org.jmol.shapebio
Class BioShape

java.lang.Object
  extended by org.jmol.shapebio.BioShape

 class BioShape
extends java.lang.Object


Field Summary
(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 Summary
BioShape(BioShapeCollection shape, int modelIndex, BioPolymer bioPolymer)
           
 
Method Summary
(package private)  void calcBfactorRange()
           
(package private)  short calcMeanPositionalDisplacement(int bFactor100)
          Calculates the mean positional displacement in milliAngstroms.
(package private)  void falsifyMesh(int index, boolean andNearby)
           
(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)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

modelIndex

int modelIndex

modelVisibilityFlags

int modelVisibilityFlags

shape

BioShapeCollection shape

bioPolymer

BioPolymer bioPolymer

meshes

Mesh[] meshes

meshReady

boolean[] meshReady

mads

short[] mads

colixes

short[] colixes

paletteIDs

byte[] paletteIDs

bsColixSet

java.util.BitSet bsColixSet

bsSizeSet

java.util.BitSet bsSizeSet

bsSizeDefault

java.util.BitSet bsSizeDefault

isActive

boolean isActive

monomerCount

int monomerCount

monomers

Monomer[] monomers

wingVectors

javax.vecmath.Vector3f[] wingVectors

leadAtomIndices

int[] leadAtomIndices

hasBfactorRange

boolean hasBfactorRange

bfactorMin

int bfactorMin

bfactorMax

int bfactorMax

range

int range

floatRange

float floatRange

eightPiSquared100

private static final double eightPiSquared100
See Also:
Constant Field Values
Constructor Detail

BioShape

BioShape(BioShapeCollection shape,
         int modelIndex,
         BioPolymer bioPolymer)
Method Detail

calcBfactorRange

void calcBfactorRange()

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. 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:
?

findNearestAtomIndex

void findNearestAtomIndex(int xMouse,
                          int yMouse,
                          Atom[] closest,
                          java.util.BitSet bsNot)

setMad

void setMad(short mad,
            java.util.BitSet bsSelected,
            float[] values)

setMad

private short setMad(int groupIndex,
                     short mad)

falsifyMesh

void falsifyMesh(int index,
                 boolean andNearby)

setColix

void setColix(short colix,
              byte pid,
              java.util.BitSet bsSelected)

setTranslucent

void setTranslucent(boolean isTranslucent,
                    java.util.BitSet bsSelected,
                    float translucentLevel)

setShapeState

void setShapeState(java.util.Hashtable temp,
                   java.util.Hashtable temp2)

setModelClickability

void setModelClickability()