Package 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 Details

    • 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

    • eightPiSquared100

      private static final double eightPiSquared100
      See Also:

  • Constructor Details

  • Method Details

    • setProperty

      public void setProperty(String propertyName, Object value, javajs.util.BS bsSelected)
      Specified by:
      setProperty in class Shape

    • 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:
      ?

    • findNearestAtomIndex

      public void findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, javajs.util.BS bsNot)
      Overrides:
      findNearestAtomIndex in class Shape

    • 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

      public void setParams(Object[] data, int[] atomMap, javajs.util.BS bsSelected)

    • setTranslucent

      void setTranslucent(boolean isTranslucent, javajs.util.BS bsSelected, float translucentLevel)

    • setAtomClickability

      public void setAtomClickability()
      Overrides:
      setAtomClickability in class AtomShape

    • getBioShapeState

      void getBioShapeState(String type, boolean translucentAllowed, Map<String,javajs.util.BS> temp, Map<String,javajs.util.BS> temp2)

    • getShapeState

      public String getShapeState()
      Overrides:
      getShapeState in class AtomShape