Package org.jmol.shapebio
Class BioShape
- java.lang.Object
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- org.jmol.shape.Shape
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- org.jmol.shape.AtomShape
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- org.jmol.shapebio.BioShape
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public class BioShape extends AtomShape
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Field Summary
Fields Modifier and Type Field Description (package private) int
bfactorMax
(package private) int
bfactorMin
BioPolymer
bioPolymer
short[]
colixesBack
private static double
eightPiSquared100
(package private) float
floatRange
(package private) boolean
hasBfactorRange
(package private) int[]
leadAtomIndices
Mesh[]
meshes
boolean[]
meshReady
int
modelIndex
int
modelVisibilityFlags
Monomer[]
monomers
(package private) int
range
(package private) BioShapeCollection
shape
javajs.util.V3[]
wingVectors
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Fields inherited from class org.jmol.shape.AtomShape
ac, atoms, bsSizeDefault, colixes, isActive, mad, mads, monomerCount, paletteIDs
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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 BioShape(BioShapeCollection shape, int modelIndex, BioPolymer bioPolymer)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) void
calcBfactorRange()
(package private) short
calcMeanPositionalDisplacement(int bFactor100)
Calculates the mean positional displacement in milliAngstroms.void
falsifyMesh()
private void
falsifyNearbyMesh(int index)
void
findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, javajs.util.BS bsNot)
(package private) void
getBioShapeState(String type, boolean translucentAllowed, Map<String,javajs.util.BS> temp, Map<String,javajs.util.BS> temp2)
private short
getMad(int groupIndex, short mad)
String
getShapeState()
void
setAtomClickability()
(package private) void
setColixBack(short colix, javajs.util.BS bsSelected)
(package private) void
setColixBS(short colix, byte pid, javajs.util.BS bsSelected)
(package private) void
setColixes(short[] atomColixes, javajs.util.BS bsSelected)
(package private) void
setMad(short mad, javajs.util.BS bsSelected, float[] values)
void
setParams(Object[] data, int[] atomMap, javajs.util.BS bsSelected)
void
setProperty(String propertyName, Object value, javajs.util.BS bsSelected)
(package private) void
setTranslucent(boolean isTranslucent, javajs.util.BS bsSelected, float translucentLevel)
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Methods inherited from class org.jmol.shape.AtomShape
checkColixLength, getInfoAsString, getSize, initModelSet, initShape, setColixAndPalette, setPropAS, setSize, setSize2, setSizeRD, setSizeRD2
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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, getSizeG, getTranslucentLabel, initializeShape, replaceGroup, setModelSet, setModelVisibilityFlags, setPropS, setShapeSizeRD, wasClicked
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Field Detail
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modelIndex
public int modelIndex
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modelVisibilityFlags
public int modelVisibilityFlags
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shape
BioShapeCollection shape
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bioPolymer
public BioPolymer bioPolymer
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meshes
public Mesh[] meshes
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meshReady
public boolean[] meshReady
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colixesBack
public short[] colixesBack
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monomers
public Monomer[] monomers
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wingVectors
public javajs.util.V3[] wingVectors
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leadAtomIndices
int[] leadAtomIndices
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hasBfactorRange
boolean hasBfactorRange
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bfactorMin
int bfactorMin
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bfactorMax
int bfactorMax
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range
int range
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floatRange
float floatRange
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eightPiSquared100
private static final double eightPiSquared100
- See Also:
- Constant Field Values
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Constructor Detail
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BioShape
BioShape(BioShapeCollection shape, int modelIndex, BioPolymer bioPolymer)
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Method Detail
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setProperty
public void setProperty(String propertyName, Object value, javajs.util.BS bsSelected)
- Specified by:
setProperty
in classShape
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calcBfactorRange
void calcBfactorRange()
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calcMeanPositionalDisplacement
short calcMeanPositionalDisplacement(int bFactor100)
Calculates the mean positional displacement in milliAngstroms.http://www.rcsb.org/pdb/lists/pdb-l/200303/000609.html
> -----Original Message----- > From: pdb-l-admin@sdsc.edu [mailto:pdb-l-admin@sdsc.edu] On > Behalf Of Philipp Heuser > Sent: Thursday, March 27, 2003 6:05 AM > To: pdb-l@sdsc.edu > Subject: pdb-l: temperature factor; occupancy > > > Hi all! > > Does anyone know where to find proper definitions for the > temperature factors > and the values for occupancy? > > Alright I do know, that the atoms with high temperature > factors are more > disordered than others, but what does a temperature factor of > a specific > value mean exactly. > > > Thanks in advance! > > Philipp > pdb-l: temperature factor; occupancy Bernhard Rupp br@llnl.gov Thu, 27 Mar 2003 08:01:29 -0800 * Previous message: pdb-l: temperature factor; occupancy * Next message: pdb-l: Structural alignment? * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Isotropic B is defined as 8*pi**2<u**2>. Meaning: eight pi squared =79 so B=79*mean square displacement (from rest position) of the atom. as u is in Angstrom, B must be in Angstrom squared. example: B=79A**2 thus, u=sqrt([79/79]) = 1 A mean positional displacement for atom. See also http://www-structure.llnl.gov/Xray/comp/comp_scat_fac.htm#Atomic for more examples. BR
- Parameters:
bFactor100
-- Returns:
- ?
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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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setMad
void setMad(short mad, javajs.util.BS bsSelected, float[] values)
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getMad
private short getMad(int groupIndex, short mad)
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falsifyMesh
public void falsifyMesh()
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falsifyNearbyMesh
private void falsifyNearbyMesh(int index)
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setColixBS
void setColixBS(short colix, byte pid, javajs.util.BS bsSelected)
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setColixBack
void setColixBack(short colix, javajs.util.BS bsSelected)
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setColixes
void setColixes(short[] atomColixes, javajs.util.BS bsSelected)
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setParams
public void setParams(Object[] data, int[] atomMap, javajs.util.BS bsSelected)
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setTranslucent
void setTranslucent(boolean isTranslucent, javajs.util.BS bsSelected, float translucentLevel)
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setAtomClickability
public void setAtomClickability()
- Overrides:
setAtomClickability
in classAtomShape
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getBioShapeState
void getBioShapeState(String type, boolean translucentAllowed, Map<String,javajs.util.BS> temp, Map<String,javajs.util.BS> temp2)
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getShapeState
public String getShapeState()
- Overrides:
getShapeState
in classAtomShape
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