Package org.jmol.shapebio
Class BioShapeCollection
java.lang.Object
org.jmol.shape.Shape
org.jmol.shapebio.BioShapeCollection
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
FieldsModifier and TypeFieldDescription(package private) Atom[]
BioShape[]
(package private) boolean
(package private) short
(package private) short
(package private) short
(package private) short
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 -
Method Summary
Modifier and TypeMethodDescriptionvoid
findNearestAtomIndex
(int xMouse, int yMouse, Atom[] closest, javajs.util.BS bsNot) getBioShape
(int i) (package private) int
int
(package private) void
final void
void
void
replaceGroup
(Group g0, Group g1) void
void
setModelVisibilityFlags
(javajs.util.BS bsModels) protected void
setPropBSC
(String propertyName, Object value, javajs.util.BS bsSelected) void
setProperty
(String propertyName, Object value, javajs.util.BS bsSelected) void
setShapeSizeRD
(int size, RadiusData rd, javajs.util.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
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Field Details
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atoms
Atom[] atoms -
madOn
short madOn -
madHelixSheet
short madHelixSheet -
madTurnRandom
short madTurnRandom -
madDnaRna
short madDnaRna -
isActive
boolean isActive -
bioShapes
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Constructor Details
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BioShapeCollection
public BioShapeCollection()
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Method Details
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initModelSet
public final void initModelSet()- Overrides:
initModelSet
in classShape
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initShape
public void initShape() -
getSizeG
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replaceGroup
- Overrides:
replaceGroup
in classShape
- Parameters:
g0
-g1
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setShapeSizeRD
- Overrides:
setShapeSizeRD
in classShape
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setProperty
- Specified by:
setProperty
in classShape
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setPropBSC
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getShapeState
- Specified by:
getShapeState
in classShape
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initialize
void initialize() -
findNearestAtomIndex
- Overrides:
findNearestAtomIndex
in classShape
- Parameters:
xMouse
-yMouse
-closest
-bsNot
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setModelVisibilityFlags
public void setModelVisibilityFlags(javajs.util.BS bsModels) - Overrides:
setModelVisibilityFlags
in classShape
- Parameters:
bsModels
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setAtomClickability
public void setAtomClickability()- Overrides:
setAtomClickability
in classShape
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getMpsShapeCount
int getMpsShapeCount() -
getBioShape
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