Package org.jmol.modelset

Class Chain

java.lang.Object
org.jmol.modelset.Chain
All Implemented Interfaces:
Structure
public final class Chain extends Object implements Structure
A Model is a collection of Chains of Groups of Atoms. Chains hold overall information relating to a Monomer, particularly whether this monomer is RNA or DNA.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    int
    chainID
    chainID is either the integer form of a single character or a pointer into a map held in Viewer that allows retrieval of a longer string
    int
    chainNo
    chainNo is for information purposes only; retrieved by {atoms}.chainNo
    int
    groupCount
     
    Group[]
    groups
    Groups form the essence of what a Chain is.
    Model
    model
     
    int
    selectedGroupCount
    Calculated just prior to coloring by group so that the range is appropriate for each chain.

  • Constructor Summary

    Constructors
    Constructor
    Description
    Chain(Model model, int chainID, int chainNo)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    (package private) void
    calcSelectedGroupsCount(javajs.util.BS bsSelected)
    prior to coloring by group, we need the chain count per chain that is selected
    (package private) void
    fixIndices(int atomsDeleted, javajs.util.BS bsDeleted)
     
    String
    getIDStr()
     
    void
    setAtomBits(javajs.util.BS bs)
     
    void
    setAtomBitsAndClear(javajs.util.BS bs, javajs.util.BS bsOut)
     

    Methods inherited from class java.lang.Object

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

  • Field Details

    • model

      public Model model

    • chainID

      public int chainID
      chainID is either the integer form of a single character or a pointer into a map held in Viewer that allows retrieval of a longer string

    • chainNo

      public int chainNo
      chainNo is for information purposes only; retrieved by {atoms}.chainNo

    • groups

      public Group[] groups
      Groups form the essence of what a Chain is. This number will be 0 if there is no chain designation in the PDB or CIF file or when the file is not of a type that would have chain designations.

    • groupCount

      public int groupCount

    • selectedGroupCount

      public int selectedGroupCount
      Calculated just prior to coloring by group so that the range is appropriate for each chain.

  • Constructor Details

    • Chain

      Chain(Model model, int chainID, int chainNo)

  • Method Details

    • getIDStr

      public String getIDStr()
      Returns:
      actual string form of the chain identifier

    • calcSelectedGroupsCount

      void calcSelectedGroupsCount(javajs.util.BS bsSelected)
      prior to coloring by group, we need the chain count per chain that is selected
      Parameters:
      bsSelected -

    • fixIndices

      void fixIndices(int atomsDeleted, javajs.util.BS bsDeleted)

    • setAtomBits

      public void setAtomBits(javajs.util.BS bs)
      Specified by:
      setAtomBits in interface Structure

    • setAtomBitsAndClear

      public void setAtomBitsAndClear(javajs.util.BS bs, javajs.util.BS bsOut)
      Specified by:
      setAtomBitsAndClear in interface Structure