AtomShape

java.lang.Object
- org.jmol.shape.Shape
- - org.jmol.shape.AtomShape

Direct Known Subclasses:

Balls, BioShape, Dots, Ellipsoids, Halos, Labels, Measures, Polyhedra, Stars, Vectors
```
public abstract class AtomShape
extends Shape
```

Field Summary

Fields
Modifier and Type	Field and Description
`int`	`ac`
`Atom[]`	`atoms`
`BS`	`bsSizeDefault`
`short[]`	`colixes`
`boolean`	`isActive`
`short`	`mad`
`short[]`	`mads`
`int`	`monomerCount`
`byte[]`	`paletteIDs`
`private RadiusData`	`rd`

Fields inherited from class org.jmol.shape.Shape
bsColixSet, bsSizeSet, isBioShape, ms, myType, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, vf, vwr

Constructor Summary

Constructors
Constructor and Description

AtomShape()

Constructors
Constructor and Description
`AtomShape()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected int`	`checkColixLength(short colix, int n)`
`String`	`getInfoAsString(int i)`
`String`	`getShapeState()`
`int`	`getSize(int atomIndex)` overridden in Dots, CGOMesh, and AtomShape
`protected void`	`initModelSet()`
`void`	`initShape()`
`void`	`setAtomClickability()`
`protected void`	`setColixAndPalette(short colix, byte paletteID, int atomIndex)`
`protected void`	`setPropAS(String propertyName, Object value, BS bs)`
`protected void`	`setSize(int size, BS bsSelected)`
`protected void`	`setSize2(int size, BS bsSelected)`
`protected void`	`setSizeRD(RadiusData rd, BS bsSelected)`
`protected void`	`setSizeRD2(int i, RadiusData rd, boolean isVisible)`

Methods inherited from class org.jmol.shape.Shape
appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, coordinateInRange, encodeColor, findNearestAtomIndex, getColix, getColixA, getColixB, getColixI, getColorCommand, getColorCommandUnk, getFontCommand, getIndexFromName, getProperty, getPropertyData, getPropShape, getShapeDetail, getSizeG, getTranslucentLabel, initializeShape, replaceGroup, setModelSet, setModelVisibilityFlags, setProperty, setPropS, setShapeSizeRD, wasClicked

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

mad
```
public short mad
```

mads
```
public short[] mads
```

colixes
```
public short[] colixes
```

paletteIDs
```
public byte[] paletteIDs
```

ac
```
public int ac
```

atoms
```
public Atom[] atoms
```

isActive
```
public boolean isActive
```

monomerCount
```
public int monomerCount
```

bsSizeDefault
```
public BS bsSizeDefault
```

rd
```
private RadiusData rd
```

Constructor Detail
- AtomShape
```
public AtomShape()
```

Method Detail

initShape
```
public void initShape()
```
Specified by:

initShape in class Shape

initModelSet
```
protected void initModelSet()
```
Overrides:

initModelSet in class Shape

getSize
```
public int getSize(int atomIndex)
```
Description copied from class: Shape

overridden in Dots, CGOMesh, and AtomShape

Overrides:

getSize in class Shape

Returns:

size

setSize

protected void setSize(int size,
                       BS bsSelected)

Overrides:: setSize in class Shape

setSize2

protected void setSize2(int size,
                        BS bsSelected)

setSizeRD

protected void setSizeRD(RadiusData rd,
                         BS bsSelected)

Overrides:: setSizeRD in class Shape

setSizeRD2

protected void setSizeRD2(int i,
                          RadiusData rd,
                          boolean isVisible)

setPropAS

protected void setPropAS(String propertyName,
                         Object value,
                         BS bs)

checkColixLength

protected int checkColixLength(short colix,
                               int n)

setColixAndPalette

protected void setColixAndPalette(short colix,
                                  byte paletteID,
                                  int atomIndex)

setAtomClickability
```
public void setAtomClickability()
```
Overrides:

setAtomClickability in class Shape

getInfoAsString
```
public String getInfoAsString(int i)
```
Parameters:

i -

Returns:

script, but only for Measures

getShapeState
```
public String getShapeState()
```
Specified by:

getShapeState in class Shape

Class AtomShape

Field Summary

Fields inherited from class org.jmol.shape.Shape

Constructor Summary

Method Summary

Methods inherited from class org.jmol.shape.Shape

Methods inherited from class java.lang.Object

Field Detail

mad

mads

colixes

paletteIDs

ac

atoms

isActive

monomerCount

bsSizeDefault

rd

Constructor Detail

AtomShape

Method Detail

initShape

initModelSet

getSize

setSize

setSize2

setSizeRD

setSizeRD2

setPropAS

checkColixLength

setColixAndPalette

setAtomClickability

getInfoAsString

getShapeState