Class NucleicMonomer

    • Constructor Detail

      • NucleicMonomer

        private NucleicMonomer()
    • Method Detail

      • validateAndAllocate

        public static Monomer validateAndAllocate​(Chain chain,
                                                  java.lang.String group3,
                                                  int seqcode,
                                                  int firstAtomIndex,
                                                  int lastAtomIndex,
                                                  int[] specialAtomIndexes)
      • set4

        private NucleicMonomer set4​(Chain chain,
                                    java.lang.String group3,
                                    int seqcode,
                                    int firstAtomIndex,
                                    int lastAtomIndex,
                                    byte[] offsets)
      • isNucleicMonomer

        public boolean isNucleicMonomer()
      • isDna

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

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

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

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

        public boolean isGuanine()
      • getC1P

        Atom getC1P()
      • getC2

        Atom getC2()
      • getC4P

        Atom getC4P()
      • getN1

        Atom getN1()
      • getN3

        Atom getN3()
      • getN2

        Atom getN2()
      • getN4

        Atom getN4()
      • getN6

        Atom getN6()
      • getO2

        Atom getO2()
      • getO4

        Atom getO4()
      • getO6

        Atom getO6()
      • getBaseRing6Points

        public void getBaseRing6Points​(javajs.util.P3[] pts)
      • getPoints

        private void getPoints​(byte[] a,
                               javajs.util.P3[] pts)
      • maybeGetBaseRing5Points

        public boolean maybeGetBaseRing5Points​(javajs.util.P3[] pts)
      • getRiboseRing5Points

        public void getRiboseRing5Points​(javajs.util.P3[] pts)
      • findNearestAtomIndex

        public void findNearestAtomIndex​(int x,
                                         int y,
                                         Atom[] closest,
                                         short madBegin,
                                         short madEnd)
        Description copied from class: Monomer
        Selects LeadAtom when this Monomer is clicked iff it is closer to the user.
        Overrides:
        findNearestAtomIndex in class Monomer
      • setRingsVisible

        public void setRingsVisible​(boolean isVisible)
      • setRingsClickable

        public void setRingsClickable()
      • getN0

        Atom getN0()
      • getHelixData

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

        public boolean getCrossLinkVector​(javajs.util.Lst<java.lang.Integer> vReturn,
                                          boolean crosslinkCovalent,
                                          boolean crosslinkHBond)
        Overrides:
        getCrossLinkVector in class Monomer
        Returns:
        T/F
      • getEdgePoints

        public boolean getEdgePoints​(javajs.util.P3[] pts)
      • addBasePair

        public void addBasePair​(BasePair bp)
      • setGroup1

        public void setGroup1​(char g)
      • getBasePairs

        public javajs.util.Lst<BasePair> getBasePairs()
        Returns:
        list of base pairs associated with this monomer, possibly more than one if noncanonical