org.jmol.shapebio

Class BioShapeCollection

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 and 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, gdata, isBioShape, ms, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, vf, vwr

Constructor Summary

Constructors

Constructor and Description
BioShapeCollection()

Method Summary

Modifier and Type	Method and 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	setModelClickability()
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)
void	setVisibilityFlags(BS bs)

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, getShapeDetail, getSize, getTranslucentLabel, getViewer, initializeShape, initShape, merge, setModelSet, setPropS, setShapeVisibility, 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

getSizeG

public int getSizeG(Group group)

Overrides:

getSizeG in class Shape

Returns:

size

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

setVisibilityFlags

public void setVisibilityFlags(BS bs)

Overrides:

setVisibilityFlags in class Shape

setModelClickability

public void setModelClickability()

Overrides:

setModelClickability in class Shape

getMpsShapeCount

int getMpsShapeCount()

getBioShape

public BioShape getBioShape(int i)