java.lang.Object
- org.jmol.shape.Shape
- - org.jmol.shapebio.BioShapeCollection

Direct Known Subclasses:

Backbone, Ribbons, Rockets, Strands, Trace
```
public abstract class BioShapeCollection
extends Shape
```
Mps stands for Model-Polymer-Shape When a Cartoon is instantiated with a call to setSize(), it creates an MpsShape for each BioPolymer in the model set. It is these shapes that are the real "shapes". Unlike other shapes, which are indexed by atom and throughout the entire model set, these shapes are indexed by residue and are restricted to a given BioPolymer within a given Model. Model

Field Summary

Fields
Modifier and Type	Field	Description
`(package private) Atom[]`	`atoms`
`BioShape[]`	`bioShapes`
`(package private) boolean`	`isActive`
`(package private) short`	`madDnaRna`
`(package private) short`	`madHelixSheet`
`(package private) short`	`madOn`
`(package private) short`	`madTurnRandom`

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

Constructor Summary

Constructors
Constructor Description

BioShapeCollection()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, BS bsNot)`
`BioShape`	`getBioShape(int i)`
`(package private) int`	`getMpsShapeCount()`
`java.lang.String`	`getShapeState()`
`int`	`getSizeG(Group group)`
`(package private) void`	`initialize()`
`void`	`initModelSet()`
`void`	`initShape()`
`void`	`replaceGroup(Group g0, Group g1)`
`void`	`setAtomClickability()`
`void`	`setModelVisibilityFlags(BS bsModels)`
`protected void`	`setPropBSC(java.lang.String propertyName, java.lang.Object value, BS bsSelected)`
`void`	`setProperty(java.lang.String propertyName, java.lang.Object value, BS bsSelected)`
`void`	`setShapeSizeRD(int size, RadiusData rd, BS bsSelected)`

Methods inherited from class org.jmol.shape.Shape
appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, coordinateInRange, encodeColor, getColix, getColixA, getColixB, getColixI, getColorCommand, getColorCommandUnk, getFontCommand, getIndexFromName, getProperty, getPropertyData, getPropShape, getShapeDetail, getSize, getTranslucentLabel, initializeShape, setModelSet, setPropS, setSize, setSizeRD, wasClicked

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

Field Detail

atoms
```
Atom[] atoms
```

madOn
```
short madOn
```

madHelixSheet
```
short madHelixSheet
```

madTurnRandom
```
short madTurnRandom
```

madDnaRna
```
short madDnaRna
```

isActive
```
boolean isActive
```

bioShapes
```
public BioShape[] bioShapes
```

Constructor Detail
- BioShapeCollection
```
public BioShapeCollection()
```

Method Detail

initModelSet
```
public final void initModelSet()
```
Overrides:

initModelSet in class Shape

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

initShape in class Shape

getSizeG
```
public int getSizeG(Group group)
```
Overrides:

getSizeG in class Shape

Returns:

size

replaceGroup

public void replaceGroup(Group g0,
                         Group g1)

Overrides:: replaceGroup in class Shape

setShapeSizeRD

public void setShapeSizeRD(int size,
                           RadiusData rd,
                           BS bsSelected)

Overrides:: setShapeSizeRD in class Shape

setProperty

public void setProperty(java.lang.String propertyName,
                        java.lang.Object value,
                        BS bsSelected)

Specified by:: setProperty in class Shape

setPropBSC

protected void setPropBSC(java.lang.String propertyName,
                          java.lang.Object value,
                          BS bsSelected)

getShapeState
```
public java.lang.String getShapeState()
```
Specified by:

getShapeState in class Shape

initialize
```
void initialize()
```

findNearestAtomIndex

public void findNearestAtomIndex(int xMouse,
                                 int yMouse,
                                 Atom[] closest,
                                 BS bsNot)

Overrides:: findNearestAtomIndex in class Shape

setModelVisibilityFlags
```
public void setModelVisibilityFlags(BS bsModels)
```
Overrides:

setModelVisibilityFlags in class Shape

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

setAtomClickability in class Shape

getMpsShapeCount
```
int getMpsShapeCount()
```

getBioShape

public BioShape getBioShape(int i)

Class BioShapeCollection

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

atoms

madOn

madHelixSheet

madTurnRandom

madDnaRna

isActive

bioShapes

Constructor Detail

BioShapeCollection

Method Detail

initModelSet

initShape

getSizeG

replaceGroup

setShapeSizeRD

setProperty

setPropBSC

getShapeState

initialize

findNearestAtomIndex

setModelVisibilityFlags

setAtomClickability

getMpsShapeCount

getBioShape