class BioShape
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static int |
ALPHA_CARBON_VISIBILITY_FLAG |
(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.Map<java.lang.String,java.util.BitSet> temp,
java.util.Map<java.lang.String,java.util.BitSet> 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
public static final int ALPHA_CARBON_VISIBILITY_FLAG
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.Map<java.lang.String,java.util.BitSet> temp, java.util.Map<java.lang.String,java.util.BitSet> temp2)
void setModelClickability()