Class BioShape
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Field Summary
FieldsModifier and TypeFieldDescription(package private) int
(package private) int
short[]
private static final double
(package private) float
(package private) boolean
(package private) int[]
Mesh[]
boolean[]
int
int
Monomer[]
(package private) int
(package private) BioShapeCollection
javajs.util.V3[]
Fields inherited from class org.jmol.shape.AtomShape
bsSizeDefault, colixes, isActive, isSet, mad, mads, monomerCount, paletteIDs
Fields inherited from class org.jmol.shape.Shape
bsColixSet, bsSizeSet, isBioShape, ms, myType, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, vf, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescription(package private) void
(package private) short
calcMeanPositionalDisplacement
(int bFactor100) Calculates the mean positional displacement in milliAngstroms.void
private void
falsifyNearbyMesh
(int index) void
findNearestAtomIndex
(int xMouse, int yMouse, Atom[] closest, javajs.util.BS bsNot) (package private) void
getBioShapeState
(String type, boolean translucentAllowed, Map<String, javajs.util.BS> temp, Map<String, javajs.util.BS> temp2) private short
getMad
(int groupIndex, short mad) void
(package private) void
setColixBack
(short colix, javajs.util.BS bsSelected) (package private) void
setColixBS
(short colix, byte pid, javajs.util.BS bsSelected) (package private) void
setColixes
(short[] atomColixes, javajs.util.BS bsSelected) (package private) void
setMad
(short mad, javajs.util.BS bsSelected, float[] values) void
void
setProperty
(String propertyName, Object value, javajs.util.BS bsSelected) (package private) void
setTranslucent
(boolean isTranslucent, javajs.util.BS bsSelected, float translucentLevel) Methods inherited from class org.jmol.shape.AtomShape
checkColixLength, getInfoAsString, getSize, initModelSet, initShape, 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, getPropShape, getShapeDetail, getSizeG, getTranslucentLabel, initializeShape, replaceGroup, setModelSet, setModelVisibilityFlags, setPropS, setShapeSizeRD, wasClicked
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Field Details
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modelIndex
public int modelIndex -
modelVisibilityFlags
public int modelVisibilityFlags -
shape
BioShapeCollection shape -
bioPolymer
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meshes
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meshReady
public boolean[] meshReady -
colixesBack
public short[] colixesBack -
monomers
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wingVectors
public javajs.util.V3[] 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:
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Constructor Details
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BioShape
BioShape(BioShapeCollection shape, int modelIndex, BioPolymer bioPolymer)
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Method Details
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setProperty
- Specified by:
setProperty
in classShape
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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<u**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:
- ?
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findNearestAtomIndex
- Overrides:
findNearestAtomIndex
in classShape
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setMad
void setMad(short mad, javajs.util.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, javajs.util.BS bsSelected) -
setColixBack
void setColixBack(short colix, javajs.util.BS bsSelected) -
setColixes
void setColixes(short[] atomColixes, javajs.util.BS bsSelected) -
setParams
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setTranslucent
void setTranslucent(boolean isTranslucent, javajs.util.BS bsSelected, float translucentLevel) -
setAtomClickability
public void setAtomClickability()- Overrides:
setAtomClickability
in classAtomShape
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getBioShapeState
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getShapeState
- Overrides:
getShapeState
in classAtomShape
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