Class AminoMonomer

All Implemented Interfaces:
Structure

public class AminoMonomer extends AlphaMonomer
  • Field Details

  • Constructor Details

    • AminoMonomer

      protected AminoMonomer()
  • Method Details

    • validateAndAllocate

      static Monomer validateAndAllocate(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)
    • isBondedCorrectlyRange

      private static boolean isBondedCorrectlyRange(int offset1, int offset2, int firstAtomIndex, byte[] offsets, Atom[] atoms)
    • isBondedCorrectly

      private static boolean isBondedCorrectly(int firstAtomIndex, byte[] offsets, Atom[] atoms)
    • isAminoMonomer

      boolean isAminoMonomer()
    • getNitrogenAtom

      public Atom getNitrogenAtom()
      Overrides:
      getNitrogenAtom in class Group
    • getCarbonylCarbonAtom

      public Atom getCarbonylCarbonAtom()
    • getCarbonylOxygenAtom

      public Atom getCarbonylOxygenAtom()
      Overrides:
      getCarbonylOxygenAtom in class Group
    • getInitiatorAtom

      Atom getInitiatorAtom()
      Overrides:
      getInitiatorAtom in class Monomer
    • getTerminatorAtom

      Atom getTerminatorAtom()
      Overrides:
      getTerminatorAtom in class Monomer
    • hasOAtom

      boolean hasOAtom()
    • isConnectedAfter

      boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
      Overrides:
      isConnectedAfter in class AlphaMonomer
    • findNearestAtomIndex

      void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
      Description copied from class: Monomer
      Selects LeadAtom when this Monomer is clicked iff it is closer to the user.
      Overrides:
      findNearestAtomIndex in class Monomer
      Parameters:
      x -
      y -
      closest -
      madBegin -
      madEnd -
    • resetHydrogenPoint

      public void resetHydrogenPoint()
    • getNitrogenHydrogenPoint

      javajs.util.P3 getNitrogenHydrogenPoint()
    • getExplicitNH

      public Atom getExplicitNH()
    • getNHPoint

      public boolean getNHPoint(javajs.util.P3 aminoHydrogenPoint, javajs.util.V3 vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens)
    • getQuaternionFrameCenter

      javajs.util.P3 getQuaternionFrameCenter(char qType)
      Overrides:
      getQuaternionFrameCenter in class AlphaMonomer
      Parameters:
      qType -
      Returns:
      center
    • getQuaternion

      public javajs.util.Quat getQuaternion(char qType)
      Overrides:
      getQuaternion in class AlphaMonomer
      Parameters:
      qType -
      Returns:
      quaternion
    • getStructureId

      public String getStructureId()
      Overrides:
      getStructureId in class Monomer
    • getProteinStructureTag

      public String getProteinStructureTag()
      Overrides:
      getProteinStructureTag in class Group
    • getBSSideChain

      public javajs.util.BS getBSSideChain()
      Overrides:
      getBSSideChain in class Group
    • clear

      private void clear(javajs.util.BS bs, Atom a, boolean andH)