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
Methods inherited from class org.jmol.shape.Shape |
appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, coordinateInRange, getColix, getColorCommand, getColorCommand, getFontCommand, getIndexFromName, getProperty, getProperty, getShapeCommands, getShapeCommands, getShapeDetail, getSize, getViewer, initializeShape, initShape, merge, setColix, setColix, setColix, setModelSet, setShapeProperty, setSize, setSize, setStateInfo, setStateInfo, wasClicked |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
atoms
Atom[] atoms
madOn
short madOn
madHelixSheet
short madHelixSheet
madTurnRandom
short madTurnRandom
madDnaRna
short madDnaRna
isActive
boolean isActive
bioShapes
BioShape[] bioShapes
BioShapeCollection
public BioShapeCollection()
initModelSet
public final void initModelSet()
- Overrides:
initModelSet
in class Shape
getSize
public int getSize(Group group)
- Overrides:
getSize
in class Shape
- Returns:
- size
setShapeSize
public void setShapeSize(int size,
RadiusData rd,
java.util.BitSet bsSelected)
- Overrides:
setShapeSize
in class Shape
setProperty
public void setProperty(java.lang.String propertyName,
java.lang.Object value,
java.util.BitSet bsSelected)
- Description copied from class:
Shape
- may come from any source -- executed AFTER a shape's own setProperty method
- Overrides:
setProperty
in class Shape
getShapeState
public java.lang.String getShapeState()
- Overrides:
getShapeState
in class Shape
initialize
void initialize()
findNearestAtomIndex
public void findNearestAtomIndex(int xMouse,
int yMouse,
Atom[] closest,
java.util.BitSet bsNot)
- Overrides:
findNearestAtomIndex
in class Shape
setVisibilityFlags
public void setVisibilityFlags(java.util.BitSet bs)
- Overrides:
setVisibilityFlags
in class Shape
setModelClickability
public void setModelClickability()
- Overrides:
setModelClickability
in class Shape
getMpsShapeCount
int getMpsShapeCount()
getBioShape
BioShape getBioShape(int i)