static method in class astex.Surface
Generate a dot surface.
DOTSURFACE - Static variable in class astex.sym
 
DOUBLE - Static variable in class astex.sym
 
DoubleArray - Class in astex
An object that implements a dynamic array.
DoubleArray(int, int) - Constructor for class astex.DoubleArray
Constructor which specifies the initial size and the capacity increment.
DoubleArray() - Constructor for class astex.DoubleArray
Default constructor.
DoubleArray(int) - Constructor for class astex.DoubleArray
Constructor which specifies the initial size.
DoubleBond - Static variable in class astex.Bond
Constant that defines a single bond.
DoubleOrAromaticBond - Static variable in class astex.Bond
Constant that defines a double or aromatic bond.
drawAngle(Atom, Atom, Atom) - Method in class astex.MoleculeRenderer
Draw an angle marker.
drawAngles() - Method in class astex.MoleculeRenderer
Draw the angle markers.
drawAntiAliasedLine(int, int, int, int, int, int, int, int) - Method in class astex.Renderer
Basic Wu antialiased line drawing.
drawAtom(Atom, int) - Method in class astex.MoleculeRenderer
Draw one atom.
drawBond(Bond, double) - Method in class astex.MoleculeRenderer
Draw one bond.
drawBox(int, int, int, int, int) - Method in class astex.Renderer
Draw a box in transformed screen coords.
drawBumpPairs() - Method in class astex.MoleculeRenderer
Draw the bump atoms.
drawCylinder(double, double, double, double, double, double, int, int, double) - Method in class astex.Renderer
Draw a cylinder.
drawDashedLine(double, double, double, double, double, double, double, double, double, int) - Method in class astex.MoleculeRenderer
Draw the distance marker line.
drawDirectString(int, int, int, String) - Method in class astex.Renderer
Draw a string at the specified point.
drawDistance(Atom, Atom, boolean) - Method in class astex.MoleculeRenderer
Draw a distance between two atoms.
drawDistanceObject(Distance) - Method in class astex.MoleculeRenderer
Draw the specific distance.
drawDistances() - Method in class astex.MoleculeRenderer
Draw the distance markers.
drawDistances2() - Method in class astex.MoleculeRenderer
Draw the distance markers.
drawDot(int, int, int, int) - Method in class astex.Renderer
Draw a dot.
drawDottedLine(Atom, Atom, double, int) - Method in class astex.MoleculeRenderer
Draw a dotted line.
drawImage(Component, Graphics) - Method in class astex.MoleculeViewer
Paint the image.
drawLabelledAtoms() - Method in class astex.MoleculeRenderer
Draw all of the labelled atoms.
drawLine(double, double, double, double, double, double, int, int, int) - Method in class astex.Renderer
World coordinate entry point for drawing lines.
drawLine(int, int, int, int, int, int, int, int, int) - Method in class astex.Renderer
Main entry point for drawing lines.
drawLoadingScreen(Graphics) - Method in class astex.MoleculeViewer
Function that paints the image when we load.
drawMap(Map) - Method in class astex.MoleculeRenderer
 
drawMaps() - Method in class astex.MoleculeRenderer
 
drawMolecules() - Method in class astex.MoleculeRenderer
Draw the molecule.
drawObjects() - Method in class astex.Renderer
Draw the tmesh objects.
drawPixels(double, double, double, int, int, int[], int) - Method in class astex.Renderer
Draw an image at the specified location.
drawSphere(double, double, double, double, int) - Method in class astex.Renderer
Draw a sphere.
drawSphere(double, double, double, double, int, int) - Method in class astex.Renderer
 
drawString(double, double, double, int, String) - Method in class astex.Renderer
Draw a string at the specified point.
drawString(double, double, double, double, int, String) - Method in class astex.Renderer
Draw a string at the specified point.
drawTorsion(Atom, Atom, Atom, Atom) - Method in class astex.MoleculeRenderer
Draw a torsion marker.
drawTorsions() - Method in class astex.MoleculeRenderer
Draw the angle markers.
drawTrace(Molecule) - Method in class astex.MoleculeRenderer
Draw the molecule as a trace.
drawTwinColourDottedLine(Atom, Atom, double, int, int) - Method in class astex.MoleculeRenderer
Draw a dotted line.
drawZImage(double, double, double, int[], int, int) - Method in class astex.Renderer
 
drow - Variable in class astex.AtomicElement
 
DynamicArray - Class in astex
An object that implements a dynamic array.
DynamicArray(int, int) - Constructor for class astex.DynamicArray
Constructor which specifies the initial size and the capacity increment.
DynamicArray() - Constructor for class astex.DynamicArray
Default constructor.
DynamicArray(int) - Constructor for class astex.DynamicArray
Constructor which specifies the initial size.
dynamicArrayCache - Static variable in class astex.Selection
Cache for DynamicArray that will return selected atoms.
DYSPROSIUM - Static variable in class astex.PeriodicTable
 

E

E - Static variable in class astex.Atom
The energy.
edit(String, String) - Method in class astex.Atom
 
EINSTEINIUM - Static variable in class astex.PeriodicTable
 
ELECTROSTATIC - Static variable in class astex.sym
 
Electrostatic - Static variable in class astex.Texgen
 
Element - Static variable in class astex.Atom
 
element(MoleculeRenderer, Vector) - Static method in class astex.Selection
Select a set of atoms on the basis of elements.
elements - Static variable in class astex.PeriodicTable
 
empty() - Method in class astex.Tmesh
Empty an object.
emulate555 - Variable in class astex.Renderer
 
energy - Variable in class astex.ModellingData
The energy associated with this object.
EnergyTerm - Class in astex
A class for representing an energy term in a force field.
EnergyTerm() - Constructor for class astex.EnergyTerm
 
ensureColorRampDefined() - Method in class astex.MoleculeRenderer
 
ensureConfigurationFileLoaded() - Static method in class astex.Arguments
Make sure we loaded the config file.
ensureMapCapacity(int) - Method in class astex.Map
Ensure we have enough room to store the map.
ensureMenusCreated() - Method in class astex.MoleculeViewer
Ensure that the close molecule menu is created.
ensurePointCapacity() - Method in class astex.Tmesh
Make sure we have room for the next point.
ensureTriangleCapacity() - Method in class astex.Tmesh
Make sure we have room for the next triangle.
ENVIRONMENT - Static variable in class astex.sym
 
EOF - Static variable in class astex.FILE
The constant that represents the end of file.
EOF - Static variable in class astex.sym
 
EQ - Static variable in class astex.Selection
Equal attribute.
equal(Point3d) - Method in class astex.Point3d
Are this point identically equal to the specified point.
equals(Matrix) - Method in class astex.Matrix
Does this matrix equal another matrix.
ERBIUM - Static variable in class astex.PeriodicTable
 
err - Static variable in class astex.FILE
 
ERROR - Static variable in class astex.Log
 
error(String, double) - Static method in class astex.Log
 
error(String, long) - Static method in class astex.Log
 
error(String) - Static method in class astex.Log
 
error - Static variable in class astex.sym
 
EUROPIUM - Static variable in class astex.PeriodicTable
 
EVALUATE - Static variable in class astex.sym
 
EXCLUDE - Static variable in class astex.sym
 
execute(String) - Method in class astex.MoleculeRenderer
 
execute(String) - Method in class astex.MoleculeViewer
Execute a command in the moleculeRenderer.
execute(MoleculeViewer, Arguments) - Static method in class astex.ViewCommand
Execute a view command.
execute(String) - Method in class MoleculeViewerApplet
 
execute2(String) - Method in class astex.MoleculeRenderer
Main interface for command processing.
execute22(String) - Method in class astex.MoleculeRenderer
 
executeAnimationFunction() - Method in class astex.AnimationObject
Execute the actual animation function.
executeFile(String) - Method in class MoleculeViewerApplet
Open a file and execute the script in it.
executeInternal(String) - Method in class astex.MoleculeRenderer
 
executeScript(String) - Method in class astex.MoleculeRenderer
Execute a script of commands.
executeScript(String) - Method in class astex.MoleculeViewer
 
expandSelection(Molecule, int[]) - Method in class astex.MoleculeRenderer
Expand the selected atoms to include the whole residue.
expandSelection1(Molecule, int[]) - Method in class astex.MoleculeRenderer
Expand the selected atoms to include the whole residue.
ExplicitBond - Static variable in class astex.Bond
Did the bond come from a CONECT record.

F

f(String) - Static method in class astex.print
 
f(Object) - Static method in class astex.print
 
f(String, double) - Static method in class astex.print
 
f(String, float) - Static method in class astex.print
 
f(String, int) - Static method in class astex.print
 
f(String, char) - Static method in class astex.print
 
f(String, String) - Static method in class astex.print
 
FALSE - Static variable in class astex.sym
 
FATAL - Static variable in class astex.Log
 
fatal(String, double) - Static method in class astex.Log
 
fatal(String, long) - Static method in class astex.Log
 
fatal(String) - Static method in class astex.Log
 
FeatureMolecule - Static variable in class astex.Molecule
 
Featurize - Class in astex
 
Featurize() - Constructor for class astex.Featurize
 
FERMIUM - Static variable in class astex.PeriodicTable
 
FETCH - Static variable in class astex.sym
 
fetch(String) - Method in class MoleculeViewerApplet
Return the contents of the specified url.
fetchSafe(String) - Method in class MoleculeViewerApplet
Safe url fetcher.
FILE - Class in astex
A class which implements a high performance byte based input stream.
FILE(OutputStream) - Constructor for class astex.FILE
Constructor for stdout stderr output.
FILE(InputStream) - Constructor for class astex.FILE
Constructor that will take an InputStream and create a FILE object that will read from it.
fill(Container, Component, int, int) - Static method in class astex.Layout
 
fill(Container, Component, int, int, int) - Static method in class astex.Layout
 
fill(Container, Component, int, int, int, int) - Static method in class astex.Layout
 
fill(Container, Component, int, int, int, int, int) - Static method in class astex.Layout
 
fillValues(String[], int) - Method in class astex.Texture
Fill values with specified colors along texture coordinate.
finalize() - Method in class astex.MoleculeViewer
 
finalize() - Method in class MoleculeViewerApplet
 
FinalRenderPass - Static variable in class astex.Renderer
 
find3Rings() - Method in class astex.Molecule
Find 3 membered rings by direct search.
findAtom(String) - Method in class astex.Residue
Default to alternate location 'A'.
findAtom(String, char) - Method in class astex.Residue
Similar to getAtom(String name) but will search in the previous residue if the name ends with '-' or the next residue if the name ends with '+'.
findChain(String, boolean) - Method in class astex.Molecule
Find or add a particular chain.
findRings() - Method in class astex.Molecule
Find rings in the structure.
findRings(int) - Method in class astex.Molecule
Find rings of a particular size.
fireAtomSelectedEvent(Atom) - Method in class astex.MoleculeRenderer
Fire an atom selected event.
firebrick - Static variable in class astex.Color32
 
fireGenericAddedEvent(Generic) - Method in class astex.MoleculeRenderer
Fire a distance added event.
fireGenericRemovedEvent(Generic) - Method in class astex.MoleculeRenderer
Fire a generic removed event.
fireMapAddedEvent(Map) - Method in class astex.MoleculeRenderer
Fire a map added event.
fireMapRemovedEvent(Map) - Method in class astex.MoleculeRenderer
Fire a map added event.
fireMoleculeAddedEvent(Molecule) - Method in class astex.MoleculeRenderer
Fire a molecule added event.
fireMoleculeRemovedEvent(Molecule) - Method in class astex.MoleculeRenderer
Fire a molecule removed event.
Fit - Class in astex
Class for least squares fitting of sets of points.
Fit() - Constructor for class astex.Fit
 
fit(double[], double[], double[], double[], double[], double[], int, Matrix) - Static method in class astex.Fit
Fit the pairs of coordinates using Kearsley's quaternion based algorithm.
fitMolecules(String, String, String) - Static method in class astex.Fit
 
FIXED - Static variable in class astex.sym
 
FixedBits - Static variable in class astex.Renderer
Number of fixed precision bits.
fixNormals(Tmesh) - Static method in class astex.Surface
Make better normals for the surface.
FloatArray - Class in astex
An object that implements a dynamic array.
FloatArray(int, int) - Constructor for class astex.FloatArray
Constructor which specifies the initial size and the capacity increment.
FloatArray() - Constructor for class astex.FloatArray
Default constructor.
FloatArray(int) - Constructor for class astex.FloatArray
Constructor which specifies the initial size.
FLUORINE - Static variable in class astex.PeriodicTable
 
forceConstant - Variable in class astex.EnergyTerm
The force constant for this term.
FORCEFIELD - Static variable in class astex.sym
 
format(int) - Static method in class astex.Color32
 
Format - Static variable in class astex.Distance
 
format(String) - Method in class astex.FILE
Format the String argument.
format(long) - Method in class astex.FILE
Format integer.
format(double) - Method in class astex.FILE
Format double.
format(char) - Method in class astex.FILE
Format the char argument.
Format - Class in astex
 
Format(String) - Constructor for class astex.Format
Formats the number following printf conventions.
format(double) - Method in class astex.Format
Formats a double into a string (like sprintf in C)
format(long) - Method in class astex.Format
Formats a long integer into a string (like sprintf in C)
format(char) - Method in class astex.Format
Formats a character into a string (like sprintf in C)
format(String) - Method in class astex.Format
Formats a string into a larger string (like sprintf in C)
formatNoQuotes(int) - Static method in class astex.Color32
 
fractionalToCartesian - Variable in class astex.Symmetry
The matrix that converts fractional to cartesian coordinates.
FRANCIUM - Static variable in class astex.PeriodicTable
 
fromQuaternion(double[]) - Method in class astex.Matrix
Generate rotation matrix from quaternion.
fromQuaternion(double, double, double, double) - Method in class astex.Matrix
Generate rotation matrix from quaternion.
front - Variable in class astex.Renderer
The distance in front of the center of the front clip plane.
frontClip - Variable in class astex.Renderer
The integer front plane.
FrontClipMoved - Static variable in class astex.RendererEvent
 
frontFaceOnly - Variable in class astex.Renderer
Do backface removal of triangles.

G

GADOLINIUM - Static variable in class astex.PeriodicTable
 
gainsboro - Static variable in class astex.Color32
 
GALLIUM - Static variable in class astex.PeriodicTable
 
GE - Static variable in class astex.Selection
Greater equal attribute.
generateAtomLabel(Atom) - Method in class astex.MoleculeRenderer
Generate the atom label.
generateAtomLabels(String, DynamicArray) - Method in class astex.MoleculeRenderer
Generate an atom label according to the format statments.
generateBondImpropers() - Method in class astex.Molecule
Generate impropers to keep bonds flat.
generateBumps(Atom) - Method in class astex.MoleculeRenderer
Generate the bump atoms around the specified atom.
generateBumps(DynamicArray) - Method in class astex.MoleculeRenderer
Generate bumps for the specified set of atoms.
generateDoubleBondImproper(Bond) - Method in class astex.Molecule
Generate the improper for this double bond.
generateLabel(String) - Method in class astex.Atom
Generate an atom label according to a format.
generateMaps() - Method in class astex.MoleculeRenderer
Generate the map display.
generateMatrices(double[], Matrix, Matrix) - Static method in class astex.Symmetry
Generate the fractional to cartesian matrices.
generateOrthonormalBasis(double[], double[], double[], boolean) - Static method in class astex.Geometry
Generate orthogonal normalised vector set.
generatePlanes(DynamicArray) - Method in class astex.Molecule
Method for CCP4Dictionary that generates list of planes.
generateRing(Ring) - Method in class astex.Molecule
Generate the impropers for one ring.
generateRingImpropers() - Method in class astex.Molecule
Generate the impropers that are due to rings.
generateSingleBondImproper(Bond) - Method in class astex.Molecule
Generate the improper for this single bond.
generateSp2Impropers() - Method in class astex.Molecule
Generate impropers for sp2 hybrid atoms.
generateSymmetry(Point3d, double) - Method in class astex.MoleculeRenderer
Generate symmetry for the molecules we are displaying.
generateSymmetry() - Method in class astex.MoleculeRenderer
Generate the symmetry copies of the molecules.
generateSymmetryMolecule(Point3d, double) - Method in class astex.MoleculeRenderer
Acutally generate the symmetry atoms.
generateTriangles - Static variable in class astex.March
 
Generic - Class in astex.generic
 
Generic(String) - Constructor for class astex.generic.Generic
 
Generic() - Constructor for class astex.generic.Generic
 
genericAdded(MoleculeRenderer, Generic) - Method in interface astex.MoleculeRendererListener
A generic was added.
genericAdded(MoleculeRenderer, Generic) - Method in class astex.MoleculeViewer
 
genericAdded(MoleculeRenderer, Generic) - Method in class astex.UserInterface
 
GenericEvent - Class in astex.generic
 
GenericEvent(String, Object, Object, Object) - Constructor for class astex.generic.GenericEvent
 
GenericEventInterface - Interface in astex.generic
 
GenericInterface - Interface in astex.generic
 
genericRemoved(MoleculeRenderer, Generic) - Method in interface astex.MoleculeRendererListener
A generic was removed.
genericRemoved(MoleculeRenderer, Generic) - Method in class astex.MoleculeViewer
 
genericRemoved(MoleculeRenderer, Generic) - Method in class astex.UserInterface
 
Geometry - Class in astex
Various involved geometrical operations for the renderer.
Geometry() - Constructor for class astex.Geometry
 
GERMANIUM - Static variable in class astex.PeriodicTable
 
get(Object, Object) - Method in class astex.Atom
Get Object representing key.
get(Object, Object) - Method in class astex.Bond
 
get(int) - Method in class astex.DoubleArray
Return a specified element from the array.
get(int) - Method in class astex.DynamicArray
Return a specified element from the array.
get(int) - Method in class astex.FloatArray
Return a specified element from the array.
get(Object, Object) - Method in class astex.generic.Generic
 
get(Object, Object) - Method in interface astex.generic.GenericInterface
Get Object representing key.
get(int) - Method in class astex.IntArray
Return a specified element from the array.
get(Object, Object) - Method in class astex.Molecule
 
get(int) - Method in class astex.Point3d
Set the specified component.
get(String, String) - Static method in class astex.Settings
The main get method.
get(String, String, Object) - Static method in class astex.Settings
 
get(int) - Method in class astex.StringArray
Return a specified element from the array.
getAmbient() - Method in class astex.Renderer
Get the ambient component.
getAngle(int) - Method in class astex.Molecule
Get the specified angle.
getAngleArray() - Method in class astex.Molecule
Get the array of angles.
getAngleCount() - Method in class astex.Molecule
Get the number of atoms for this molecule.
getAntiAlias() - Method in class astex.Renderer
Return the current antialiasing setting.
getApplet(Component) - Static method in class astex.Util
Return the applet that contains the specified component.
getArray() - Method in class astex.DoubleArray
Return the reference to the object array.
getArray() - Method in class astex.DynamicArray
Return the reference to the object array.
getArray() - Method in class astex.FloatArray
Return the reference to the object array.
getArray() - Method in class astex.IntArray
Return the reference to the object array.
getArray() - Method in class astex.StringArray
Return the reference to the object array.
getAtom(int) - Method in class astex.Angle
Get the specified atom.
getAtom(int) - Method in class astex.Bond
Get the specified atom.
getAtom(int) - Method in class astex.Improper
Get the specified atom.
getAtom(int) - Method in class astex.Molecule
Return the specified atom.
getAtom(int) - Method in class astex.Residue
Return the specified atom.
getAtom(String) - Method in class astex.Residue
Return the atom with the given name.
getAtom(String, char) - Method in class astex.Residue
Return the atom with the given name.
getAtom(int) - Method in class astex.Ring
Get an atom.
getAtomArray() - Method in class astex.Molecule
Return the atom array.
getAtomCount() - Method in class astex.Molecule
Return the number of atoms in the molecule.
getAtomCount() - Method in class astex.MoleculeRenderer
Return the total number of atoms in the renderer.
getAtomCount() - Method in class astex.Residue
Return the number of atoms in the molecule.
getAtomCount() - Method in class astex.Ring
Return the atom count.
getAtomIndex(Atom) - Method in class astex.Ring
Return the index of the atom in the ring or -1 if not present.
getAtomIterator() - Method in class astex.MoleculeRenderer
Get a atom iterator.
getAtomLabel() - Method in class astex.Atom
Get the atom label.
getAtomLabelFormat() - Method in class astex.MoleculeRenderer
Get the atom label format.
getAtomName(char, char, char, char) - Static method in class astex.MoleculeIO
Look up the atom name.
getAtoms() - Method in class astex.Residue
Return the DynamicArray of atoms.
getAtomsAroundSelection(DynamicArray, double, boolean) - Method in class astex.MoleculeRenderer
Return atoms in a shell around the specified selection.
getAtomsInLigands(DynamicArray) - Method in class astex.MoleculeRenderer
Get atoms that are part of ligands.
getAtomsInLigands() - Method in class astex.MoleculeRenderer
Wrapper around getAtomsInLigands.
getAtomsInResidue(String) - Method in class astex.MoleculeRenderer
Return the atoms in a particular residue.
getAtomsInSelection(String) - Method in class astex.MoleculeRenderer
Evaluate a selection expression.
getAtomsInSphere(Point3d, double) - Method in class astex.MoleculeRenderer
Return the atoms in the specified sphere.
getAtomSymbol() - Method in class astex.Atom
Get the atomic symbol for this atom.
getAtomSymbolFromElement(int) - Static method in class astex.PeriodicTable
returns the symbol for the specified atom type
getAtomType() - Method in class astex.Atom
Get the atomType.
getAtomWithId(int) - Method in class astex.Molecule
Return the atom with the specified id.
getAttribute(int) - Method in class astex.Atom
Get an attribute.
getAWTColor(int) - Static method in class astex.Color32
Return AWT color of this.
getBackClip() - Method in class astex.Renderer
 
getBackface() - Method in class astex.Tmesh
Get the value of backface.
getBackgroundColor() - Method in class astex.Renderer
Get the background colour.
getBallRadius() - Method in class astex.Atom
Get the vdw radius.
getBestRingContainingBond(Bond) - Method in class astex.Molecule
Return the best ring containing this bond.
getBFactor() - Method in class astex.Atom
Return the bFactor.
getBiggestDisplayedRadius() - Method in class astex.Atom
Get the biggest radius that is displayed.
getBlue(int) - Static method in class astex.Color32
Returns the blue component.
getBond(int) - Method in class astex.Atom
Return a specified bond or null if it doesn't exist.
getBond(Atom) - Method in class astex.Atom
Does this atom have a bond to the specified atom.
getBond(int) - Method in class astex.Molecule
Return the specified bond.
getBond(int) - Method in class astex.Ring
Get a bond.
getBondArray() - Method in class astex.Molecule
Return the bond array.
getBondColor() - Method in class astex.Bond
Get the value of bondColor.
getBondCount() - Method in class astex.Atom
Return the total number of bonds.
getBondCount() - Method in class astex.Molecule
Return the number of bonds in the molecule.
getBondCount() - Method in class astex.Ring
Return the bond count.
getBondedAtom(int) - Method in class astex.Atom
Return the specified bonded atom.
getBondedAtom(String) - Method in class astex.Atom
Get bonded atom with this name.
getBondingRadius() - Method in class astex.Atom
Get the bonding radius for the atom.
getBondIterator() - Method in class astex.MoleculeRenderer
Get a bond iterator.
getBondLength() - Method in class astex.Bond
Get the actual bond length.
getBondOrder() - Method in class astex.Bond
Get the bond order.
getBondsInSelection(DynamicArray) - Method in class astex.MoleculeRenderer
Return bonds where both atoms are in selectedAtoms.
getBondSymbol() - Method in class astex.Bond
Return a smiles style symbol for the bond.
getBondWidth() - Method in class astex.Bond
Get the value of bondWidth.
getBondWithOrder(int) - Method in class astex.Atom
Return a bond with the specified order.
getBoolean(String, boolean) - Method in class astex.Arguments
Lookup value of String arg or return default.
getBoolean(Object, boolean) - Method in class astex.generic.Generic
Get a boolean.
getBoolean(String, String) - Static method in class astex.Settings
 
getBoolean(String, String, boolean) - Static method in class astex.Settings
Lookup value of String arg or return default.
getBoundingSphere(double[]) - Method in class astex.Tmesh
Find simple bounding sphere of the tmesh.
getBumpAtoms() - Method in class astex.MoleculeRenderer
Get the bump atoms.
getCartesianToFractionalMatrix() - Method in class astex.Symmetry
Get the fractionalising matrix.
getCartoonNormalCutoff() - Method in class astex.Renderer
Get the cartoon normal cutoff.
getCellContents(int, IntArray) - Method in class astex.Lattice
Get the contents of the cell.
getCellContents(int, IntArray) - Method in class astex.NeighbourGrid
Get the contents of the cell.
getCellCount() - Method in class astex.Lattice
Get the number of occupied cells.
getCenter(Point3d, DynamicArray) - Method in class astex.Distance
Calculate the center of the group.
getCenter() - Method in class astex.Molecule
Find the center of the molecule.
getCenter(DynamicArray) - Method in class astex.MoleculeRenderer
Return the geometric center of the atoms in the selection.
getCenter() - Method in class astex.Renderer
Get the center point.
getCenter0() - Method in class astex.Distance
Calculate the center of group 0.
getCenter1() - Method in class astex.Distance
Calculate the center of group 1.
getCentralAtomCount() - Method in class astex.Molecule
Get the number of central atoms.
getChain(int) - Method in class astex.Molecule
Return the specified chain.
getChainCount() - Method in class astex.Molecule
Return the number of chains.
getChar(int) - Method in class astex.FILE
Return the specified character from the current line.
getCharge() - Method in class astex.Atom
Get the atom charge.
getChildren(Object) - Method in class astex.Atom
Get an enumeration of our children.
getChildren(Object) - Method in class astex.generic.Generic
 
getChildren(Object) - Method in interface astex.generic.GenericInterface
Get an enumeration of our children.
getClampColor(int, int, int) - Static method in class astex.Color32
Clamp components to 0,255 and return rgb color.
getClassname() - Method in class astex.Atom
Get our class description.
getClassname() - Method in class astex.Bond
 
getClassname() - Method in class astex.generic.Generic
 
getClassname() - Method in interface astex.generic.GenericInterface
Get our class description.
getClip() - Method in class astex.Renderer
Set the clip.
getColor(String, int) - Method in class astex.Arguments
Return argument interpreted as a color.
getColor() - Method in class astex.Atom
Get the atom color.
getColor(int, int) - Method in class astex.ColorButton
Instruct AstexViewer to display its color gadget so that a JavaScript interface can use it for picking colours.
getColor(int, int) - Method in class astex.MoleculeViewer
Instruct AstexViewer to display its color gadget so that a JavaScript interface can use it for picking colours.
getColor() - Method in class astex.Tmesh
Get the value of color.
getColor() - Method in class astex.UserInterface
 
getColor(int, int) - Method in class MoleculeViewerApplet
Instruct AstexViewer to display its color gadget so that something can use it for picking colours.
getColorFromName(String) - Static method in class astex.Color32
Return packed color value from string name.
getColorStyle() - Method in class astex.Tmesh
Get the object color style.
getComponent(int, int) - Static method in class astex.Color32
 
getContourColor(int) - Method in class astex.Map
Get the specified contour color.
getContourDisplayed(int) - Method in class astex.Map
Get if the specified contour is displayed.
getContourGraphicalObject(Map, int) - Method in class astex.MoleculeRenderer
Get tmesh of contour for particular map.
getContourGraphicalObjectName(Map, int) - Method in class astex.MoleculeRenderer
Get name of contour for particular map.
getContourLevel(int) - Method in class astex.Map
Get the specified contour level.
getContourStyle(int) - Method in class astex.Map
Get the specified contour color.
getCoordinates() - Method in class MoleculeViewerApplet
 
getCurrentChain() - Method in class astex.Molecule
Get the current chain.
getCurrentLineAsString() - Method in class astex.FILE
Return the current line as a String.
getCurrentResidue() - Method in class astex.Chain
Return the current residue.
getCustomLabel() - Method in class astex.Atom
Set whether the atom is solvent.
getCylinderWidth() - Method in class astex.Bond
Get the value of cylinderWidth.
getDataArray() - Method in class astex.Map
Get the actual data array.
getDescription() - Method in interface astex.UserInterfacePanel
 
getDisplayBumps() - Method in class astex.MoleculeRenderer
Return the state of bump display.
getDisplayDistances() - Method in class astex.MoleculeRenderer
Return the distance display flag.
getDisplayed() - Method in class astex.Molecule
Is the molecule displayed?
getDisplayStyle() - Method in class astex.Molecule
Get the display style.
getDisplayStyle(int) - Method in class astex.Molecule
Get the display style.
getDistance(int) - Method in class astex.MoleculeRenderer
Return a specific distance.
getDistanceCount() - Method in class astex.MoleculeRenderer
Return how many distances.
getDouble(String, double) - Method in class astex.Arguments
Lookup value of double arg or return default.
getDouble(int) - Method in class astex.FILE
Synonym for readDoubleFromField.
getDouble(Object, double) - Method in class astex.generic.Generic
Get a double.
getDouble(String, String) - Static method in class astex.Settings
 
getDouble(String, String, double) - Static method in class astex.Settings
Lookup value of double arg or return default.
getElement() - Method in class astex.Atom
Get the element type of this atom.
getElement(char, char) - Static method in class astex.PeriodicTable
Decode element string to atomic number.
getElementFromPDBAtomLabel(char, char) - Static method in class astex.MoleculeIO
Assign element type from pdb atom label.
getElementFromSymbol(String) - Static method in class astex.PeriodicTable
Find the atomic number (atom type) given a symbol.
getElementFromSymbol(char, char) - Static method in class astex.PeriodicTable
Get element from characters from pdb file.
getException() - Static method in class astex.FILE
Get the exception (if any) that was thrown when FILE.open() was called.
getField(int) - Method in class astex.FILE
Get the field as a string.
getFieldChar(int, int) - Method in class astex.FILE
Get the specified character from the field.
getFieldCount() - Method in class astex.FILE
Return the number of fields on the current line.
getFieldLength(int) - Method in class astex.FILE
Get the start position of the field.
getFieldStart(int) - Method in class astex.FILE
Get the start position of the field.
getFile() - Method in class astex.Map
Get the filename.
getFilename() - Method in class astex.Molecule
Get the filename.
getFirstAtom() - Method in class astex.Angle
Return the first atom in a angle.
getFirstAtom() - Method in class astex.Bond
Return the first atom in a bond.
getFirstAtom() - Method in class astex.Improper
Return the first atom in a improper.
getFloat(int) - Method in class astex.FILE
 
getFourthAtom() - Method in class astex.Improper
Return the fourth atom in a improper.
getFractionalToCartesianMatrix() - Method in class astex.Symmetry
Get the defractionalising matrix.
getFrame(Component) - Static method in class astex.Util
Return the frame that contains the specified component.
getFrontClip() - Method in class astex.Renderer
 
getGraphicalObject(int) - Method in class astex.Renderer
Get the number of graphical objects.
getGraphicalObject(String) - Method in class astex.Renderer
Return a GraphicalObject with the specified name.
getGraphicalObjectCount() - Method in class astex.Renderer
Get the number of graphical objects.
getGraphicalObjects(String) - Method in class astex.Renderer
Return a DynamicArray of objects that match the pattern.
getGrayScale(int) - Static method in class astex.Color32
 
getGreen(int) - Static method in class astex.Color32
Returns the green component.
getHybridisation() - Method in class astex.Atom
Return the hybridisation state of the atom.
getId() - Method in class astex.Atom
Get the id for this atom.
getIdealBondAngle() - Method in class astex.Angle
Get the ideal angle angle.
getIdealBondLength() - Method in class astex.Bond
Get the ideal bond length.
getIdealImproperAngle() - Method in class astex.Improper
Get the ideal improper angle.
getImproper(int) - Method in class astex.Molecule
Get the specified improper.
getImproperArray() - Method in class astex.Molecule
Get the array of impropers.
getImproperCount() - Method in class astex.Molecule
Get the number of atoms for this molecule.
getIndex(double) - Method in class astex.DoubleArray
Return the location of the object or -1 if its not present.
getIndex(Object) - Method in class astex.DynamicArray
Return the location of the object or -1 if its not present.
getIndex(float) - Method in class astex.FloatArray
Return the location of the object or -1 if its not present.
getIndex(int) - Method in class astex.IntArray
Return the location of the object or -1 if its not present.
getIndex(String) - Method in class astex.StringArray
Return the location of the object or -1 if its not present.
getInputStream() - Method in class astex.FILE
Get the input stream associated with this file.
getInsertionCode() - Method in class astex.Atom
Get the insertion code.
getInsertionCode() - Method in class astex.Chain
Get the insertion code.
getInsertionCode() - Method in class astex.Residue
Get the insertion code.
getInstance(Frame, String, MoleculeRenderer) - Static method in class astex.ObjectPropertyDialog
Create the instance of the opd.
getInteger(String, int) - Method in class astex.Arguments
Lookup value of int arg or return default.
getInteger(int) - Method in class astex.FILE
Synonym for readIntegerFromField.
getInteger(Object, int) - Method in class astex.generic.Generic
Get an int.
getInteger(String, String) - Static method in class astex.Settings
 
getInteger(String, String, int) - Static method in class astex.Settings
Lookup value of int arg or return default.
getIntegerValue() - Method in class astex.ColorButton
Return the selected color as a packed integer.
getIntensity(int) - Static method in class astex.Color32
 
getInteractive() - Method in class astex.Animate
Are we interactive.
getInverseTexture(int, double) - Method in class astex.Tmesh
Get inverse texture coordinate.
getItem() - Method in class astex.RendererEvent
Get the value of item.
getLabelledAtoms() - Method in class astex.MoleculeRenderer
Return the atoms that are currently labelled.
getLightingModel() - Method in class astex.Renderer
 
getLineLength() - Method in class astex.FILE
Return the length of the current line.
getLineWidth() - Method in class astex.Tmesh
Set the linewidth.
getLoggingLevel(int) - Static method in class astex.Log
Get the logging level.
getLogo() - Method in class astex.Renderer
Get the current logo.
getMap(int) - Method in class astex.MoleculeRenderer
Return the specified map.
getMap(String) - Method in class astex.MoleculeRenderer
Return the specified map from its name.
getMapBoxDimensions(int[]) - Method in class astex.Map
Return the size of map we have loaded.
getMapCount() - Method in class astex.MoleculeRenderer
Return the total count of maps.
getMaps(String) - Method in class astex.MoleculeRenderer
Return the specified map from its name.
getMapType() - Method in class astex.Map
Get the value of mapType.
getMass() - Method in class astex.Atom
Get the default mass for the atom.
getMaximumDistance() - Method in class astex.Lattice
Return the maximum search distance.
getMaximumId() - Method in class astex.Molecule
Get the maximum id for this molecule.
getMaximumIntensity(int) - Static method in class astex.Color32
 
getMaximumResidueId() - Method in class astex.Chain
Get maximum residue id.
getMolecule() - Method in class astex.Atom
Get the molecule to which the atom belongs.
getMolecule(int) - Method in class astex.MoleculeRenderer
Return the specified molecule.
getMolecule(String) - Method in class astex.MoleculeRenderer
Return the first molecule that matches the specified name.
getMoleculeCount() - Method in class astex.MoleculeRenderer
Return the total number of molecules.
getMoleculeRenderer() - Method in class astex.MoleculeViewer
Get the molecule renderer that we contain.
getMolecules() - Method in class astex.MoleculeRenderer
Return the DynamicArray of molecules.
getMoleculeType() - Method in class astex.Molecule
Return what type of molecule this is.
getName() - Method in class astex.Chain
Get the chain name.
getName() - Method in class astex.Map
Get the map name.
getName() - Method in class astex.Molecule
Get the molecule name.
getName() - Method in class astex.Residue
Get the residue name.
getName() - Method in class astex.Tmesh
Get the value of name.
getNearestAtom(int, int) - Method in class astex.MoleculeRenderer
Find atom with screen coordinates nearest to the specified point.
getNextAtom() - Method in class astex.AtomIterator
Get the next atom.
getNextBond() - Method in class astex.BondIterator
Get the next bond.
getNextMapName() - Method in class astex.MoleculeRenderer
Return the name for the next molecule.
getNextMoleculeName() - Method in class astex.MoleculeRenderer
Return the name for the next molecule.
getNextResidue() - Method in class astex.ResidueIterator
Get the next residue.
getnPoints() - Method in class astex.Tmesh
Get the number of points.
getNumber() - Method in class astex.Chain
Get the chain number.
getNumber() - Method in class astex.Residue
Get the residue number.
getObjectCount() - Method in class astex.Lattice
Return the number of objects.
getOccupancy() - Method in class astex.Atom
Get the occupancy.
getOriginalSpaceGroupName() - Method in class astex.Symmetry
Get the original space group name.
getOtherAtom(Atom) - Method in class astex.Bond
Given one atom in a bond return the other atom from the bond.
getOverallScale() - Method in class astex.Renderer
Return the overall scale.
getParent() - Method in class astex.Chain
Get the parent.
getParent() - Method in class astex.Residue
Get the parent.
getParents(Object) - Method in class astex.Atom
Get an Enumeration of our parents.
getParents(Object) - Method in class astex.generic.Generic
 
getParents(Object) - Method in interface astex.generic.GenericInterface
Get an Enumeration of our parents.
getPartialCharge() - Method in class astex.Atom
Get the value of partialCharge.
getPixel(int, int) - Method in class astex.Renderer
Get a pixel value checking for on screen.
getPossibleCellNeighbours(int, IntArray) - Method in class astex.Lattice
Get the possible pairs of neighbours from a cell.
getPossibleNeighbours(int, double, double, double, IntArray, boolean) - Method in class astex.Lattice
Return the possible neighbours of the point.
getPossibleNeighbours(int, double, double, double, IntArray, boolean) - Method in class astex.NeighbourGrid
Return the possible neighbours of the point.
getPossibleNeighbours(int, double, double, double, IntArray, boolean) - Method in class astex.NeighbourGrid2D
Return the possible neighbours of the point.
getPreferredSize() - Method in class astex.ColorSpace
 
getPreferredSize() - Method in class astex.ContourScrollbar
 
getPreferredSize() - Method in class astex.LightCanvas
 
getPreferredSize() - Method in class astex.MoleculeViewer
Return the preferred size.
getProperties() - Method in class astex.Atom
Return an enumeration of our properties.
getProperties() - Method in class astex.Bond
 
getProperties() - Method in class astex.generic.Generic
 
getProperties() - Method in interface astex.generic.GenericInterface
Return an enumeration of our properties.
getProperties() - Method in class astex.Molecule
 
getProperties() - Method in class astex.Residue
 
getRadius() - Method in class astex.Map
Get the radius of the current map region.
getRadius() - Method in class astex.Molecule
Get the radius of the molecule.
getRadius(DynamicArray) - Method in class astex.MoleculeRenderer
Return the radius of the atoms in the selection.
getRadius(DynamicArray, Point3d) - Method in class astex.MoleculeRenderer
Return the radius of the atoms in the selection.
getRadius() - Method in class astex.Renderer
Get the radius.
getRed(int) - Static method in class astex.Color32
Returns the red component.
getRelativeGridIndex(int, int, int) - Method in class astex.Map
Calculate the relative grid index.
getRelativePath(String) - Static method in class astex.FILE
Try and make path relative to current directory.
getRenderer() - Method in class astex.Tmesh
Get the MoleculeRenderer value.
getRenderPass() - Method in class astex.Tmesh
Get the RenderPass value.
getResidue() - Method in class astex.Atom
Get the residue to which the atom belongs.
getResidue(int) - Method in class astex.Chain
Return the specified atom.
getResidueCount() - Method in class astex.Chain
Return the number of atoms in the molecule.
getResidueCount() - Method in class astex.Molecule
Get the total number of residues.
getResidueIterator() - Method in class astex.MoleculeRenderer
Get a residue iterator.
getResidueName(char, char, char) - Static method in class astex.MoleculeIO
Look up the residue name.
getReverse(int) - Method in class astex.DoubleArray
Return a specified element from the array end of the array.
getReverse(int) - Method in class astex.DynamicArray
Return a specified element from the array end of the array.
getReverse(int) - Method in class astex.FloatArray
Return a specified element from the array end of the array.
getReverse(int) - Method in class astex.IntArray
Return a specified element from the array end of the array.
getReverse(int) - Method in class astex.StringArray
Return a specified element from the array end of the array.
getRGB(int, int) - Method in class astex.ColorSpace
 
getRGB2(int, int) - Method in class astex.ColorSpace
 
getRing(int) - Method in class astex.Molecule
Return the specified ring.
getRingCenter() - Method in class astex.Ring
Get the ring center.
getRingCount() - Method in class astex.Molecule
Return the number of rings.
getSamples() - Method in class astex.Renderer
Get the number of samples.
getScale() - Method in class astex.Renderer
Get the scale.
getSecondaryStructure() - Method in class astex.Residue
Get the value of secondaryStructure.
getSecondAtom() - Method in class astex.Angle
Return the second atom in a angle.
getSecondAtom() - Method in class astex.Bond
Return the second atom in a bond.
getSecondAtom() - Method in class astex.Improper
Return the second atom in a improper.
getSelectCount() - Method in class astex.MoleculeRenderer
Return whether we are printing select counts.
getSelectedAtomCount() - Method in class astex.MoleculeRenderer
Return the number of selected atoms.
getSelectedAtoms() - Method in class astex.MoleculeRenderer
Return the atoms that are currently selected.
getSelectedAtoms() - Method in class MoleculeViewerApplet
 
getSelectedColor() - Method in class astex.Atom
Get the color or selected color if selected.
getSelectedOrLabelledAtoms() - Method in class astex.MoleculeRenderer
Return the atoms that are currently labelled or selected.
getSelectedResidues() - Method in class astex.MoleculeRenderer
Return the residues that are currently selected.
getSelection() - Method in class MoleculeViewerApplet
 
getSequentialNumber() - Method in class astex.Residue
Get the sequential residue number.
getSigma() - Method in class astex.Map
Return the sigma value for the map.
getSleepDuration() - Method in class astex.AnimationObject
Get the sleep duration.
getSomeAtoms(boolean, boolean) - Method in class astex.MoleculeRenderer
Return the atoms that are currently labelled.
getSpaceGroupName(String) - Static method in class astex.Symmetry
Return the symmetry name from the spage group line.
getSpaceGroupName() - Method in class astex.Symmetry
Get the space group name.
getSpaceGroupNumber() - Method in class astex.Symmetry
Get the space group number.
getSpacing() - Method in class astex.NeighbourGrid2D
Get the spacing.
getStatusLabelFormat() - Method in class astex.MoleculeRenderer
Get the status label format.
getStatusString() - Method in class astex.Renderer
Get the current StatusString.
getStepCount() - Method in class astex.Animate
Return the total number of steps in the animation.
getSteps() - Method in class astex.AnimationObject
Get the number of steps in this animation.
getStickWidth() - Method in class astex.Bond
Get the value of stickWidth.
getString(String, String) - Method in class astex.Arguments
Lookup value of String arg or return default.
getString(Object, String) - Method in class astex.generic.Generic
Get a String.
getString(String, String) - Static method in class astex.Settings
 
getString(String, String, String) - Static method in class astex.Settings
Lookup value of String arg or return default.
getStringOption(String, String[], int[], int) - Method in class astex.Arguments
Return lookup of string argument from array of possibles.
getSubstring(int, int) - Method in class astex.FILE
Return a substring of the current line.
getSymbol() - Method in class astex.Atom
Get the atom symbol for the element.
getSymbol(int) - Static method in class astex.PeriodicTable
 
getSymmetry() - Method in class astex.Molecule
Get the symmetry object.
getSymmetryOperators() - Method in class astex.Symmetry
Get the symmetry operators for the specified space group.
getTextureScalingMode() - Method in class astex.Tmesh
Get the texture scaling mode.
getThirdAtom() - Method in class astex.Angle
Return the third atom in a angle.
getThirdAtom() - Method in class astex.Improper
Return the third atom in a improper.
getTransparency() - Method in class astex.Atom
Get the transparency.
getTryFiles() - Static method in class astex.FILE
 
getType() - Method in class astex.Molecule
Get the type.
getType() - Method in class astex.RendererEvent
Get the value of type.
getTypeFromExtension(String) - Static method in class astex.MoleculeIO
Static mapping of file extensions to AstexViewer molecule types.
getUnitCellCode() - Method in class astex.Symmetry
Get the coding.
getUnitVector() - Method in class astex.Bond
Get unit vector.
getUOffset() - Method in class astex.Tmesh
Get the uoffset.
getUScale() - Method in class astex.Tmesh
Get the uscale.
getValue() - Method in class astex.ColorButton
Return the selected color as a string.
getValueAtRelativeGrid(int, int, int) - Method in class astex.Map
Get the map value at relative grid point.
getVDWRadius() - Method in class astex.Atom
Get the VDW radius of this atom.
getVersion() - Static method in class astex.Version
 
getVertex(int, double[], double[]) - Method in class astex.Tmesh
Get the vertex info for the specified point.
getView() - Method in class astex.MoleculeViewer
Return scripting description of the view.
getView() - Method in class MoleculeViewerApplet
Return scripting language to restore the current view.
getVOffset() - Method in class astex.Tmesh
Get the voffset.
getVScale() - Method in class astex.Tmesh
Get the vscale.
getX() - Method in class astex.Point3d
Return the x coordinate.
getY() - Method in class astex.Point3d
Return the y coordinate.
getZ() - Method in class astex.Point3d
Return the z coordinate.
getZoom() - Method in class astex.Renderer
Get the zoom.
gold - Static variable in class astex.Color32
 
GOLD - Static variable in class astex.PeriodicTable
 
goldenrod - Static variable in class astex.Color32
 
GoogleFont - Class in astex
Prepare an image of a string that looks like the rather groovy outlined font that Google maps uses.
GoogleFont() - Constructor for class astex.GoogleFont
 
gradient - Variable in class astex.ModellingData
The gradient associated with this object.
graph(MoleculeRenderer, byte[]) - Static method in class astex.Selection
Return a set of atoms in a connected graph.
GRAPH - Static variable in class astex.sym
 
GraphicalObject - Class in astex
 
GraphicalObject() - Constructor for class astex.GraphicalObject
Create a GraphicalObject.
GraphicalObject(Renderer) - Constructor for class astex.GraphicalObject
Create a GraphicalObject.
gray - Static variable in class astex.Color32
 
Green - Static variable in class astex.Color32
Green bits.
green - Static variable in class astex.Color32
 
grey - Static variable in class astex.Color32
 
grid - Variable in class astex.Map
Size of map grid.
group - Class in astex
 
group() - Constructor for class astex.group
 
group(MoleculeRenderer, Hashtable) - Static method in class astex.Selection
Select a set of atoms in a group.
group0 - Variable in class astex.Distance
Atoms at one end of the distance.
group1 - Variable in class astex.Distance
Atoms at the other end of the distance.
groupbox(String) - Static method in class astex.UI
Create a group box with nice insets.
groups - Variable in class astex.MoleculeRenderer
The set of defined groups.
GT - Static variable in class astex.Selection
Greater than attribute.

H

HAFNIUM - Static variable in class astex.PeriodicTable
 
handleAnimation(Arguments) - Method in class astex.MoleculeViewer
Get the animation thread.
handleCommand(MoleculeViewer, MoleculeRenderer, Arguments) - Static method in class astex.Featurize
 
handleCommand(MoleculeViewer, MoleculeRenderer, Arguments) - Static method in class astex.group
 
handleCommand(MoleculeViewer, MoleculeRenderer, Arguments) - Static method in class astex.javascript
 
handleCommand(MoleculeViewer, MoleculeRenderer, Arguments) - Static method in class astex.MouseTracker
 
handleCommand(MoleculeViewer, MoleculeRenderer, Arguments) - Static method in class astex.Spin
 
handleDeleteCommand(DynamicArray) - Method in class astex.MoleculeRenderer
Handle a delete atoms command.
handleDistanceCommand(Arguments) - Method in class astex.MoleculeRenderer
Handle a distance command.
handleEditCommand(String, String, DynamicArray) - Method in class astex.MoleculeRenderer
Handle an atom edit command.
handleEvent(GenericEvent) - Method in interface astex.generic.GenericEventInterface
Handle a GenericEvent.
handleEvent(Event) - Method in class astex.ImageButton
 
handleHbondCommand(Arguments) - Method in class astex.MoleculeRenderer
Handle a hydrogen bond command.
handleLightCommand(int, Arguments) - Method in class astex.MoleculeRenderer
Handle a light command.
handleMapCommand(String, Arguments) - Method in class astex.MoleculeRenderer
Interpret a new style map command.
handleMenuAction(ActionEvent, String) - Method in class astex.MoleculeViewer
Handle more complex menu actions.
handleMouseOver(MouseEvent) - Method in class astex.MoleculeViewer
 
handleMouseOverCommand(MouseEvent) - Method in class astex.MoleculeViewer
 
handleObjectCommand(String, Arguments) - Method in class astex.MoleculeRenderer
Handle an object command.
handlePick(Atom) - Method in class astex.MoleculeRenderer
Handle a pick on the screen and label the appropriate item.
handlePrint(String) - Method in class astex.MoleculeViewer
Handle a print command in the scripting language.
handleRendererEvent(RendererEvent) - Method in interface astex.RendererEventListener
 
handleRendererEvent(RendererEvent) - Method in class astex.UserInterface
Handle events in the renderer.
handleSelectionCommand(String, Arguments) - Method in class astex.MoleculeRenderer
Handle a selection stack command.
handleSlideCommand(Arguments) - Method in class astex.MoleculeRenderer
Handle a slide command.
handleTextureCommand(Arguments) - Method in class astex.MoleculeRenderer
Interpret a texture command.
handleUpdateCommand(Arguments, FloatArray) - Method in class astex.MoleculeRenderer
Handle a command that updates the properties of atoms.
handleUserCommand(String, Arguments) - Method in class astex.MoleculeRenderer
Handle a user command.
handleWriteCommand(Arguments) - Method in class astex.MoleculeRenderer
Interpret a molecule write command.
hasAttributes() - Method in class astex.Atom
Does the atom have any attributes set?
hasBond(Atom) - Method in class astex.Atom
Does this atom have a bond to the other atom.
hasBondWithOrder(int) - Method in class astex.Atom
Does this atom have a bond of the specified bond order.
hasContoursDisplayed() - Method in class astex.Map
 
hasExplicitBond() - Method in class astex.Atom
Does this atom have bonds that came from an explicit bond.
hasMoreElements() - Method in class astex.AtomIterator
Do we have more elements.
hasMoreElements() - Method in class astex.BondIterator
Do we have more elements.
hasMoreElements() - Method in class astex.ResidueIterator
Do we have more elements.
hasSelectedAtoms() - Method in class astex.Residue
 
HBOND - Static variable in class astex.sym
 
hbondEnergy(Atom, Point3d, Atom, Atom, double) - Static method in class astex.MoleculeRenderer
Calculate the energy of an hbond as defined in Kabsch and Sander, 'Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features', Biopolymers, 22, 2577-2637 (1983).
headerInitialised - Variable in class astex.Map
Is header initialised.
height - Static variable in class astex.AstexLogo
 
HELIUM - Static variable in class astex.PeriodicTable
 
Helix - Static variable in class astex.Residue
Helix secondary structure type.
Helix310 - Static variable in class astex.Residue
Helix secondary structure type.
hermite_single(Point3d, Point3d, Point3d, double, Point3d, double, double, Point3d) - Static method in class astex.Schematic
Interpolate hermite spline.
hersheyFonts - Variable in class astex.MoleculeRenderer
 
Hetero - Static variable in class astex.Atom
The atom is an heteroatom.
hideContourLevelDialog() - Method in class astex.MoleculeViewer
Hide the contour level dialog.
HOLMIUM - Static variable in class astex.PeriodicTable
 
honeydew - Static variable in class astex.Color32
 
HORIZONTAL - Static variable in class astex.UI
 
hsv2packed(double[]) - Static method in class astex.Color32
Convert hsv to packed int color.
hsv2rgb(double[], double[]) - Static method in class astex.Color32
Convert hsv format colour to rgb.
HYDROGEN - Static variable in class astex.PeriodicTable
 

I

ID - Static variable in class astex.Atom
The ID attribute.
id(MoleculeRenderer, Vector) - Static method in class astex.Selection
Select a set of atoms on the basis of ids.
ID - Static variable in class astex.sym
 
ImageButton - Class in astex
 
ImageButton(Image, int, String) - Constructor for class astex.ImageButton
 
ImageIO - Class in astex
Write a pixel format image to a file.
ImageIO() - Constructor for class astex.ImageIO
 
Improper - Class in astex
A class for storing information about an improper torsion torsion.
in - Static variable in class astex.FILE
 
INCREASE - Static variable in class astex.sym
 
incrementClip() - Method in class astex.Renderer
Increment the clip plane distance.
incrementFrontClip() - Method in class astex.Renderer
Increment the clip plane distance.
INDIUM - Static variable in class astex.PeriodicTable
 
INFO - Static variable in class astex.Log
 
info(String, double) - Static method in class astex.Log
 
info(String, long) - Static method in class astex.Log
 
info(String) - Static method in class astex.Log
 
init() - Method in class MoleculeViewerApplet
 
initialise() - Method in class astex.AnimationObject
Initialise the animation object.
initialise() - Method in class astex.Atom
Initialise an atom.
initialise() - Method in class astex.Molecule
Initialise the molecule.
initialise() - Method in class astex.MoleculeRenderer
Initialise the MoleculeRenderer.
initialise() - Method in class astex.Point3d
Initialise a point.
initialiseApplet() - Method in class MoleculeViewerApplet
Initialise the applet.
initialiseCenter() - Method in class astex.MoleculeRenderer
Figure out the molecule center and scale to make it just fit.
initialiseContours - Variable in class astex.Map
 
initialiseGrid(double) - Static method in class astex.Surface
Find the size of the atoms that we will surface.
initialList - Static variable in class astex.ShadowCache
 
inSameplanarRing(Atom, Atom) - Method in class astex.MoleculeRenderer
Are the two atoms in the same planar ring.
insertion(MoleculeRenderer, String) - Static method in class astex.Selection
Select a set of atoms on the basis of insertion code.
INSERTION - Static variable in class astex.sym
 
insertionCode - Variable in class astex.Atom
Insertion code if any.
INSIGHT_ASCII - Static variable in class astex.Map
 
install(Object) - Method in class astex.MoleculeViewer
 
IntArray - Class in astex
An object that implements a dynamic array.
IntArray(int, int) - Constructor for class astex.IntArray
Constructor which specifies the initial size and the capacity increment.
IntArray() - Constructor for class astex.IntArray
Default constructor.
IntArray(int) - Constructor for class astex.IntArray
Constructor which specifies the initial size.
INTEGER - Static variable in class astex.sym
 
intensitySpecularise(int, int, int) - Static method in class astex.Color32
multiply by intensity between 0 and 255 and specularise.
interactiveAnimation() - Method in class astex.MoleculeViewer
 
interpolate(Matrix, Matrix, double) - Static method in class astex.Matrix
Interpolate a new matrix.
interpolate(Matrix, Matrix, double, Matrix) - Static method in class astex.Matrix
Interpolate a new matrix.
interpolate(Point3d, Point3d, Point3d, double) - Static method in class astex.Schematic
Linear interoplation between p1 and p2.
intersect_triangle(double[], double[], double[], double[], double[], double[]) - Static method in class astex.ShadowCache
 
invert(Matrix, Matrix) - Static method in class astex.Matrix
invert( original_matrix, inverse_matrix ) calculate the inverse of a 4x4 matrix -1 A = ___1__ adjoint A det A
INVERT - Static variable in class astex.sym
 
IODINE - Static variable in class astex.PeriodicTable
 
ionNames - Static variable in class astex.Selection
Residue names for ions.
ions(MoleculeRenderer) - Static method in class astex.Selection
Ions expression.
IONS - Static variable in class astex.sym
 
IRIDIUM - Static variable in class astex.PeriodicTable
 
IRON - Static variable in class astex.PeriodicTable
 
isAliphaticHydrogen() - Method in class astex.Atom
Is this an aliphatic hydrogen.
isApplication() - Method in class astex.MoleculeViewer
Are we running in application.
isAromatic() - Method in class astex.Ring
Is this ring aromatic?
isAtomIn3MemberedRing(Atom) - Method in class astex.Molecule
Is this atom in a 3 membered ring.
isBondIn6Ring(Bond) - Method in class astex.Molecule
Is this bond in a 6 membered ring.
isBondInAromaticRing(Bond) - Method in class astex.Molecule
Is this bond in an aromatic ring.
isDisplayed() - Method in class astex.Atom
Has this atom been displayed.
isExplicitBond() - Method in class astex.Bond
Is bond an explicit bond.
isHBondAcceptor() - Method in class astex.Atom
Is this atom an HBond donor.
isHBondDonor() - Method in class astex.Atom
Is this atom an HBond donor.
isHeteroAtom() - Method in class astex.Atom
Is this atom a heteroatom.
isIdentity() - Method in class astex.Matrix
Does this matrix equal another matrix.
isIdentity(double) - Method in class astex.Matrix
 
isIon() - Method in class astex.Residue
Is this residue an ion.
isIsolated() - Method in class astex.Residue
Does this residue contain bonds to atoms in any other residues.
isLabelled() - Method in class astex.Atom
Is this atom a solvent atom.
isNonRotatable() - Method in class astex.Bond
Is this bond non rotatable.
isNucleicAcid() - Method in class astex.Residue
Is this a solvent residue.
isNullVector() - Method in class astex.Point3d
Are all the components of this vector 0.
isPlanar() - Method in class astex.Ring
Is this ring planar, but not necessarily aromatic.
isQueryBond() - Method in class astex.Bond
Is the bond a query bond.
isRingBond() - Method in class astex.Bond
Is the bond in a ring.
isSelected() - Method in class astex.Atom
Is this atom selected.
isSimpleDisplayed() - Method in class astex.Atom
Has this atom been displayed.
isSolvent() - Method in class astex.Atom
Is this atom a solvent atom.
isSolvent() - Method in class astex.Residue
Is this a solvent residue.
isSolventAtom() - Static method in class astex.MoleculeIO
Is the atom label a solvent label.
isSpecialAtom(Atom) - Method in class astex.Molecule
Does this atom need treating specially for bonding.
isStandardAminoAcid() - Method in class astex.Residue
Is this residue a standard amino acid.
isSymmetryMolecule() - Method in class astex.Molecule
Is this a symmetry molecule.
isTemporarilySelected() - Method in class astex.Atom
Is this atom temporarily selected.
isTerminalBond() - Method in class astex.Bond
Is this a terminal bond.
isVisible() - Method in class astex.Tmesh
Get the value of visible.
isVisited() - Method in class astex.Atom
Has this atom been visited.
isWide() - Method in class astex.Atom
Has this atom been wide.
isWideBond() - Method in class astex.Bond
Is the bond wide.
itemStateChanged(ItemEvent) - Method in class astex.MoleculeViewer
Implementation of ItemListener.
itemStateChanged(JCItemEvent) - Method in class astex.ObjectControl
Listen for events on the object.
itemStateChanged(ItemEvent) - Method in class astex.UserInterface
 
itemStateChanged(JCItemEvent) - Method in class astex.UserInterface
 
ivory - Static variable in class astex.Color32
 

J

javascript - Class in astex
 
javascript() - Constructor for class astex.javascript
 

K

keyDefinitions - Variable in class astex.MoleculeViewer
Definition of key bindings.
keyPressed(KeyEvent) - Method in class astex.MoleculeViewer
Implementation of KeyListener.
keyReleased(KeyEvent) - Method in class astex.MoleculeViewer
 
keyTyped(KeyEvent) - Method in class astex.MoleculeViewer
 
khaki - Static variable in class astex.Color32
 
KRYPTON - Static variable in class astex.PeriodicTable
 

L

l2cx(double) - Method in class astex.LightCanvas
 
l2cy(double) - Method in class astex.LightCanvas
 
LABEL - Static variable in class astex.sym
 
LabelColor - Static variable in class astex.Distance
 
Labelled - Static variable in class astex.Atom
The atom is labelled.
labelled(MoleculeRenderer) - Static method in class astex.Selection
Return the current selection.
LABELLED - Static variable in class astex.sym
 
labelledAtomsContains(Atom) - Method in class astex.MoleculeRenderer
Do we already have a label for this atom.
LANTHANUM - Static variable in class astex.PeriodicTable
 
lastClip - Static variable in class astex.Surface
The last atom that clipped a point.
lastScriptFile - Variable in class astex.MoleculeRenderer
The last script we executed.
Lattice - Class in astex
 
Lattice(double) - Constructor for class astex.Lattice
Create an empty lattice object.
lavender - Static variable in class astex.Color32
 
LAWRENCIUM - Static variable in class astex.PeriodicTable
 
Layout - Class in astex
 
Layout() - Constructor for class astex.Layout
 
LAZY - Static variable in class astex.sym
 
LCURLY - Static variable in class astex.sym
 
LE - Static variable in class astex.Selection
Less equal attribute.
LEAD - Static variable in class astex.PeriodicTable
 
length() - Method in class astex.Point3d
Return the length of the vector.
length(double[]) - Static method in class astex.Point3d
Return length of double[] vector.
Light - Class in astex
Store the data for a light source.
Light(boolean, double, double, double, int, int, double) - Constructor for class astex.Light
Default constructor.
LIGHT - Static variable in class astex.sym
 
LightCanvas - Class in astex
 
LightCanvas(MoleculeViewer) - Constructor for class astex.LightCanvas
 
lightMapCalculated - Variable in class astex.Renderer
Have we calcualated our light map?
lights - Variable in class astex.Renderer
The list of lights.
linen - Static variable in class astex.Color32
 
Lines - Static variable in class astex.Map
Types for the display style.
LINES - Static variable in class astex.sym
 
lines - Variable in class astex.Tmesh
Sphere graphical object.
LINES - Static variable in class astex.Tmesh
Types for style.
LIPOPHILICITY - Static variable in class astex.sym
 
Lipophilicity - Static variable in class astex.Texgen
 
lipophilicityTexture() - Static method in class astex.Texture
 
LITHIUM - Static variable in class astex.PeriodicTable
 
LOAD - Static variable in class astex.sym
 
loadConfigurationFile(String) - Static method in class astex.Arguments
Load a set of properties from a configuration file.
loadFile(String) - Method in class astex.MoleculeViewer
Convenience method for loading a file.
loadImage(String) - Static method in class astex.Texture
Create an image from a file/url as appropriate.
loadMap(String) - Method in class astex.MoleculeViewer
Load a map given the name of its file.
loadMolecule(String) - Method in class astex.MoleculeViewer
Load a molecule given the name of its file.
loadProperties(String) - Static method in class astex.FILE
Convenience method to load a properties file.
loadTexture(String) - Static method in class astex.Texture
Load a texture from file/url as appropriate.
Log - Class in astex
Lightweight logging interface.
Log() - Constructor for class astex.Log
 
logStrings - Static variable in class astex.Log
The hard wired log level labels.
lowerRelativeGrid(Point3d, int[]) - Method in class astex.Map
Find nearest relative grid point to the specified point.
LPAREN - Static variable in class astex.sym
 
LT - Static variable in class astex.Selection
Less than attribute.
LUTETIUM - Static variable in class astex.PeriodicTable
 

M

MAC - Static variable in class astex.FILE
 
magenta - Static variable in class astex.Color32
 
MAGNESIUM - Static variable in class astex.PeriodicTable
 
main(String[]) - Static method in class astex.Apollo
 
main(String[]) - Static method in class astex.ColorChooser
 
main(String[]) - Static method in class astex.ColorSpace
 
main(String[]) - Static method in class astex.CRC32
Tests CRC32.
main(String[]) - Static method in class astex.FILE
Test program for the FILE class.
main(String[]) - Static method in class astex.Fit
Test harness.
main(String[]) - Static method in class astex.Format
a test stub for the format class
main(String[]) - Static method in class astex.generic.Generic
 
main(String[]) - Static method in class astex.Lattice
Test harness for the lattice construction.
main(String[]) - Static method in class astex.Log
 
main(String[]) - Static method in class astex.Map
Test program.
main(String[]) - Static method in class astex.March
main.
main(String[]) - Static method in class astex.match
Test method for the matcher.
main(String[]) - Static method in class astex.MoleculeViewer
Main entry point.
main(String[]) - Static method in class astex.ObjectControl
 
main(String[]) - Static method in class astex.Settings
Test method.
main(String[]) - Static method in class astex.ShadowCache
 
main(String[]) - Static method in class astex.Symmetry
Test method for the symmetry code.
main(String[]) - Static method in class astex.Tmesh
Test program.
main(String[]) - Static method in class astex.UI
 
makeFontImage(String, int, int, int[]) - Static method in class astex.GoogleFont
 
MANGANESE - Static variable in class astex.PeriodicTable
 
Map - Class in astex
A class for storing an electron density map.
MAP - Static variable in class astex.sym
 
mapAdded(MoleculeRenderer, Map) - Method in interface astex.MoleculeRendererListener
A map was added.
mapAdded(MoleculeRenderer, Map) - Method in class astex.MoleculeViewer
Respond to a map added event.
mapAdded(MoleculeRenderer, Map) - Method in class astex.UserInterface
A map was added.
mapAtomColors(Tmesh, DynamicArray, int, double, double) - Method in class astex.MoleculeRenderer
Map the colors of a set of atoms to the object.
mapRemoved(MoleculeRenderer, Map) - Method in interface astex.MoleculeRendererListener
A map was removed.
mapRemoved(MoleculeRenderer, Map) - Method in class astex.MoleculeViewer
Respond to a map added event.
mapRemoved(MoleculeRenderer, Map) - Method in class astex.UserInterface
A map was removed.
March - Class in astex
A class for (hopefully) implementing marching cubes algorithm for isosurfaces.
March() - Constructor for class astex.March
 
markRingBonds() - Method in class astex.Molecule
Mark the bonds that are part of a ring.
maroon - Static variable in class astex.Color32
 
maskToArray(MoleculeRenderer, byte[]) - Static method in class astex.Selection
Return a DynamicArray from a selection mask.
match - Class in astex
Instances of this class represents a wildcard expression, which can be matched against String objects.
match() - Constructor for class astex.match
 
matches(String, String) - Static method in class astex.match
Return true if string matches pattern.
matches(String, String, int) - Static method in class astex.match
Return true if string matches pattern.
matricesAssigned - Variable in class astex.Symmetry
Have we precalculated the f2c and c2f matrices from SCALE.
Matrix - Class in astex
A class for storing and manipulating a 4x4 matrix.
Matrix() - Constructor for class astex.Matrix
Default constructor.
Matrix(Matrix) - Constructor for class astex.Matrix
Default constructor.
MATRIX - Static variable in class astex.sym
 
max(Point3d) - Method in class astex.Point3d
Find the vector maximum of the x, y and z coordinates of this point and another Point3d.
MAX_VALENCE_STATES - Static variable in class astex.AtomicElement
The maximum number of valence states that any of our atoms exist in.
MaximumContourLevels - Static variable in class astex.Map
Maximum number of contour levels.
maximumGrid - Variable in class astex.Map
The maximum grid point for the current stored map data.
MDLMol - Static variable in class astex.MoleculeIO
MDL mol file.
MENDELEVIUM - Static variable in class astex.PeriodicTable
 
MERCURY - Static variable in class astex.PeriodicTable
 
mid(Point3d, Point3d) - Static method in class astex.Point3d
Construct a point with the x, y and z coordinates equal to the midpoint of two other Point3ds.
mid(Point3d, Point3d, Point3d) - Static method in class astex.Point3d
Construct a point with the x, y and z coordinates equal to the midpoint of two other Point3ds.
mid(double[], int, int) - Method in class astex.Tmesh
Find mid point of two vertices.
min(Point3d) - Method in class astex.Point3d
Find the vector minimum of the x, y and z coordinates of this point and another Point3d.
minimumGrid - Variable in class astex.Map
The minimum grid point for the current stored map data.
minimumSize() - Method in class astex.ImageButton
 
MinMaxScalingMode - Static variable in class astex.Tmesh
The min,max textureScalingMode.
moccasin - Static variable in class astex.Color32
 
Mode - Static variable in class astex.Distance
Properties for a Distance object.
MODELLING - Static variable in class astex.sym
 
ModellingActive - Static variable in class astex.Atom
Atom is active in energy calculations.
modellingData - Variable in class astex.Atom
 
ModellingData - Class in astex
 
ModellingData() - Constructor for class astex.ModellingData
 
ModellingEnvironment - Static variable in class astex.Atom
Atom is environment in energy calculations.
ModellingFixed - Static variable in class astex.Atom
Atom is fixed in energy calculations.
ModellingXray - Static variable in class astex.Atom
Atom is xray terms in energy calculations.
modulo(MoleculeRenderer, int) - Static method in class astex.Selection
Select a set of atoms on the basis of ids.
Molecule - Class in astex
 
Molecule() - Constructor for class astex.Molecule
Constructor which prepares a standard molecule.
molecule(MoleculeRenderer, Vector) - Static method in class astex.Selection
Select a set of atoms on the basis of molecule name.
MOLECULE - Static variable in class astex.sym
 
MoleculeAdded - Static variable in class astex.MoleculeEvent
 
moleculeAdded(MoleculeRenderer, Molecule) - Method in interface astex.MoleculeRendererListener
A molecule was added.
moleculeAdded(MoleculeRenderer, Molecule) - Method in class astex.MoleculeViewer
Respond to a molecule added event.
moleculeAdded(MoleculeRenderer, Molecule) - Method in class astex.UserInterface
A molecule was added.
MoleculeAnimation - Static variable in class astex.AnimationObject
Constant to indicate that we are recentering.
MoleculeChanged - Static variable in class astex.MoleculeEvent
 
MoleculeEvent - Class in astex
Molecule Object Model Event.
MoleculeEvent() - Constructor for class astex.MoleculeEvent
 
MoleculeEventMask - Static variable in class astex.MoleculeEvent
 
moleculeExact(MoleculeRenderer, Vector) - Static method in class astex.Selection
Select a set of atoms on the basis of molecule name.
MoleculeIO - Class in astex
22-05-01 mjh add .sdf as a file type for mol files.
MoleculeIO() - Constructor for class astex.MoleculeIO
 
moleculeMatches(String, Molecule) - Method in class astex.MoleculeRenderer
 
MoleculeRemoved - Static variable in class astex.MoleculeEvent
 
moleculeRemoved(MoleculeRenderer, Molecule) - Method in interface astex.MoleculeRendererListener
A molecule was removed.
moleculeRemoved(MoleculeRenderer, Molecule) - Method in class astex.MoleculeViewer
Respond to a molecule removed event.
moleculeRemoved(MoleculeRenderer, Molecule) - Method in class astex.UserInterface
A molecule was removed.
MoleculeRenderer - Class in astex
Class for drawing a molecule into our renderer.
MoleculeRenderer() - Constructor for class astex.MoleculeRenderer
Default constructor.
moleculeRenderer - Variable in class astex.MoleculeViewer
The molecule renderer that this viewer will use.
MoleculeRendererListener - Interface in astex
An interface that allows objects to listen to changes in a MoleculeRenderer.
moleculeViewer - Variable in class astex.Animate
The MoleculeViewer we are associated with.
moleculeViewer - Variable in class astex.MoleculeRenderer
The moleucle viewer class that we are drawing for.
MoleculeViewer - Class in astex
A component that can draw a molecule.
MoleculeViewer() - Constructor for class astex.MoleculeViewer
Default constructor.
moleculeViewer - Variable in class MoleculeViewerApplet
The MoleculeViewer.
MoleculeViewerApplet - Class in <Unnamed>
An applet container for the MoleculeViewer.
MoleculeViewerApplet() - Constructor for class MoleculeViewerApplet
 
MoleculeViewerAppletBeanInfo - Class in astex
 
MoleculeViewerAppletBeanInfo() - Constructor for class astex.MoleculeViewerAppletBeanInfo
 
MOLEXACT - Static variable in class astex.sym
 
MOLYBDENUM - Static variable in class astex.PeriodicTable
 
Monitor - Class in astex
 
Monitor() - Constructor for class astex.Monitor
 
mouseClicked(MouseEvent) - Method in class astex.ColorChooser
 
mouseClicked(MouseEvent) - Method in class astex.LightCanvas
 
mouseClicked(MouseEvent) - Method in class astex.MoleculeViewer
 
mouseClicked(MouseEvent) - Method in class astex.UserInterface
 
mouseDragged(MouseEvent) - Method in class astex.ColorChooser
 
mouseDragged(MouseEvent) - Method in class astex.LightCanvas
 
mouseDragged(MouseEvent) - Method in class astex.MoleculeViewer
Handle the mouse being dragged.
mouseEntered(MouseEvent) - Method in class astex.ColorChooser
 
mouseEntered(MouseEvent) - Method in class astex.LightCanvas
 
mouseEntered(MouseEvent) - Method in class astex.MoleculeViewer
 
mouseEntered(MouseEvent) - Method in class astex.UserInterface
 
mouseExited(MouseEvent) - Method in class astex.ColorChooser
 
mouseExited(MouseEvent) - Method in class astex.LightCanvas
 
mouseExited(MouseEvent) - Method in class astex.MoleculeViewer
 
mouseExited(MouseEvent) - Method in class astex.UserInterface
 
mouseMoved(MouseEvent) - Method in class astex.ColorChooser
 
mouseMoved(MouseEvent) - Method in class astex.LightCanvas
 
mouseMoved(MouseEvent) - Method in class astex.MoleculeViewer
 
mousePressed(MouseEvent) - Method in class astex.ColorChooser
 
mousePressed(MouseEvent) - Method in class astex.LightCanvas
 
mousePressed(MouseEvent) - Method in class astex.MoleculeViewer
Handle a mousePressed event.
mousePressed(MouseEvent) - Method in class astex.UserInterface
 
mouseReleased(MouseEvent) - Method in class astex.ColorChooser
 
mouseReleased(MouseEvent) - Method in class astex.LightCanvas
 
mouseReleased(MouseEvent) - Method in class astex.MoleculeViewer
Handle a mouseReleased event.
mouseReleased(MouseEvent) - Method in class astex.UserInterface
Override the behaviour of the outliner component.
MouseTracker - Class in astex
 
MouseTracker() - Constructor for class astex.MouseTracker
 
moveAtom(Atom, int, int) - Method in class astex.MoleculeRenderer
Move an atom in the plane of the screen.
multiply(int, int) - Static method in class astex.Color32
 

N

Name - Static variable in class astex.generic.GenericEvent
 
Name - Static variable in interface astex.generic.GenericInterface
Some defined property constants.
name(MoleculeRenderer, Vector) - Static method in class astex.Selection
Select a set of atoms on the basis of residue names.
NAME - Static variable in class astex.sym
 
name - Variable in class astex.Tmesh
The name of the object.
NameLeftJustified - Static variable in class astex.Atom
Atom is fixed in energy calculations.
navy - Static variable in class astex.Color32
 
NE - Static variable in class astex.Selection
Not equal attribute.
nearestRelativeGrid(Point3d, int[]) - Method in class astex.Map
Find nearest relative grid point to the specified point.
needNewResidue(int, char, char, char, char) - Static method in class astex.MoleculeIO
Do we need a new residue?
needsReading() - Method in class astex.Map
Does the map need reading.
negate() - Method in class astex.Point3d
Negate the x, y and z coordinates of this point.
NeighbourGrid - Class in astex
 
NeighbourGrid(double, double, double, double, double, double, double, int) - Constructor for class astex.NeighbourGrid
Construct a neighbour grid with the following specification.
NeighbourGrid2D - Class in astex
 
NeighbourGrid2D() - Constructor for class astex.NeighbourGrid2D
Construct a neighbour grid with the following specification.
NEODYMIUM - Static variable in class astex.PeriodicTable
 
NEON - Static variable in class astex.PeriodicTable
 
NEPTUNIUM - Static variable in class astex.PeriodicTable
 
newRow() - Static method in class astex.UI
 
nextElement() - Method in class astex.AtomIterator
Get the next element.
nextElement() - Method in class astex.BondIterator
Get the next element.
nextElement() - Method in class astex.ResidueIterator
Get the next element.
nextLine() - Method in class astex.FILE
Advance the FILE object to the next line.
ngrid - Variable in class astex.Map
The number of grid points along each axis.
NICKEL - Static variable in class astex.PeriodicTable
 
NIOBIUM - Static variable in class astex.PeriodicTable
 
NITROGEN - Static variable in class astex.PeriodicTable
 
nitrogenNeedsImproper(Atom) - Method in class astex.Molecule
Does this nitrogen atom need a improper.
NOBELIUM - Static variable in class astex.PeriodicTable
 
nofill(Container, Component, int, int) - Static method in class astex.Layout
 
none(MoleculeRenderer) - Static method in class astex.Selection
Select all the atoms.
NONE - Static variable in class astex.sym
 
NONE - Static variable in class astex.UI
 
Normal - Static variable in class astex.Molecule
Normal display style.
NORMAL_PICK - Static variable in class astex.MoleculeRenderer
Normal picking mode.
normalise(double[]) - Static method in class astex.Geometry
Normalise the vector.
normalise() - Method in class astex.Point3d
Make the position vector of this point have unit length.
normalisePos() - Method in class astex.Light
 
NormalMolecule - Static variable in class astex.Molecule
Type for a normal molecule.
normalToLine(Point3d) - Static method in class astex.Point3d
Construct a unit vector that is perpendicular to the vector.
normalToLine(Point3d, Point3d) - Static method in class astex.Point3d
Construct a unit vector that is perpendicular to the vector.
normalToLine(double, double, double, double, double) - Static method in class astex.Point3d
Generate a line perpendicular to the line described by the set of points xa,ya xb,yb.
normalToLine(double, double) - Static method in class astex.Point3d
 
not(byte[]) - Static method in class astex.Selection
Not a selection mask.
NOT - Static variable in class astex.sym
 
np - Variable in class astex.Tmesh
The number of points in the object.
npalloc - Variable in class astex.Tmesh
The number of points allocated for the object.
nt - Variable in class astex.Tmesh
The number of triangles in the object.
nx - Variable in class astex.Tmesh
The normal vectors of the points.
ny - Variable in class astex.Tmesh
The normal vectors of the points.
nz - Variable in class astex.Tmesh
The normal vectors of the points.

O

O - Static variable in class astex.Atom
The O coordinate attribute.
O_BINARY - Static variable in class astex.Map
 
OAttribute - Static variable in class astex.Atom
 
OBJECT - Static variable in class astex.sym
 
ObjectAdded - Static variable in class astex.RendererEvent
 
ObjectColor - Static variable in class astex.Tmesh
The color style possibilities.
objectContainer - Variable in class astex.UserInterface
 
ObjectControl - Class in astex
 
ObjectControl(UserInterface, Tmesh) - Constructor for class astex.ObjectControl
Public constructor.
ObjectPropertyDialog - Class in astex
 
ObjectPropertyDialog(Frame, String, MoleculeRenderer) - Constructor for class astex.ObjectPropertyDialog
Create a dialog that lets us edit the texture based properties of a tmesh object.
ObjectRemoved - Static variable in class astex.RendererEvent
 
objects - Variable in class astex.Renderer
The list of objects to render.
obscured(double, double, double, int, int) - Static method in class astex.Surface
Is the point within one of the atoms in the list.
obscuredBySphere(int, double, double, double) - Static method in class astex.ShadowCache
 
Off - Static variable in class astex.Distance
 
Off - Static variable in class astex.Molecule
Completely off.
OFF - Static variable in class astex.sym
 
On - Static variable in class astex.Distance
 
on - Variable in class astex.Light
Is the light on?
ON - Static variable in class astex.sym
 
onClickLabel - Variable in class astex.MoleculeViewer
 
Opacity - Static variable in class astex.Atom
 
opbuffer - Variable in class astex.Renderer
The original pixel buffer.
open(String) - Static method in class astex.FILE
Return a FILE object for reading the specified resource.
open(File) - Static method in class astex.FILE
Create a FILE object to read from the specified File object.
open(URL) - Static method in class astex.FILE
Create a FILE object to read from the specified URL.
openFile(String) - Static method in class astex.FILE
Create a FILE object to read from the specified filename.
openURL(String) - Static method in class astex.FILE
Create a FILE object to read from the specified urlname.
OPERATOR - Static variable in class astex.sym
 
or(byte[], byte[]) - Static method in class astex.Selection
Or two selection masks together.
OR - Static variable in class astex.sym
 
orange - Static variable in class astex.Color32
 
orchid - Static variable in class astex.Color32
 
origin - Variable in class astex.Map
The position of the first grid point.
OriginalScalingMode - Static variable in class astex.Tmesh
The original textureScalingMode.
OSMIUM - Static variable in class astex.PeriodicTable
 
out - Static variable in class astex.FILE
Wrapper allowing write to stdout and stderr.
outlinerFolderStateChangeBegin(JCOutlinerEvent) - Method in class astex.UserInterface
 
outlinerFolderStateChangeEnd(JCOutlinerEvent) - Method in class astex.UserInterface
 
outlinerNodeSelectBegin(JCOutlinerEvent) - Method in class astex.UserInterface
 
outlinerNodeSelectEnd(JCOutlinerEvent) - Method in class astex.UserInterface
 
outlinerNodeUnselectBegin(JCOutlinerEvent) - Method in class astex.UserInterface
 
outlinerNodeUnselectEnd(JCOutlinerEvent) - Method in class astex.UserInterface
 
output(String) - Method in class astex.Tmesh
Prints the tmesh to a file.
overallMatrix - Variable in class astex.Renderer
 
overallScale - Static variable in class astex.ShadowCache
Overall scale factor in the renderer.
OXYGEN - Static variable in class astex.PeriodicTable
 

P

pack(int, int, int) - Static method in class astex.Color32
Pack r,g,b triple into a single int.
packed2hsv(int, double[]) - Static method in class astex.Color32
Convert a packed rgb number to hsv.
paint(Graphics) - Method in class astex.ColorSpace
 
paint(Graphics) - Method in class astex.ImageButton
 
paint(Graphics) - Method in class astex.LightCanvas
 
paint() - Method in class astex.MoleculeRenderer
Paint the rendered image into the screen.
paint(Graphics) - Method in class astex.MoleculeViewer
Override the paint method.
paint(Graphics) - Method in class MoleculeViewerApplet
 
paint2(Graphics) - Method in class astex.ColorSpace
Methods below here implement the GIMP watercolor chooser.
Pairs - Static variable in class astex.Distance
The pair distance mode.
PALLADIUM - Static variable in class astex.PeriodicTable
 
Parent - Static variable in class astex.generic.GenericEvent
 
ParentAdded - Static variable in class astex.generic.GenericEvent
 
ParentRemoved - Static variable in class astex.generic.GenericEvent
 
pbuffer - Variable in class astex.Renderer
The pixel buffer.
PC - Static variable in class astex.FILE
 
PDBFile - Static variable in class astex.MoleculeIO
PDB file.
peekSelection(int) - Method in class astex.MoleculeRenderer
Peek a selection on the stack.
PeriodicTable - Class in astex
 
PeriodicTable() - Constructor for class astex.PeriodicTable
 
peru - Static variable in class astex.Color32
 
phong - Variable in class astex.Renderer
Do phong shading.
PHOSPHORUS - Static variable in class astex.PeriodicTable
 
pickedAtoms - Variable in class astex.MoleculeRenderer
The list of atoms that have been picked so far.
pickMode - Variable in class astex.MoleculeRenderer
The current pick mode.
pink - Static variable in class astex.Color32
 
pixelCount - Variable in class astex.Renderer
Number of pixels.
pixelHeight - Variable in class astex.Renderer
Height of the renderer.
pixels - Static variable in class astex.AstexLogo
 
pixelWidth - Variable in class astex.Renderer
Width of the renderer.
planeEquation(Point3d, Point3d, Point3d) - Static method in class astex.Point3d
Evaluate the plane equation for the specified vectors.
PLATINUM - Static variable in class astex.PeriodicTable
 
plum - Static variable in class astex.Color32
 
PLUTONIUM - Static variable in class astex.PeriodicTable
 
Point3d - Class in astex
A class for manipulating 3d points and vectors.
Point3d() - Constructor for class astex.Point3d
Default constructor.
Point3d(double, double, double) - Constructor for class astex.Point3d
Constructor which allows the x, y, and z coordinates to be specified.
Point3d(double, double) - Constructor for class astex.Point3d
Construct a 2D point with specified x and y coordinates.
Point3d(double) - Constructor for class astex.Point3d
Construct a 3D point with equal x, y and z coordinates.
Point3d(Point3d) - Constructor for class astex.Point3d
Construct a 3D point from the coordinates of another Point3d.
pointInSphere(double, double, double) - Static method in class astex.ShadowCache
Is this point in another sphere.
pointShadowed(double, double, double) - Static method in class astex.ShadowCache
Is this point shadowed by stuff in the shadow cache.
POLONIUM - Static variable in class astex.PeriodicTable
 
pop() - Static method in class astex.UI
 
popSelection() - Method in class astex.MoleculeRenderer
Pop a selection from the selection stack.
pos - Variable in class astex.Light
Position of the light.
possiblyCreateRing(Atom[], Bond[], int) - Method in class astex.Molecule
Create a ring if the atoms are in the right order.
postProcess() - Method in class astex.Renderer
Post process the buffers.
PostRenderPass - Static variable in class astex.Renderer
 
POTASSIUM - Static variable in class astex.PeriodicTable
 
power - Variable in class astex.Light
Sheen of highlight.
powFactor - Variable in class astex.Renderer
 
PRASEODYMIUM - Static variable in class astex.PeriodicTable
 
preferredSize() - Method in class astex.ImageButton
 
prepareCylinderCacheList(double, double, double, double, double, double, double) - Static method in class astex.ShadowCache
Prepare shadow cache list for cylinder, by making bounding volume a sphere that encloses the whole cylinder.
prepareSphereCacheList(double, double, double, double, boolean) - Static method in class astex.ShadowCache
Prepare a list of objects that may obscure points on _this_ sphere.
prepareSymmetry() - Method in class astex.Symmetry
Generate the cartesian/fractional interconversion matrices.
prepareTriangleCacheList(double, double, double, double, double, double, double, double, double, boolean) - Static method in class astex.ShadowCache
Prepare shadow cache list for triangle, by making bounding volume a sphere that encloses the whole triangle.
PreRenderPass - Static variable in class astex.Renderer
Different settings for the render passes.
pretranslate(double, double, double) - Method in class astex.Matrix
Translate the transformation matrix the other way.
print(String, int) - Static method in class astex.Color32
Print a colour representation.
print(String, int, int, int) - Static method in class astex.Color32
Print a colour representation.
print(String, DoubleArray) - Static method in class astex.DoubleArray
Print a CLASSNAME contents.
print(String, DynamicArray) - Static method in class astex.DynamicArray
Print a CLASSNAME contents.
print(char) - Method in class astex.FILE
Print a char.
print(int, int, double) - Method in class astex.FILE
Quick print function for floats/doubles.
print(int, long) - Method in class astex.FILE
Quick print function for ints/long
print(String, double, double, double) - Method in class astex.FILE
Print function for 3 floats/doubles.
print(String, long, long, long) - Method in class astex.FILE
Print function for 3 ints/longs.
print(String) - Method in class astex.FILE
print function.
print(String, String) - Method in class astex.FILE
Print a formatted String.
print(String, char) - Method in class astex.FILE
Print a formatted char.
print(String, long) - Method in class astex.FILE
Print a formatted integer.
print(String, double) - Method in class astex.FILE
Print a formatted double.
print(String, FloatArray) - Static method in class astex.FloatArray
Print a CLASSNAME contents.
print(PrintStream, String, double) - Static method in class astex.Format
prints a formatted number following printf conventions
print(PrintStream, String, long) - Static method in class astex.Format
prints a formatted number following printf conventions
print(PrintStream, String, char) - Static method in class astex.Format
prints a formatted number following printf conventions
print(PrintStream, String, String) - Static method in class astex.Format
prints a formatted number following printf conventions
print(String, IntArray) - Static method in class astex.IntArray
Print a CLASSNAME contents.
print() - Method in class astex.Matrix
Print a default message with the matrix.
print(String) - Method in class astex.Matrix
Print the matrix.
print(String, double[]) - Static method in class astex.Point3d
 
print - Class in astex
03-01-99 tmm made class public (required for move to packages) made methods public 06-09-98 tmm added javadoc header comments/change comment section 03-01-98 mh created
print() - Constructor for class astex.print
 
print(String, StringArray) - Static method in class astex.StringArray
Print a CLASSNAME contents.
PRINT - Static variable in class astex.sym
 
printArray(String, int[]) - Static method in class astex.Map
Print an array.
printArray(String, double[]) - Static method in class astex.Map
Print an array.
printHeader(PrintStream) - Method in class astex.Map
Print the header for the map.
println(String) - Method in class astex.FILE
println function.
printMatrix() - Method in class astex.MoleculeRenderer
Print the matrix out.
printStatistics(int) - Method in class astex.Lattice
Print info about the Lattice object.
processCommand(String) - Method in class astex.AnimationObject
Introduce variables etc.
projectPoints() - Static method in class astex.Surface
Project the points inside the atoms onto the surface.
projectTorii() - Static method in class astex.Surface
Project the points inside the atoms onto the surface.
projectTorus(int, int) - Static method in class astex.Surface
Project the points of a torus onto the grid.
PROMETHIUM - Static variable in class astex.PeriodicTable
 
propagateCycleSearch(Atom, Atom, int) - Method in class astex.Molecule
Propagate the search for cycles.
Property - Static variable in class astex.Atom
The property set flag.
property(MoleculeRenderer, int) - Static method in class astex.Selection
Return atoms that have the specified property.
PROPERTY - Static variable in class astex.sym
 
property_map(Tmesh, DynamicArray, int, double, boolean, int) - Static method in class astex.Texgen
Generate potential.
PropertyChanged - Static variable in class astex.generic.GenericEvent
 
propertyGet(String) - Static method in class astex.Arguments
Return a property from the builtin file.
PROTACTINIUM - Static variable in class astex.PeriodicTable
 
publicInit() - Method in class MoleculeViewerApplet
 
publicRedraw() - Method in class astex.Renderer
Public redrawing operations that can be overridden.
purple - Static variable in class astex.Color32
 
pushSelection(DynamicArray) - Method in class astex.MoleculeRenderer
Push a selection onto the stack.

Q

Q - Static variable in class astex.Atom
The partial charge attribute.
QAttribute - Static variable in class astex.Atom
 
QUESTION_MARK - Static variable in class astex.match
This flag represents the question mark (`?') wildcard character.

R

radicalSymbols - Static variable in class astex.PeriodicTable
Symbols used for displaying radical states of atoms.
RADIUM - Static variable in class astex.PeriodicTable
 
radius - Variable in class astex.Atom
The radius of the atom.
Radius - Static variable in class astex.Atom
 
Radius - Static variable in class astex.Distance
 
radius - Variable in class astex.ModellingData
The radius for non-bonded interactions.
RADIUS - Static variable in class astex.sym
 
RADON - Static variable in class astex.PeriodicTable
 
rayCapsuleInt(double[], double[], double[], double[], boolean) - Static method in class astex.Geometry
Peform ray-cylinder intersection and normal generation.
rayCapsuleIntInit(double[], double[], double, double) - Static method in class astex.Geometry
Initialise cylinder calculations.
raySphereInt(double[], double[], double, double, double, double, double[], double[], boolean) - Static method in class astex.Geometry
Peform ray-sphere intersection and normal generation.
RCURLY - Static variable in class astex.sym
 
read() - Method in class astex.FILE
Read a single character.
read() - Method in class astex.Map
Read a map from the specified file object.
read(String) - Static method in class astex.MoleculeIO
Convenience method that will try and determine a file type from its extension (not foolproof).
read(String, FILE) - Static method in class astex.MoleculeIO
Main entry point for reading a molecule file.
read(String) - Static method in class astex.Tmesh
Create a tmesh from a file.
readAtomBlock(FILE, int, Molecule) - Static method in class astex.MoleculeIO
Read the Sybyl atom block.
readBitmap(String, int[]) - Static method in class astex.ImageIO
Read a windows bitmap file.
readBondBlock(FILE, int, Molecule, boolean) - Static method in class astex.MoleculeIO
Read the Sybyl atom block.
readDouble(int, int) - Method in class astex.FILE
Read a double precision number from the specified region.
readDouble(String) - Static method in class astex.FILE
Read a double value from a string.
readDoubleFromField(int) - Method in class astex.FILE
Read a double from the specified field.
readFrom(FILE) - Static method in class astex.FILE
Read the data from the specified FILE object.
readHeader() - Method in class astex.Map
Read a map from the specified file object.
readInteger(int, int) - Method in class astex.FILE
Read an integer from the current line buffer.
readInteger(String) - Static method in class astex.FILE
Read an integer from the specified string.
readInteger3(int) - Method in class astex.FILE
Specific method for reading a 3 column integer.
readIntegerFromField(int) - Method in class astex.FILE
Read an integer from the specified field.
readKeyDefinitions() - Method in class astex.MoleculeViewer
 
readLine() - Method in class astex.FILE
Provide a method that will return the current line as a String.
readMap(Map) - Method in class astex.MoleculeRenderer
Read the maps that we are displaying.
readMaps() - Method in class astex.MoleculeRenderer
 
readMDLMol(FILE) - Static method in class astex.MoleculeIO
Read an an MDL mol file.
readMol2(FILE) - Static method in class astex.MoleculeIO
Read a SYBYL mol file.
readPDB(FILE) - Static method in class astex.MoleculeIO
Read a PDB file from the input.
readPDBAtom(FILE, Molecule) - Static method in class astex.MoleculeIO
Read a pdb atom from the current record.
readPly(FILE) - Static method in class astex.Tmesh
Read a ply file.
readRegion() - Method in class astex.Map
Read the determined region from the map.
readScaleRecord(Molecule, FILE) - Static method in class astex.MoleculeIO
Read a scale record from the input file.
readSimple(FILE) - Static method in class astex.MoleculeIO
Read an an MDL mol file.
readSymmetryOperator(String, DynamicArray) - Static method in class astex.Symmetry
Decode one symmetry operator.
readTmesh(FILE) - Static method in class astex.MoleculeIO
 
readUnitCell(Molecule, FILE) - Static method in class astex.MoleculeIO
Read the unit cell info from the current line.
readXyzr(FILE) - Static method in class astex.MoleculeIO
 
ready - Variable in class astex.MoleculeViewer
Are we initialised?
recalculateNormals() - Method in class astex.Tmesh
Recalculate normals.
Recenter - Static variable in class astex.AnimationObject
Constant to indicate that we are recentering.
RECTANGULAR - Static variable in class astex.sym
 
rectangular(Tmesh) - Static method in class astex.Texgen
Create rectangular texture coordinates.
Red - Static variable in class astex.Color32
Red bits.
red - Static variable in class astex.Color32
 
redraw() - Method in class astex.Renderer
Redraw the image.
reExecute() - Method in class astex.MoleculeRenderer
 
relativeGridToCartesian(double, double, double, Point3d) - Method in class astex.Map
Convert grid coordiantes to cartesian.
release() - Method in class astex.Atom
Release an atom after we finished with it.
remove(double) - Method in class astex.DoubleArray
Remove an object from the CLASSNAME.
remove(Object) - Method in class astex.DynamicArray
Remove an object from the CLASSNAME.
remove(float) - Method in class astex.FloatArray
Remove an object from the CLASSNAME.
remove(int) - Method in class astex.IntArray
Remove an object from the CLASSNAME.
remove(String) - Method in class astex.StringArray
Remove an object from the CLASSNAME.
REMOVE - Static variable in class astex.sym
 
removeAllAngles() - Method in class astex.MoleculeRenderer
Remove all the angles.
removeAllBonds() - Method in class astex.Atom
Remove all bonds.
removeAllBumpAtoms() - Method in class astex.MoleculeRenderer
Remove all bump atoms.
removeAllDistances() - Method in class astex.MoleculeRenderer
Remove all the distance monitors.
removeAllElements() - Method in class astex.DoubleArray
Remove all elements from the dynamic array.
removeAllElements() - Method in class astex.DynamicArray
Remove all elements from the dynamic array.
removeAllElements() - Method in class astex.FloatArray
Remove all elements from the dynamic array.
removeAllElements() - Method in class astex.IntArray
Remove all elements from the dynamic array.
removeAllElements() - Method in class astex.StringArray
Remove all elements from the dynamic array.
removeAllLabelledAtoms() - Method in class astex.MoleculeRenderer
Remove all labelled atoms.
removeAllSelectedAtoms() - Method in class astex.MoleculeRenderer
Remove all selected atoms.
removeAllTorsions() - Method in class astex.MoleculeRenderer
Remove all the torsion monitors.
removeAnimationThread(Thread) - Method in class astex.MoleculeViewer
Try and remove a thread after it has finished running.
removeAtom(Atom) - Method in class astex.Molecule
Remove an atom from the molecule.
removeAtom(Atom) - Method in class astex.Residue
Remove an atom from the residue.
removeBond(Bond) - Method in class astex.Atom
Remove a bond from this atom.
removeBond(Bond) - Method in class astex.Molecule
Remove a bond from the molecule.
removeChild(GenericInterface) - Method in class astex.Atom
Remove a child.
removeChild(GenericInterface) - Method in class astex.generic.Generic
 
removeChild(GenericInterface) - Method in interface astex.generic.GenericInterface
Remove a child.
removeContourLevels() - Method in class astex.MoleculeRenderer
Remove the displayed maps.
removeElement(int) - Method in class astex.DoubleArray
Remove a specified element from the CLASSNAME.
removeElement(int) - Method in class astex.DynamicArray
Remove a specified element from the CLASSNAME.
removeElement(int) - Method in class astex.FloatArray
Remove a specified element from the CLASSNAME.
removeElement(int) - Method in class astex.IntArray
Remove a specified element from the CLASSNAME.
removeElement(int) - Method in class astex.StringArray
Remove a specified element from the CLASSNAME.
removeGraphicalObjects(String) - Method in class astex.MoleculeRenderer
 
removeGraphicalObjects(String) - Method in class astex.Renderer
Remove objects that match a pattern.
removeGraphicalObjects(Tmesh) - Method in class astex.Renderer
Remove specific graphical object.
removeGraphicalObjectsBeginningWith(String) - Method in class astex.MoleculeRenderer
 
removeGraphicalObjectsBeginningWith(String) - Method in class astex.Renderer
Remove objects that begin with the specified string.
removeListener(GenericEventInterface) - Method in class astex.Atom
Remove a listener.
removeListener(GenericEventInterface) - Method in class astex.generic.Generic
 
removeListener(GenericEventInterface) - Method in interface astex.generic.GenericInterface
Remove a listener.
removeMap(String) - Method in class astex.MoleculeRenderer
Remove maps.
removeMap(Map) - Method in class astex.MoleculeRenderer
 
removeMap(Map) - Method in class astex.MoleculeViewer
Remove a map from the renderer.
removeMaps() - Method in class astex.MoleculeRenderer
Remove the maps rather than the contour levels.
removeMolecule(String) - Method in class astex.MoleculeRenderer
Remove a molecule.
removeMoleculeByName(String) - Method in class astex.MoleculeRenderer
Remove a molecule.
removeMoleculeRendererListener(MoleculeRendererListener) - Method in class astex.MoleculeRenderer
Remove a MoleculeRendererListener.
removeParent(GenericInterface) - Method in class astex.Atom
Remove a parent.
removeParent(GenericInterface) - Method in class astex.generic.Generic
 
removeParent(GenericInterface) - Method in interface astex.generic.GenericInterface
Remove a parent.
removeRendererEventListener(RendererEventListener) - Method in class astex.Renderer
Remove a listener for renderer events.
removeRepaintListener(Component) - Method in class astex.MoleculeViewer
 
removeResidue(Residue) - Method in class astex.Chain
Remove a residue from the chain.
removeSpaceGroup() - Method in class astex.MoleculeRenderer
Remove the stored space group information.
removeSymmetry() - Method in class astex.MoleculeRenderer
Remove the symmetry molecule if there is one.
render() - Method in class astex.Tmesh
Called when the Tmesh needs to draw itself.
renderer - Variable in class astex.MoleculeRenderer
The Renderer that will do the work.
Renderer - Class in astex
 
Renderer() - Constructor for class astex.Renderer
Default renderer.
RendererEvent - Class in astex
Events fired from the renderer.
RendererEvent(int, Object) - Constructor for class astex.RendererEvent
 
RendererEventListener - Interface in astex
Class for monitoring renderer events.
rendererEventListeners - Variable in class astex.Renderer
 
RenderPass - Static variable in class astex.Renderer
 
reorderAtoms() - Method in class astex.Molecule
Reorder the atoms in a molecule.
repaint() - Method in class astex.MoleculeRenderer
 
REPAINT - Static variable in class astex.sym
 
replace(String, String, String) - Static method in class astex.Util
 
reset() - Method in class astex.MoleculeRenderer
Remove everything from the renderer.
reset(double, double, double, double, double) - Method in class astex.NeighbourGrid2D
Reset and reuse a neighbour grid.
reset() - Static method in class astex.UI
 
resetAwtImage() - Method in class astex.MoleculeViewer
Force the awt image to get replaced.
resetCenterAndRadius() - Method in class astex.Renderer
Reset the center and radius of the view.
resetColor() - Method in class astex.Atom
Set color back to undefined.
resetContourLevels() - Method in class astex.MoleculeRenderer
Reset the contour levels.
resetTransformationMatrix() - Method in class astex.MoleculeRenderer
Reset the transformation matrix.
resetView() - Method in class astex.MoleculeRenderer
Reset the view of the renderer.
resetWideBonds() - Method in class astex.MoleculeRenderer
Reset the wide bonds flags.
Residue - Class in astex
A class for storing a group of atoms that form part of a protein residue.
residue(MoleculeRenderer, Vector) - Static method in class astex.Selection
Select a set of atoms on the basis of ids.
RESIDUE - Static variable in class astex.sym
 
residue2(MoleculeRenderer, Vector) - Static method in class astex.Selection
Select a set of atoms on the basis of ids.
ResidueColor - Static variable in class astex.Residue
 
ResidueIterator - Class in astex
Iterate over the residues in a scene.
ResidueIterator(MoleculeRenderer) - Constructor for class astex.ResidueIterator
The only public constructor.
retrieve() - Static method in class astex.Selection
Retrieve the result of a selection expression.
returnScript() - Method in class astex.Matrix
 
rgb - Variable in class astex.ColorChooser
 
rgb - Variable in class astex.Renderer
Do RGB Gouraud shading rather than Phong lookup.
rgb2hsv(double[], double[]) - Static method in class astex.Color32
Convert rgb to hsv.
RHENIUM - Static variable in class astex.PeriodicTable
 
RHODIUM - Static variable in class astex.PeriodicTable
 
ribbon(Arguments, Tmesh) - Static method in class astex.Schematic
Add ribbon to graphical object.
Ring - Static variable in class astex.Atom
 
Ring - Class in astex
Class for holding information about ring systems in molecular structures.
ringBond - Static variable in class astex.Bond
Is the bond in a ring of any description.
Rock - Static variable in class astex.AnimationObject
Constant to indicate that we are rocking.
Roll - Static variable in class astex.AnimationObject
Constant to indicate that we are rolling.
rotateAroundVector(Point3d, double) - Method in class astex.Matrix
Rotate around a line.
rotateAroundVector(double, double, double, double) - Method in class astex.Matrix
Rotate around a line.
rotateX(double) - Method in class astex.Renderer
Rotate the transform around the x axis.
rotateXdegrees(double) - Method in class astex.Matrix
Rotate around x in degrees.
rotateY(double) - Method in class astex.Renderer
Rotate the transform around the x axis.
rotateYdegrees(double) - Method in class astex.Matrix
Rotate around y in degrees.
rotateZ(double) - Method in class astex.Renderer
Rotate the transform around the x axis.
rotateZdegrees(double) - Method in class astex.Matrix
Rotate around Z in degrees.
rotationMatrix - Variable in class astex.Renderer
 
RPAREN - Static variable in class astex.sym
 
RUBIDIUM - Static variable in class astex.PeriodicTable
 
run() - Method in class astex.Animate
The run method.
run() - Method in class astex.Spin
Implement the Runnable interface.
run() - Method in class MoleculeViewerApplet
 
RUTHENIUM - Static variable in class astex.PeriodicTable
 
rwb0 - Static variable in class astex.Color32
 
rwb1 - Static variable in class astex.Color32
 
rwb2 - Static variable in class astex.Color32
 
rwb3 - Static variable in class astex.Color32
 
rwb4 - Static variable in class astex.Color32
 
rwb5 - Static variable in class astex.Color32
 
rwb6 - Static variable in class astex.Color32
 
rwb7 - Static variable in class astex.Color32
 

S

salmon - Static variable in class astex.Color32
 
SAMARIUM - Static variable in class astex.PeriodicTable
 
saveAndExit() - Method in class astex.MoleculeViewer
Save the whole state.
saveFile(String, String[]) - Method in class astex.MoleculeViewer
Get a file name to save to.
saveMolecule(Molecule) - Method in class astex.MoleculeViewer
Save this molecule.
saveMoleculeByName(String) - Method in class astex.MoleculeViewer
Save this molecule.
saveMolecules() - Method in class astex.MoleculeViewer
Save the small molecules.
saveScript(String) - Method in class astex.MoleculeViewer
 
scacher - Static variable in class astex.ShadowCache
 
scachex - Static variable in class astex.ShadowCache
Sphere cache for shadows.
scachey - Static variable in class astex.ShadowCache
 
scachez - Static variable in class astex.ShadowCache
 
scale(int, int) - Static method in class astex.Color32
 
scale(double) - Method in class astex.Matrix
Scale the transformation matrix.
scale(double, double, double) - Method in class astex.Matrix
Apply non uniform scale.
scale(double) - Method in class astex.Point3d
Scale the point by the specified amount.
scale - Variable in class astex.Renderer
The current scale.
scale - Variable in class astex.Symmetry
The SCALE matrix from the PDB file if one exists.
scaleTexture(String, int, double) - Method in class astex.Renderer
Scale texture to the specified objects.
SCANDIUM - Static variable in class astex.PeriodicTable
 
Schematic - Class in astex
 
Schematic() - Constructor for class astex.Schematic
 
SCHEMATIC - Static variable in class astex.sym
 
scr - Static variable in class astex.ShadowCache
 
scx - Static variable in class astex.ShadowCache
References for sphere centers.
scy - Static variable in class astex.ShadowCache
 
scz - Static variable in class astex.ShadowCache
 
seashell - Static variable in class astex.Color32
 
SecondaryStructure - Class in astex
Class for assigning secondary structure to a protein molecule.
SecondaryStructure() - Constructor for class astex.SecondaryStructure
 
SECSTRUC - Static variable in class astex.sym
 
select(int) - Method in class astex.Atom
Set the selection state.
select(int) - Method in class astex.Chain
Apply a selection recursively.
select(int) - Method in class astex.Molecule
Apply a selection recursively.
select(int) - Method in class astex.Residue
Apply a selection recursively.
select(int) - Method in interface astex.Selectable
 
SELECT - Static variable in class astex.sym
 
Selectable - Interface in astex
 
Selected - Static variable in class astex.Atom
The atom is selected.
Selection - Class in astex
Class for evaluating selection expressions.
Selection() - Constructor for class astex.Selection
 
selectStatement() - Method in class astex.Atom
 
selectStatement() - Method in class astex.Chain
 
selectStatement() - Method in class astex.Molecule
 
selectStatement() - Method in class astex.Residue
 
selectStatement() - Method in interface astex.Selectable
 
SELENIUM - Static variable in class astex.PeriodicTable
 
selfShadowed(double, double, double, double) - Static method in class astex.ShadowCache
Is the surface at this point self shadowing.
SEMI - Static variable in class astex.sym
 
sequential(MoleculeRenderer, Vector) - Static method in class astex.Selection
Select a set of atoms on the basis of ids.
SEQUENTIAL - Static variable in class astex.sym
 
set(Object, Object) - Method in class astex.Atom
Set an object value.
set(Object, Object) - Method in class astex.Bond
 
set(int, double) - Method in class astex.DoubleArray
Set a specified element in the array.
set(int, Object) - Method in class astex.DynamicArray
Set a specified element in the array.
set(int, float) - Method in class astex.FloatArray
Set a specified element in the array.
set(Object, Object) - Method in class astex.generic.Generic
 
set(Object, Object) - Method in interface astex.generic.GenericInterface
Set an object value.
set(int, int) - Method in class astex.IntArray
Set a specified element in the array.
set(Matrix) - Method in class astex.Matrix
Set matrix from another.
set(int, int, double) - Method in class astex.Matrix
 
set(Object, Object) - Method in class astex.Molecule
 
set(double, double, double) - Method in class astex.Point3d
Set the x, y and z coordinates of this Point3d.
set(double) - Method in class astex.Point3d
Set the x, y and z coordinates to the same value.
set(Point3d) - Method in class astex.Point3d
Set the x, y and z coordinates to the values from another Point3d.
set(int, double) - Method in class astex.Point3d
Set the specified component.
set(int, String) - Method in class astex.StringArray
Set a specified element in the array.
SET - Static variable in class astex.sym
 
setActiveLight(int, Light) - Method in class astex.MoleculeViewer
 
setActiveLight(int, Light) - Method in class astex.UserInterface
 
setAmbient(int) - Method in class astex.Renderer
Set the ambient component of the lighting model.
setAnimateThread(Thread) - Method in class astex.AnimationObject
Set the animate thread.
setAntiAlias(boolean) - Method in class astex.Renderer
Set the current antialiasing setting.
setApplication(boolean) - Method in class astex.MoleculeViewer
Set whether we are running in application.
setArrayCopy(boolean) - Method in class astex.MoleculeViewer
Should the renderer use arraycopy for clearing its buffers.
setAtomLabel(String) - Method in class astex.Atom
Set the atom label.
setAtomLabelFormat(String) - Method in class astex.MoleculeRenderer
Set the label format that is used for atoms on screen.
setAtomType(String) - Method in class astex.Atom
Set the atomType.
setautoFlush(boolean) - Method in class astex.FILE
sets the autoFlush flag.
setBackClip(double) - Method in class astex.Renderer
Set the back clip plane.
setBackClip(double, boolean) - Method in class astex.Renderer
 
setBackface(String, boolean) - Method in class astex.Renderer
Set backface on or off.
setBackface(boolean) - Method in class astex.Tmesh
Set the value of backface.
setBackgroundColor(int) - Method in class astex.Renderer
Set the background colour.
setBallRadius(double) - Method in class astex.Atom
Set the vdw radius.
setBFactor(double) - Method in class astex.Atom
Set the bFactor.
setBondColor(int) - Method in class astex.Bond
Set the value of bondColor.
setBondOrder(int) - Method in class astex.Bond
Set the bond order.
setBondWidth(int) - Method in class astex.Bond
Set the value of bondWidth.
setBoolean(Object, boolean) - Method in class astex.generic.Generic
Set a Boolean.
setBounds(Rectangle) - Method in class astex.MoleculeViewer
Handle a resize in a different way.
setBounds(int, int, int, int) - Method in class astex.MoleculeViewer
Handle a resize.
setBumpInSameMolecule(boolean) - Method in class astex.MoleculeRenderer
 
setCapacity(int) - Method in class astex.DoubleArray
Set the capacity for the object.
setCapacity(int) - Method in class astex.DynamicArray
Set the capacity for the object.
setCapacity(int) - Method in class astex.FloatArray
Set the capacity for the object.
setCapacity(int) - Method in class astex.IntArray
Set the capacity for the object.
setCapacity(int) - Method in class astex.StringArray
Set the capacity for the object.
setCartoonNormalCutoff(double) - Method in class astex.Renderer
Set the cartoon normal cutoff.
setCenter(double, double, double) - Method in class astex.Map
Set the center point of the region we will contour.
setCenter(Point3d) - Method in class astex.Map
Set the center point of the region we will contour.
setCenter(double, double, double) - Method in class astex.MoleculeRenderer
Set the center for the renderer.
setCenter(Point3d) - Method in class astex.MoleculeRenderer
 
setCenter(Point3d, boolean) - Method in class astex.MoleculeRenderer
Set the center for the renderer.
setCenter(DynamicArray) - Method in class astex.MoleculeRenderer
Set the center from a set of atoms.
setCenter(Point3d) - Method in class astex.MoleculeViewer
Set the center point of the underlying renderer.
setCenter(Point3d) - Method in class astex.Renderer
Set the center point.
setCentralAtomCount(int) - Method in class astex.Molecule
Set the number of central atoms.
setCharactersInBuffer(int) - Method in class astex.FILE
 
setCharge(int) - Method in class astex.Atom
Set the atom charge.
setClassname(String) - Method in class astex.Atom
Set our classname.
setClassname(String) - Method in class astex.generic.Generic
 
setClassname(String) - Method in interface astex.generic.GenericInterface
Set our classname.
setClip(double) - Method in class astex.MoleculeRenderer
Set the clip distance allowing for minimum clip distance.
setClip(double, double) - Method in class astex.Renderer
Set the clip.
setClip(double) - Method in class astex.Renderer
Set the clip.
setClipIncrement(double) - Method in class astex.Renderer
Set the clip increment.
setClipped(int, boolean) - Method in class astex.Tmesh
Set whether this point is clipped.
setCodeBase(URL) - Static method in class astex.FILE
Set the docuemnt base.
setColor(int) - Method in class astex.Atom
Set the atom color.
setColor(int) - Method in class astex.Renderer
Set the material color.
setColor(int) - Method in class astex.Tmesh
Set the value of color.
setColorStyle(int) - Method in class astex.Tmesh
Set the object color style.
setCommand(String) - Method in class astex.AnimationObject
Set the command.
setComponent(Component) - Static method in class astex.GoogleFont
 
setContourColor(int, int) - Method in class astex.Map
Set the specified contour color.
setContourDisplayed(int, boolean) - Method in class astex.Map
Set if the specified contour is displayed.
setContourLevel(int, double) - Method in class astex.Map
Set the specified contour level.
setContourSize(int) - Method in class astex.MoleculeRenderer
 
setContourStyle(int, int) - Method in class astex.Map
Set the specified contour color.
setCustomLabel(String) - Method in class astex.Atom
Set whether the atom is solvent.
setCylinderWidth(double) - Method in class astex.Bond
Set the value of cylinderWidth.
setDebug(boolean) - Static method in class astex.FILE
Set the debug state.
setDebug(boolean) - Static method in class astex.Surface
Turn debugging on/off.
setDisplayAtomLabel(boolean) - Method in class astex.MoleculeRenderer
Set whether we should display the atom label.
setDisplayBumps(boolean) - Method in class astex.MoleculeRenderer
Set whether we display bumps.
setDisplayDistances(boolean) - Method in class astex.MoleculeRenderer
Set the distance display flag.
setDisplayed(boolean) - Method in class astex.Atom
Set whether the atom has been displayed.
setDisplayed(int) - Method in class astex.Molecule
Set if the molecule is on or off.
setDisplayMaps(boolean) - Method in class astex.MoleculeRenderer
Should we display maps.
setDisplaySolvent(boolean) - Method in class astex.MoleculeRenderer
Set whether we display solvent.
setDisplayStatusString(boolean) - Method in class astex.MoleculeRenderer
Should we display status strings.
setDisplayStatusString(boolean) - Method in class astex.Renderer
Set whether or not to display the status string.
setDisplayStyle(int) - Method in class astex.Molecule
Set Display style.
setDocumentBase(URL) - Static method in class astex.FILE
Set the docuemnt base.
setDocumentBase(URL) - Static method in class astex.Texture
Set the document base.
setDouble(Object, double) - Method in class astex.generic.Generic
Set a double.
setDrawGamma(double) - Method in class astex.Renderer
 
setElement(int) - Method in class astex.Atom
Set the element of this atom.
setEolIdentifier(int) - Method in class astex.FILE
Set the eond of line characters explicitily.
setExplicitBond(boolean) - Method in class astex.Bond
Set whehter this bond was an explicit bond.
setExtensions(String[]) - Method in class astex.UniversalFilenameFilter
Set the accepted file name extensions.
setFile(String) - Method in class astex.Map
Set the filename.
setFilename(String) - Method in class astex.Molecule
Set the filename.
setFinishCenter(double, double, double, double, double, double) - Method in class astex.AnimationObject
Set the start view.
setFinishMatrix(Matrix) - Method in class astex.AnimationObject
Set the start matrix for view change.
setFirstAtom(Atom) - Method in class astex.Angle
Set the first atom in the angle.
setFirstAtom(Atom) - Method in class astex.Bond
Set the first atom in the bond.
setFirstAtom(Atom) - Method in class astex.Improper
Set the first atom in the improper.
setFourthAtom(Atom) - Method in class astex.Improper
Set the fourth atom in the improper.
setFrontClip(double) - Method in class astex.Renderer
Set the front clip plane.
setFrontClip(double, boolean) - Method in class astex.Renderer
 
setGradient(boolean) - Method in class astex.Renderer
Set top of background colour gradient.
setGradientBottom(int) - Method in class astex.Renderer
Set top of background colour gradient.
setGradientTop(int) - Method in class astex.Renderer
Set top of background colour gradient.
setGraphicalObjectsColour(String, int) - Method in class astex.Renderer
Change the visibility state of GraphicalObjects.
setGraphicalObjectsVisibility(String, int) - Method in class astex.Renderer
Change the visibility state of GraphicalObjects.
setHeteroAtom(boolean) - Method in class astex.Atom
Set whether the atom is a heteroatom.
setId(int) - Method in class astex.Atom
Set the id for this atom.
setIdealBondAngle(double) - Method in class astex.Angle
Set the ideal angle angle.
setIdealBondLength(double) - Method in class astex.Bond
Set the ideal bond length.
setIdealImproperAngle(double) - Method in class astex.Improper
Set the ideal improper angle.
setIdentity() - Method in class astex.Matrix
Set the matrix to the identity matrix.
setInsertionCode(char) - Method in class astex.Atom
Set the insertion code.
setInsertionCode(char) - Method in class astex.Chain
Set the insertion code.
setInsertionCode(char) - Method in class astex.Residue
Set the insertion code.
setInteger(Object, int) - Method in class astex.generic.Generic
Set an int.
setInteractive(boolean) - Method in class astex.Animate
Set whether we are in interactive mode.
setItem(Object) - Method in class astex.RendererEvent
Set the value of item.
setLabelled(boolean) - Method in class astex.Atom
Set whether the atom is solvent.
setLightingModel(int) - Method in class astex.Renderer
Set the lighting model.
setLineWidth(double) - Method in class astex.Tmesh
Set the linewidth.
setLoggingLevel(int) - Static method in class astex.Log
Set the logging level for this class.
setLogo(String) - Method in class astex.Renderer
Set the current logo.
setMapContourColour(String, int, int) - Method in class astex.MoleculeRenderer
Change the value of a contour level.
setMapContourDisplayed(String, int, int) - Method in class astex.MoleculeRenderer
Turn contour level on/off of a contour level.
setMapContourLevel(String, int, double) - Method in class astex.MoleculeRenderer
Change the value of a contour level.
setMapContourLineWidth(String, int, double) - Method in class astex.MoleculeRenderer
Change the line width.
setMapContourTransparency(String, int, int) - Method in class astex.MoleculeRenderer
Change the line width.
setMapType(int) - Method in class astex.Map
Set the value of mapType.
setMaximumDistance(double) - Method in class astex.Lattice
Set the maximum search distance.
setMaximumGridsize(int) - Static method in class astex.Surface
Set the maximum grid size.
setMinimumSpacing(double) - Static method in class astex.Surface
Set the minimum grid spacing.
setMinMax() - Method in class astex.ObjectPropertyDialog
Set the min max values for this object.
setMinMax(int) - Method in class astex.Tmesh
Set min and max for the specified texture coordinate.
setMode(int) - Method in class astex.AnimationObject
Set the current mode.
setMoleculeType(int) - Method in class astex.Molecule
Set what type of molecule this is.
setMoleculeVariable(String, String, String) - Method in class astex.MoleculeRenderer
 
setMoleculeViewer(MoleculeViewer) - Method in class astex.Animate
Set the MoleculeViewer.
setMoleculeViewer(MoleculeViewer) - Method in class astex.AnimationObject
The MoleculeViewer.
setMoleculeViewer(MoleculeViewer) - Method in interface astex.UserInterfacePanel
 
setMoleculeVisibility(String, String) - Method in class astex.MoleculeRenderer
Change molecule visibility.
setName(String) - Method in class astex.Chain
Set the chain name.
setName(String) - Method in class astex.Map
Set the map name.
setName(String) - Method in class astex.Molecule
Set the molecule name
setName(String) - Method in class astex.Residue
Set the residue name.
setName(String) - Method in class astex.Tmesh
Set the value of name.
setNeedsReading(boolean) - Method in class astex.Map
Set whether the map needs reading.
setNumber(int) - Method in class astex.Chain
Set the chain number.
setNumber(int) - Method in class astex.Residue
Set the residue number.
setOccupancy(double) - Method in class astex.Atom
Set the occupancy.
setOrClearAttribute(int, boolean) - Method in class astex.Atom
Set or clear a particular attribute.
setOriginalSpaceGroupName(String) - Method in class astex.Symmetry
Set the original space group name (with spaces).
setOutputStream(OutputStream) - Method in class astex.FILE
Set the output stream.
setParent(Residue) - Method in class astex.Atom
Set the residues to which the atom belongs.
setParent(Molecule) - Method in class astex.Chain
Set the parent molecule.
setParent(Chain) - Method in class astex.Residue
Set the parent chain.
setPartialCharge(double) - Method in class astex.Atom
Set the value of partialCharge.
setPickMode(int) - Method in class astex.MoleculeRenderer
Set the picking mode.
setPixel(int, int, int, int) - Method in class astex.Renderer
Set a pixel checking for on screen and z-buffer.
setPixel(int, int, int) - Method in class astex.Renderer
Set a pixel checking for on screen.
setPointCapacity(int) - Method in class astex.Tmesh
Set the initial capacity for points.
setPowFactor(double) - Method in class astex.Renderer
 
setPreferredSize(int, int) - Method in class astex.MoleculeViewer
Set the preferred size.
setProbeRadius(double) - Static method in class astex.Surface
Set the probe radius.
setRadius(double) - Method in class astex.Map
Set the radis of the region we will contour.
setRadius(double) - Method in class astex.MoleculeRenderer
Set the radius allowing for minimum value for renderer.
setRadius(double) - Method in class astex.MoleculeViewer
Set the radius of the underlying renderer.
setRadius(double) - Method in class astex.Renderer
Set the radius.
setRenderer(Renderer) - Method in class astex.Tmesh
Set the Renderer value.
setRenderPass(int) - Method in class astex.Tmesh
Set the RenderPass value.
setRingBond(boolean) - Method in class astex.Bond
Set the bond ring status.
setRockAngle(double) - Method in class astex.AnimationObject
Set the rock angle.
setRockRate(double) - Method in class astex.AnimationObject
Set the rock rate.
setSamples(int) - Method in class astex.Renderer
Set the number of samples.
setScale(double) - Method in class astex.Renderer
Set the scale.
setSecondaryStructure(int) - Method in class astex.Residue
Set the value of secondaryStructure.
setSecondAtom(Atom) - Method in class astex.Angle
Set the second atom in the angle.
setSecondAtom(Atom) - Method in class astex.Bond
Set the second atom in the bond.
setSecondAtom(Atom) - Method in class astex.Improper
Set the second atom in the improper.
setSelectCount(boolean) - Method in class astex.MoleculeRenderer
Set whether or not we print select counts.
setSelected(boolean) - Method in class astex.Atom
Set whether the atom is selected.
setSelected(DynamicArray) - Method in class astex.MoleculeRenderer
Set the specified atoms as selected.
setSelected(DynamicArray, boolean) - Method in class astex.MoleculeRenderer
Set the specified atoms as selected.
setSequentialNumber(int) - Method in class astex.Residue
 
setShowVersion(boolean) - Method in class astex.MoleculeViewer
Should we show the version.
setSigma(double) - Method in class astex.Map
Set the sigma level.
setSize(int, int) - Method in class astex.Renderer
Resize the renderer.
setSize(int, int) - Method in class astex.Texture
Resample the texture to the specified size.
setSleepDuration(int) - Method in class astex.AnimationObject
Set the sleep duration.
setSolvent(boolean) - Method in class astex.Atom
Set whether the atom is solvent.
setSpaceGroupName(String) - Method in class astex.Molecule
Set the space group name.
setSpaceGroupName(String) - Method in class astex.Symmetry
Set the space group name.
setSpaceGroupNumber(int) - Method in class astex.Symmetry
Set the space group number.
setStages(Vector) - Method in class astex.Animate
Set the stages.
setStartCenter(double, double, double, double, double, double) - Method in class astex.AnimationObject
Set the start view.
setStartMatrix(Matrix) - Method in class astex.AnimationObject
Set the start matrix for view change.
setStatusAtom(Atom) - Method in class astex.MoleculeRenderer
Set the atom that will produce the status label.
setStatusLabelFormat(String) - Method in class astex.MoleculeRenderer
Set the status label format.
setStatusString(String) - Method in class astex.Renderer
Set the current StatusString.
setSteps(int) - Method in class astex.AnimationObject
Set the number of steps.
setStickWidth(double) - Method in class astex.Bond
Set the value of stickWidth.
setString(Object, String) - Method in class astex.generic.Generic
Set a String.
setSymmetry(Symmetry) - Method in class astex.Molecule
Set the symmetry entry for this molecule.
setSymmetry(boolean) - Method in class astex.MoleculeRenderer
Set whether we display symmetry.
setSymmetry(boolean) - Method in class astex.MoleculeViewer
Set whether we are displaying symmetry.
setTemporarilySelected(boolean) - Method in class astex.Atom
Set whether the atom is temporarily selected.
setTextureRange(int, double, double) - Method in class astex.Tmesh
Set the texture range.
setTextureScalingMode(int) - Method in class astex.Tmesh
Set the texture scaling mode.
setThirdAtom(Atom) - Method in class astex.Angle
Set the second atom in the angle.
setThirdAtom(Atom) - Method in class astex.Improper
Set the third atom in the improper.
Settings - Class in astex
 
Settings() - Constructor for class astex.Settings
 
setTmesh(Tmesh) - Method in class astex.ObjectPropertyDialog
Set the tmesh object that is being edited.
setTransparency(int) - Method in class astex.Atom
Set the transparency.
setTransparency(int) - Method in class astex.Tmesh
Set the transparency.
setTriangleCapacity(int) - Method in class astex.Tmesh
Set the initial capacity for triangles.
setTryFiles(boolean) - Static method in class astex.FILE
 
setType(String) - Method in class astex.Molecule
Set the type.
setType(int) - Method in class astex.RendererEvent
Set the value of type.
setUnitCell(double[]) - Method in class astex.Molecule
Set the unit cell.
setUnitCell(double[]) - Method in class astex.Symmetry
Set the unit cell.
setUnitCellCode(int) - Method in class astex.Symmetry
Set the coding.
setUOffset(double) - Method in class astex.Tmesh
Set the uoffset.
setupContourLevels(String) - Method in class astex.MoleculeRenderer
Setup the contour levels from the passed string.
setupShadowCaches(Light, double) - Static method in class astex.ShadowCache
Set up the shadow cache data structures for renderering.
setUScale(double) - Method in class astex.Tmesh
Set the uscale.
setUsePopupMenu(boolean) - Method in class astex.MoleculeViewer
Set whether we should use the popup menu.
setVDWRadius(double) - Method in class astex.Atom
Set the vdw radius.
setVertex(int, double[], double[]) - Method in class astex.Tmesh
Set the vertex info for the specified point.
setVisible(boolean) - Method in class astex.Tmesh
Set the value of visible.
setVisited(boolean) - Method in class astex.Atom
Set whether the atom has been visited.
setVOffset(double) - Method in class astex.Tmesh
Set the voffset.
setVScale(double) - Method in class astex.Tmesh
Set the vscale.
setWide(boolean) - Method in class astex.Atom
Set whether the atom has been wide.
setWideBond(boolean) - Method in class astex.Bond
Set the bond to be wide or not.
setWideBonds() - Method in class astex.MoleculeRenderer
Set which bonds are drawn wide.
setWideBonds(DynamicArray) - Method in class astex.MoleculeRenderer
Set wide bonds for the atoms in the selection.
setWrapAngle(double) - Method in class astex.Renderer
 
setX(double) - Method in class astex.Point3d
Set the x coordinate.
setY(double) - Method in class astex.Point3d
Set the y coordinate.
setZ(double) - Method in class astex.Point3d
Set the x coordinate.
setZoom(double) - Method in class astex.Renderer
Set the zoom.
ShadowCache - Class in astex
 
ShadowCache() - Constructor for class astex.ShadowCache
 
shadowMode - Variable in class astex.Renderer
Shadow mode for the renderer.
shadows - Variable in class astex.MoleculeRenderer
Are shadows on.
ShadowsAccumulate - Static variable in class astex.Renderer
 
ShadowsOff - Static variable in class astex.Renderer
Defines for the shadowing states.
ShadowsOn - Static variable in class astex.Renderer
 
Sheet - Static variable in class astex.Residue
Sheet secondary structure type.
showAt(Dialog, int, int) - Static method in class astex.MoleculeViewer
Show the dialog at the position.
showContourLevelDialog() - Method in class astex.MoleculeViewer
Popup a dialog which allow us to alter contour levels.
sienna - Static variable in class astex.Color32
 
signalAtoms - Variable in class astex.EnergyTerm
The atoms we will optimise to the density.
SILICON - Static variable in class astex.PeriodicTable
 
SILVER - Static variable in class astex.PeriodicTable
 
SIMPLE - Static variable in class astex.sym
 
SimpleMol - Static variable in class astex.MoleculeIO
simple mol file.
simpleTexture() - Static method in class astex.Texture
 
SingleBond - Static variable in class astex.Bond
Constant that defines a single bond.
singleBondRequiresImproper(Bond) - Method in class astex.Molecule
Does this single bond require a improper.
SingleOrAromaticBond - Static variable in class astex.Bond
Constant that defines a single or aromatic bond.
SingleOrDoubleBond - Static variable in class astex.Bond
Constant that defines a single or double bond.
size() - Method in class astex.DoubleArray
Return the number of objects in the object array.
size() - Method in class astex.DynamicArray
Return the number of objects in the object array.
size() - Method in class astex.FloatArray
Return the number of objects in the object array.
size() - Method in class astex.IntArray
Return the number of objects in the object array.
size() - Method in class astex.StringArray
Return the number of objects in the object array.
SKELETON - Static variable in class astex.sym
 
SkeletonMolecule - Static variable in class astex.Molecule
 
skip(int) - Method in class astex.FILE
Skip some bytes.
slerp(double[], double[], double, double[]) - Static method in class astex.Matrix
The famous quaternion slerp.
smooth(double) - Method in class astex.Tmesh
Smooth the tmesh object.
snow - Static variable in class astex.Color32
 
SODIUM - Static variable in class astex.PeriodicTable
 
Solvent - Static variable in class astex.Atom
The atom is solvent.
solvent(MoleculeRenderer) - Static method in class astex.Selection
Solvent expression.
SOLVENT - Static variable in class astex.sym
 
solventNames - Static variable in class astex.Selection
Residue names for solvent.
sp - Static variable in class astex.Atom
 
sp2 - Static variable in class astex.Atom
 
sp3 - Static variable in class astex.Atom
Hybridisation states.
spacing - Variable in class astex.Map
The spacing along each axis.
specular - Variable in class astex.Light
Packed specular colour.
sphere(MoleculeRenderer, double, double, double, double) - Static method in class astex.Selection
Return a set of atoms withinin a sphere.
sphere(MoleculeRenderer, double, byte[]) - Static method in class astex.Selection
Return a set of atoms withinin a sphere.
SPHERE - Static variable in class astex.sym
 
sphereGen(int) - Static method in class astex.Surface
Initialise the dot sphere structures.
sphereOcclusionCacheList - Static variable in class astex.ShadowCache
 
SPHERES - Static variable in class astex.sym
 
spheres - Variable in class astex.Tmesh
Sphere graphical object.
SPHERES - Static variable in class astex.Tmesh
Types for style.
sphereShadowCacheList - Static variable in class astex.ShadowCache
Cache and occlusion lists.
Spin - Class in astex
 
Spin() - Constructor for class astex.Spin
 
Spin(MoleculeViewer, MoleculeRenderer) - Constructor for class astex.Spin
 
spinbox(int, int, int, int, int, int, JCSpinBoxListener) - Static method in class astex.UI
Create a spin box.
spinBoxChangeBegin(JCSpinBoxEvent) - Method in class astex.ColorChooser
 
spinBoxChangeBegin(JCSpinBoxEvent) - Method in class astex.ObjectPropertyDialog
 
spinBoxChangeBegin(JCSpinBoxEvent) - Method in class astex.UserInterface
 
spinBoxChangeEnd(JCSpinBoxEvent) - Method in class astex.ColorChooser
 
spinBoxChangeEnd(JCSpinBoxEvent) - Method in class astex.ObjectPropertyDialog
 
spinBoxChangeEnd(JCSpinBoxEvent) - Method in class astex.UserInterface
 
splashImage - Variable in class astex.MoleculeViewer
Are we initialised?
split(String) - Static method in class astex.FILE
Convenience methods for splitting strings into fields.
split(String, String) - Static method in class astex.FILE
Convenience methods for splitting strings into fields.
spr - Static variable in class astex.FILE
 
sprint(String, double) - Static method in class astex.FILE
Return a formatted double as String.
sprint(String, long) - Static method in class astex.FILE
Return a formatted long as String.
sprint(String, String) - Static method in class astex.FILE
Return a formatted String as String.
SQ(double) - Static method in class astex.Symmetry
Return the square of the argument.
stages - Variable in class astex.Animate
The list of animation objects.
start() - Method in class MoleculeViewerApplet
 
startTimer(int) - Static method in class astex.Util
Start the specified time.
stepMultiple - Static variable in class astex.ViewCommand
 
STICK_COLOR - Static variable in class astex.sym
 
STICK_RADIUS - Static variable in class astex.sym
 
STICKS - Static variable in class astex.sym
 
stop() - Method in class MoleculeViewerApplet
 
stopTimer(String, int) - Static method in class astex.Util
Stop the current timer and return its delta in milliseconds.
store(DynamicArray) - Static method in class astex.Selection
Store the result of a selection expression.
STRING - Static variable in class astex.sym
 
string2level(String) - Static method in class astex.Log
Map a string level name to the corresponding int.
StringArray - Class in astex
An object that implements a dynamic array.
StringArray(int, int) - Constructor for class astex.StringArray
Constructor which specifies the initial size and the capacity increment.
StringArray() - Constructor for class astex.StringArray
Default constructor.
StringArray(int) - Constructor for class astex.StringArray
Constructor which specifies the initial size.
stringIsURL(String) - Static method in class astex.FILE
Does the resource look like it is a URL?
STRONTIUM - Static variable in class astex.PeriodicTable
 
style - Variable in class astex.Tmesh
Renderering Style.
subtract(Point3d) - Method in class astex.Point3d
Subtract the x, y and z coordinates from another Point3d from the coordinates of this point.
SULPHUR - Static variable in class astex.PeriodicTable
 
summariseMolecule(Molecule) - Static method in class astex.MoleculeIO
Summarise the contents of a molecule.
Surface - Static variable in class astex.Atom
The surfaced atom flag.
Surface - Static variable in class astex.Map
 
surface(float[], int, int, int, float, boolean, Tmesh) - Static method in class astex.March
Constructor.
Surface - Class in astex
A class for generating three dimensional surfaces.
Surface() - Constructor for class astex.Surface
 
SURFACE - Static variable in class astex.sym
 
SurfaceContext - Static variable in class astex.Atom
The surface context flag.
suspendAnimationThread(boolean) - Method in class astex.MoleculeViewer
Handle (de)activation of animation thread.
swapAxes(Point3d, Map) - Method in class astex.MoleculeRenderer
Map the point coordinates back into the map ordering.
SYBYL_ASCII - Static variable in class astex.Map
 
SybylMol2 - Static variable in class astex.MoleculeIO
SYBYL mol file.
sym - Class in astex
CUP generated class containing symbol constants.
sym() - Constructor for class astex.sym
 
symbol - Variable in class astex.AtomicElement
 
Symmetry - Class in astex
A class for generating symmetry related copies of molecules.
Symmetry() - Constructor for class astex.Symmetry
 
SymmetryMolecule - Static variable in class astex.Molecule
 

T

t0 - Variable in class astex.Tmesh
The indices of the points in the triangles.
t1 - Variable in class astex.Tmesh
The indices of the points in the triangles.
t2 - Variable in class astex.Tmesh
The indices of the points in the triangles.
tan - Static variable in class astex.Color32
 
tangentSphere(double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double[]) - Static method in class astex.Apollo
 
tangentSphere(double[][], double[], double[]) - Static method in class astex.Apollo
 
TANTALUM - Static variable in class astex.PeriodicTable
 
Target - Static variable in class astex.generic.GenericEvent
 
targetValue - Variable in class astex.EnergyTerm
The target value e.g.
tc2x - Static variable in class astex.ShadowCache
References to the triangle bounding sphere info.
tc2y - Static variable in class astex.ShadowCache
 
tcachex0 - Static variable in class astex.ShadowCache
Triangle cache for shadows.
tcachex1 - Static variable in class astex.ShadowCache
 
tcachex2 - Static variable in class astex.ShadowCache
 
tcachey0 - Static variable in class astex.ShadowCache
 
tcachey1 - Static variable in class astex.ShadowCache
 
tcachey2 - Static variable in class astex.ShadowCache
 
tcachez0 - Static variable in class astex.ShadowCache
 
tcachez1 - Static variable in class astex.ShadowCache
 
tcachez2 - Static variable in class astex.ShadowCache
 
tcen2dx - Static variable in class astex.ShadowCache
 
tcen2dy - Static variable in class astex.ShadowCache
 
tcenr - Static variable in class astex.ShadowCache
 
tcenx - Static variable in class astex.ShadowCache
 
tceny - Static variable in class astex.ShadowCache
 
tcenz - Static variable in class astex.ShadowCache
 
tcolor - Variable in class astex.Tmesh
The indices of the points in the triangles.
tcr - Static variable in class astex.ShadowCache
 
tcx - Static variable in class astex.ShadowCache
 
tcy - Static variable in class astex.ShadowCache
 
tcz - Static variable in class astex.ShadowCache
 
TECHNETIUM - Static variable in class astex.PeriodicTable
 
TELLURIUM - Static variable in class astex.PeriodicTable
 
TemporarilySelected - Static variable in class astex.Atom
The atom is temporarily selected.
TERBIUM - Static variable in class astex.PeriodicTable
 
Texgen - Class in astex
Class for generating various sorts of texture coordinates.
Texgen() - Constructor for class astex.Texgen
 
texture - Variable in class astex.Renderer
The current texture.
TEXTURE - Static variable in class astex.sym
 
Texture - Class in astex
 
Texture(int, int) - Constructor for class astex.Texture