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 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.

  • Method Details

    • getIDStr

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

    • setAtomBits

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

    • setAtomBitsAndClear

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

    • addGroup

      public Group addGroup(Group group, int groupIndex)