Package org.jmol.shapebio
Class BioShapeCollection
- java.lang.Object
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- org.jmol.shape.Shape
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- org.jmol.shapebio.BioShapeCollection
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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
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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
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Fields inherited from class org.jmol.shape.Shape
bsColixSet, bsSizeSet, isBioShape, ms, myType, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, vf, vwr
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Constructor Summary
Constructors Constructor Description BioShapeCollection()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, javajs.util.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(javajs.util.BS bsModels)
protected void
setPropBSC(java.lang.String propertyName, java.lang.Object value, javajs.util.BS bsSelected)
void
setProperty(java.lang.String propertyName, java.lang.Object value, javajs.util.BS bsSelected)
void
setShapeSizeRD(int size, RadiusData rd, javajs.util.BS bsSelected)
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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
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Method Detail
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initModelSet
public final void initModelSet()
- Overrides:
initModelSet
in classShape
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replaceGroup
public void replaceGroup(Group g0, Group g1)
- Overrides:
replaceGroup
in classShape
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setShapeSizeRD
public void setShapeSizeRD(int size, RadiusData rd, javajs.util.BS bsSelected)
- Overrides:
setShapeSizeRD
in classShape
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setProperty
public void setProperty(java.lang.String propertyName, java.lang.Object value, javajs.util.BS bsSelected)
- Specified by:
setProperty
in classShape
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setPropBSC
protected void setPropBSC(java.lang.String propertyName, java.lang.Object value, javajs.util.BS bsSelected)
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getShapeState
public java.lang.String getShapeState()
- Specified by:
getShapeState
in classShape
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initialize
void initialize()
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findNearestAtomIndex
public void findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, javajs.util.BS bsNot)
- Overrides:
findNearestAtomIndex
in classShape
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setModelVisibilityFlags
public void setModelVisibilityFlags(javajs.util.BS bsModels)
- Overrides:
setModelVisibilityFlags
in classShape
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setAtomClickability
public void setAtomClickability()
- Overrides:
setAtomClickability
in classShape
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getMpsShapeCount
int getMpsShapeCount()
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getBioShape
public BioShape getBioShape(int i)
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