Class AlphaMonomer

All Implemented Interfaces:
Structure
Direct Known Subclasses:
AminoMonomer

public class AlphaMonomer extends Monomer
  • Field Details

    • alphaOffsets

      static final byte[] alphaOffsets
    • proteinStructure

      public ProteinStructure proteinStructure
    • nitrogenHydrogenPoint

      protected javajs.util.P3 nitrogenHydrogenPoint
  • Constructor Details

    • AlphaMonomer

      protected AlphaMonomer()
  • Method Details

    • isProtein

      public boolean isProtein()
      Description copied from class: Group
      group ID-based definition
      Overrides:
      isProtein in class Group
      Returns:
      boolean
    • validateAndAllocateA

      static Monomer validateAndAllocateA(Chain chain, String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
    • isAlphaMonomer

      boolean isAlphaMonomer()
    • getStructure

      public Structure getStructure()
      Overrides:
      getStructure in class Group
    • setStructure

      void setStructure(ProteinStructure ps)
    • setStrucNo

      public void setStrucNo(int n)
      Overrides:
      setStrucNo in class Monomer
    • getProteinStructureType

      public STR getProteinStructureType()
      Overrides:
      getProteinStructureType in class Monomer
    • getProteinStructureSubType

      public STR getProteinStructureSubType()
      Overrides:
      getProteinStructureSubType in class Group
    • getStrucNo

      public int getStrucNo()
      Overrides:
      getStrucNo in class Group
    • isHelix

      public boolean isHelix()
      Overrides:
      isHelix in class Monomer
    • isSheet

      public boolean isSheet()
      Overrides:
      isSheet in class Monomer
    • setProteinStructureType

      public int setProteinStructureType(STR type, int monomerIndexCurrent)
      Overrides:
      setProteinStructureType in class Group
      Parameters:
      type -
      monomerIndexCurrent - a pointer to the current ProteinStructure
      Returns:
      a pointer to this ProteinStructure
    • getAtom

      public final Atom getAtom(byte specialAtomID)
    • getAtomPoint

      public final javajs.util.P3 getAtomPoint(byte specialAtomID)
    • isConnectedAfter

      boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
      Specified by:
      isConnectedAfter in class Monomer
    • getQuaternionFrameCenter

      javajs.util.P3 getQuaternionFrameCenter(char qType)
      Overrides:
      getQuaternionFrameCenter in class Monomer
      Returns:
      center
    • isWithinStructure

      public boolean isWithinStructure(STR type)
      Overrides:
      isWithinStructure in class Group
      Returns:
      T/F
    • getQuaternionFrameCenterAlpha

      protected javajs.util.P3 getQuaternionFrameCenterAlpha(char qType)
    • getHelixData

      public Object getHelixData(int tokType, char qType, int mStep)
      Overrides:
      getHelixData in class Group
      Returns:
      helix data of some sort
    • getQuaternion

      public javajs.util.Quat getQuaternion(char qType)
      Overrides:
      getQuaternion in class Group
      Returns:
      quaternion
    • getQuaternionAlpha

      protected javajs.util.Quat getQuaternionAlpha(char qType)