org.jmol.shapebio

Class BioShape

class BioShape extends Object

Field Summary
intbfactorMax
intbfactorMin
BioPolymerbioPolymer
BitSetbsColixSet
BitSetbsSizeDefault
BitSetbsSizeSet
short[]colixes
static doubleeightPiSquared100
floatfloatRange
booleanhasBfactorRange
booleanisActive
int[]leadAtomIndices
short[]mads
Mesh[]meshes
boolean[]meshReady
intmodelIndex
intmodelVisibilityFlags
intmonomerCount
Monomer[]monomers
byte[]paletteIDs
intrange
BioShapeCollectionshape
Vector3f[]wingVectors
Constructor Summary
BioShape(BioShapeCollection shape, int modelIndex, BioPolymer bioPolymer)
Method Summary
voidcalcBfactorRange()
shortcalcMeanPositionalDisplacement(int bFactor100)
Calculates the mean positional displacement in milliAngstroms.
voidfalsifyMesh(int index, boolean andNearby)
voidfindNearestAtomIndex(int xMouse, int yMouse, Atom[] closest)
voidsetColix(short colix, byte pid, BitSet bsSelected)
voidsetMad(short mad, BitSet bsSelected)
shortsetMad(int groupIndex, short mad)
voidsetModelClickability()
voidsetShapeState(Hashtable temp, Hashtable temp2)
voidsetTranslucent(boolean isTranslucent, BitSet bsSelected, float translucentLevel)

Field Detail

bfactorMax

int bfactorMax

bfactorMin

int bfactorMin

bioPolymer

BioPolymer bioPolymer

bsColixSet

BitSet bsColixSet

bsSizeDefault

BitSet bsSizeDefault

bsSizeSet

BitSet bsSizeSet

colixes

short[] colixes

eightPiSquared100

private static final double eightPiSquared100

floatRange

float floatRange

hasBfactorRange

boolean hasBfactorRange

isActive

boolean isActive

leadAtomIndices

int[] leadAtomIndices

mads

short[] mads

meshes

Mesh[] meshes

meshReady

boolean[] meshReady

modelIndex

int modelIndex

modelVisibilityFlags

int modelVisibilityFlags

monomerCount

int monomerCount

monomers

Monomer[] monomers

paletteIDs

byte[] paletteIDs

range

int range

shape

BioShapeCollection shape

wingVectors

Vector3f[] wingVectors

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: ?

falsifyMesh

void falsifyMesh(int index, boolean andNearby)

findNearestAtomIndex

void findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest)

setColix

void setColix(short colix, byte pid, BitSet bsSelected)

setMad

void setMad(short mad, BitSet bsSelected)

setMad

private short setMad(int groupIndex, short mad)

setModelClickability

void setModelClickability()

setShapeState

void setShapeState(Hashtable temp, Hashtable temp2)

setTranslucent

void setTranslucent(boolean isTranslucent, BitSet bsSelected, float translucentLevel)