org.jmol.shapebio

Class BioShape

java.lang.Object

org.jmol.shape.Shape

org.jmol.shape.AtomShape

org.jmol.shapebio.BioShape

public class BioShape
extends AtomShape

Field Summary

Fields

Modifier and Type	Field and Description
private static int	ALPHA_CARBON_VISIBILITY_FLAG
(package private) int	bfactorMax
(package private) int	bfactorMin
BioPolymer	bioPolymer
static int	CARTOON_VISIBILITY_FLAG
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

Fields inherited from class org.jmol.shape.AtomShape

ac, atoms, bsSizeDefault, colixes, isActive, mad, mads, monomerCount, paletteIDs

Fields inherited from class org.jmol.shape.Shape

bsColixSet, bsSizeSet, gdata, isBioShape, ms, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, vf, vwr

Constructor Summary

Constructors

Constructor and Description
BioShape(BioShapeCollection shape, int modelIndex, BioPolymer bioPolymer)

Method Summary

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()
(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	setModelClickability()
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)

Methods inherited from class org.jmol.shape.AtomShape

getInfoAsString, getShapeState, getSize, initModelSet, setColixAndPalette, setPropAS, setSize, setSize2, setSizeRD, setSizeRD2

Methods inherited from class org.jmol.shape.Shape

appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, coordinateInRange, encodeColor, getColix, getColixA, getColixB, getColixI, getColorCommand, getColorCommandUnk, getFontCommand, getIndexFromName, getProperty, getPropertyData, getShapeDetail, getSizeG, getTranslucentLabel, getViewer, initializeShape, initShape, merge, setModelSet, setPropS, setShapeSizeRD, setShapeVisibility, setVisibilityFlags, wasClicked

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

modelIndex

public int modelIndex

modelVisibilityFlags

public int modelVisibilityFlags

shape

BioShapeCollection shape

bioPolymer

public BioPolymer bioPolymer

meshes

public Mesh[] meshes

meshReady

public boolean[] meshReady

colixesBack

public short[] colixesBack

monomers

public Monomer[] monomers

wingVectors

public javajs.util.V3[] wingVectors

leadAtomIndices

int[] leadAtomIndices

hasBfactorRange

boolean hasBfactorRange

bfactorMin

int bfactorMin

bfactorMax

int bfactorMax

range

int range

floatRange

float floatRange

CARTOON_VISIBILITY_FLAG

public static final int CARTOON_VISIBILITY_FLAG

ALPHA_CARBON_VISIBILITY_FLAG

private static final int ALPHA_CARBON_VISIBILITY_FLAG

eightPiSquared100

private static final double eightPiSquared100

See Also:

Constant Field Values

Constructor Detail

BioShape

BioShape(BioShapeCollection shape,
         int modelIndex,
         BioPolymer bioPolymer)

Method Detail

setProperty

public void setProperty(java.lang.String propertyName,
                        java.lang.Object value,
                        BS bsSelected)

Specified by:

setProperty in class Shape

getMonomers

public Group[] getMonomers()

Overrides:

getMonomers in class AtomShape

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

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

Overrides:

findNearestAtomIndex in class Shape

setMad

void setMad(short mad,
            BS bsSelected,
            float[] values)

getMad

private short getMad(int groupIndex,
                     short mad)

falsifyMesh

public void falsifyMesh()

falsifyNearbyMesh

private void falsifyNearbyMesh(int index)

setColixBS

void setColixBS(short colix,
                byte pid,
                BS bsSelected)

setColixes

void setColixes(short[] atomColixes,
                BS bsSelected)

setParams

public void setParams(java.lang.Object[] data,
                      int[] atomMap,
                      BS bsSelected)

setColixBack

void setColixBack(short colix,
                  BS bsSelected)

setTranslucent

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

setModelClickability

public void setModelClickability()

Overrides:

setModelClickability in class AtomShape