class BioShape
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
(package private) int |
bfactorMax |
(package private) int |
bfactorMin |
(package private) BioPolymer |
bioPolymer |
(package private) java.util.BitSet |
bsColixSet |
(package private) java.util.BitSet |
bsSizeDefault |
(package private) java.util.BitSet |
bsSizeSet |
(package private) short[] |
colixes |
private static double |
eightPiSquared100 |
(package private) float |
floatRange |
(package private) boolean |
hasBfactorRange |
(package private) boolean |
isActive |
(package private) int[] |
leadAtomIndices |
(package private) short[] |
mads |
(package private) Mesh[] |
meshes |
(package private) boolean[] |
meshReady |
(package private) int |
modelIndex |
(package private) int |
modelVisibilityFlags |
(package private) int |
monomerCount |
(package private) Monomer[] |
monomers |
(package private) byte[] |
paletteIDs |
(package private) int |
range |
(package private) BioShapeCollection |
shape |
(package private) javax.vecmath.Vector3f[] |
wingVectors |
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.
|
(package private) void |
falsifyMesh() |
private void |
falsifyNearbyMesh(int index) |
(package private) void |
findNearestAtomIndex(int xMouse,
int yMouse,
Atom[] closest,
java.util.BitSet bsNot) |
(package private) void |
setColix(short colix,
byte pid,
java.util.BitSet bsSelected) |
private short |
setMad(int groupIndex,
short mad) |
(package private) void |
setMad(short mad,
java.util.BitSet bsSelected,
float[] values) |
(package private) void |
setModelClickability() |
(package private) void |
setShapeState(java.util.Hashtable temp,
java.util.Hashtable temp2) |
(package private) void |
setTranslucent(boolean isTranslucent,
java.util.BitSet bsSelected,
float translucentLevel) |
int modelIndex
int modelVisibilityFlags
BioShapeCollection shape
BioPolymer bioPolymer
Mesh[] meshes
boolean[] meshReady
short[] mads
short[] colixes
byte[] paletteIDs
java.util.BitSet bsColixSet
java.util.BitSet bsSizeSet
java.util.BitSet bsSizeDefault
boolean isActive
int monomerCount
Monomer[] monomers
javax.vecmath.Vector3f[] 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)
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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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
- void findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, java.util.BitSet bsNot)
void setMad(short mad, java.util.BitSet bsSelected, float[] values)
private short setMad(int groupIndex, short mad)
void falsifyMesh()
private void falsifyNearbyMesh(int index)
void setColix(short colix, byte pid, java.util.BitSet bsSelected)
void setTranslucent(boolean isTranslucent, java.util.BitSet bsSelected, float translucentLevel)
void setShapeState(java.util.Hashtable temp, java.util.Hashtable temp2)
void setModelClickability()