Class PhosphorusMonomer

    • Field Detail

      • phosphorusOffsets

        private static final byte[] phosphorusOffsets
      • MAX_ADJACENT_PHOSPHORUS_DISTANCE

        private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE
    • Constructor Detail

      • PhosphorusMonomer

        protected PhosphorusMonomer()
    • Method Detail

      • isNucleic

        public final boolean isNucleic()
        Description copied from class: Group
        group ID-based definition
        Overrides:
        isNucleic in class Group
        Returns:
        boolean
      • validateAndAllocateP

        static Monomer validateAndAllocateP​(Chain chain,
                                            java.lang.String group3,
                                            int seqcode,
                                            int firstIndex,
                                            int lastIndex,
                                            int[] specialAtomIndexes)
      • isDna

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

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

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

        public boolean isPyrimidine()
        Description copied from class: Group
        group ID-based definition
        Overrides:
        isPyrimidine in class Group
        Returns:
        boolean
      • isCA2

        protected boolean isCA2​(Monomer possiblyPreviousMonomer)
      • getQuaternion

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

        protected javajs.util.Quat getQuaternionP()
      • getHelixData

        public java.lang.Object getHelixData​(int tokType,
                                             char qType,
                                             int mStep)
        Overrides:
        getHelixData in class Group
        Returns:
        helix data of some sort