Field Detail

• alphaOffsets

  static final byte[] alphaOffsets

• proteinStructure

  public ProteinStructure proteinStructure

• nitrogenHydrogenPoint

  protected javajs.util.P3 nitrogenHydrogenPoint

Constructor Detail

• AlphaMonomer

  protected AlphaMonomer()

Method Detail

• 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,
                                      java.lang.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 java.lang.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)