public class BioShape extends AtomShape
Modifier and Type | Field and 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 |
ac, atoms, bsSizeDefault, colixes, isActive, mad, mads, monomerCount, paletteIDs
bsColixSet, bsSizeSet, isBioShape, ms, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, vf, vwr
Constructor and Description |
---|
BioShape(BioShapeCollection shape,
int modelIndex,
BioPolymer bioPolymer) |
Modifier and Type | Method and 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,
BS bsNot) |
private short |
getMad(int groupIndex,
short mad) |
Group[] |
getMonomers() |
void |
setAtomClickability() |
(package private) void |
setColixBack(short colix,
BS bsSelected) |
(package private) void |
setColixBS(short colix,
byte pid,
BS bsSelected) |
(package private) void |
setColixes(short[] atomColixes,
BS bsSelected) |
(package private) void |
setMad(short mad,
BS bsSelected,
float[] values) |
void |
setParams(java.lang.Object[] data,
int[] atomMap,
BS bsSelected) |
void |
setProperty(java.lang.String propertyName,
java.lang.Object value,
BS bsSelected) |
(package private) void |
setTranslucent(boolean isTranslucent,
BS bsSelected,
float translucentLevel) |
getInfoAsString, getShapeState, getSize, initModelSet, setColixAndPalette, setPropAS, setSize, setSize2, setSizeRD, setSizeRD2
appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, coordinateInRange, encodeColor, getColix, getColixA, getColixB, getColixI, getColorCommand, getColorCommandUnk, getFontCommand, getIndexFromName, getProperty, getPropertyData, getShapeDetail, getSizeG, getTranslucentLabel, initializeShape, initShape, merge, setModelSet, setModelVisibilityFlags, setPropS, setShapeSizeRD, setShapeVisibility, wasClicked
public int modelIndex
public int modelVisibilityFlags
BioShapeCollection shape
public BioPolymer bioPolymer
public Mesh[] meshes
public boolean[] meshReady
public short[] colixesBack
public Monomer[] monomers
public javajs.util.V3[] wingVectors
int[] leadAtomIndices
boolean hasBfactorRange
int bfactorMin
int bfactorMax
int range
float floatRange
private static final double eightPiSquared100
BioShape(BioShapeCollection shape, int modelIndex, BioPolymer bioPolymer)
public void setProperty(java.lang.String propertyName, java.lang.Object value, BS bsSelected)
setProperty
in class Shape
public Group[] getMonomers()
getMonomers
in class AtomShape
void calcBfactorRange()
short calcMeanPositionalDisplacement(int bFactor100)
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
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* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Isotropic B is defined as 8*pi**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
bFactor100
- public void findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, BS bsNot)
findNearestAtomIndex
in class Shape
void setMad(short mad, BS bsSelected, float[] values)
private short getMad(int groupIndex, short mad)
public void falsifyMesh()
private void falsifyNearbyMesh(int index)
void setColixBS(short colix, byte pid, BS bsSelected)
void setColixes(short[] atomColixes, BS bsSelected)
public void setParams(java.lang.Object[] data, int[] atomMap, BS bsSelected)
void setColixBack(short colix, BS bsSelected)
void setTranslucent(boolean isTranslucent, BS bsSelected, float translucentLevel)
public void setAtomClickability()
setAtomClickability
in class AtomShape