Class AminoMonomer

    • Constructor Detail

      • AminoMonomer

        protected AminoMonomer()
    • Method Detail

      • validateAndAllocate

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

        private static boolean isBondedCorrectlyRange​(int offset1,
                                                      int offset2,
                                                      int firstAtomIndex,
                                                      byte[] offsets,
                                                      Atom[] atoms)
      • isBondedCorrectly

        private static boolean isBondedCorrectly​(int firstAtomIndex,
                                                 byte[] offsets,
                                                 Atom[] atoms)
      • isAminoMonomer

        boolean isAminoMonomer()
      • getCarbonylCarbonAtom

        public Atom getCarbonylCarbonAtom()
      • hasOAtom

        boolean hasOAtom()
      • findNearestAtomIndex

        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
      • resetHydrogenPoint

        public void resetHydrogenPoint()
      • getNitrogenHydrogenPoint

        javajs.util.P3 getNitrogenHydrogenPoint()
      • getExplicitNH

        public Atom getExplicitNH()
      • getNHPoint

        public boolean getNHPoint​(javajs.util.P3 aminoHydrogenPoint,
                                  javajs.util.V3 vNH,
                                  boolean jmolHPoint,
                                  boolean dsspIgnoreHydrogens)
      • getQuaternion

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

        private void clear​(BS bs,
                           Atom a,
                           boolean andH)