org.jmol.shapebio

Class BioShapeCollection

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
Atom[]atoms
BioShape[]bioShapes
booleanisActive
shortmadDnaRna
shortmadHelixSheet
shortmadOn
shortmadTurnRandom
Method Summary
voidfindNearestAtomIndex(int xMouse, int yMouse, Atom[] closest)
BioShapegetBioShape(int i)
intgetMpsShapeCount()
StringgetShapeState()
voidinitialize()
voidinitModelSet()
voidsetModelClickability()
voidsetProperty(String propertyName, Object value, BitSet bsSelected)
voidsetSize(int size, BitSet bsSelected)
voidsetVisibilityFlags(BitSet bs)

Field Detail

atoms

Atom[] atoms

bioShapes

BioShape[] bioShapes

isActive

boolean isActive

madDnaRna

short madDnaRna

madHelixSheet

short madHelixSheet

madOn

short madOn

madTurnRandom

short madTurnRandom

Method Detail

findNearestAtomIndex

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

getBioShape

BioShape getBioShape(int i)

getMpsShapeCount

int getMpsShapeCount()

getShapeState

public String getShapeState()

initialize

void initialize()

initModelSet

public final void initModelSet()

setModelClickability

public void setModelClickability()

setProperty

public void setProperty(String propertyName, Object value, BitSet bsSelected)

setSize

public void setSize(int size, BitSet bsSelected)

setVisibilityFlags

public void setVisibilityFlags(BitSet bs)