Class Chain

  • All Implemented Interfaces:
    Structure

    public final class Chain
    extends java.lang.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

      All Methods Instance Methods Concrete Methods 
      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)  
      java.lang.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 Detail

      • 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 Detail

      • Chain

        Chain​(Model model,
              int chainID,
              int chainNo)
    • Method Detail

      • getIDStr

        public java.lang.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