Package org.jmol.modelsetbio

Class AlphaMonomer

java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
org.jmol.modelsetbio.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)