Class AlphaMonomer

    • Field Detail

      • alphaOffsets

        static final byte[] alphaOffsets
      • 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()
      • setStrucNo

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