Package org.jmol.util

Class Edge

    • Constructor Detail

      • Edge

        public Edge()
    • Method Detail

      • getAtomIndex1

        public abstract int getAtomIndex1()
      • getAtomIndex2

        public abstract int getAtomIndex2()
      • getCovalentOrder

        public abstract int getCovalentOrder()
        Specified by:
        getCovalentOrder in interface SimpleEdge
        Returns:
        the bond order 1-4 if it is covalent, or 0 if not.
      • isCovalent

        public abstract boolean isCovalent()
        Specified by:
        isCovalent in interface SimpleEdge
      • isHydrogen

        public abstract boolean isHydrogen()
      • getArgbHbondType

        public static int getArgbHbondType​(int order)
      • getBondOrderNumberFromOrder

        public static final java.lang.String getBondOrderNumberFromOrder​(int order)
        used for formatting labels and in the connect PARTIAL command
        Parameters:
        order -
        Returns:
        a string representation to preserve float n.m
      • getCmlBondOrder

        public static final java.lang.String getCmlBondOrder​(int order)
      • getBondOrderNameFromOrder

        public static final java.lang.String getBondOrderNameFromOrder​(int order)
      • getAtropismOrder

        public static int getAtropismOrder​(int nn,
                                           int mm)
      • getAtropismOrder12

        public static int getAtropismOrder12​(int nnmm)
      • getAtropismCode

        private static int getAtropismCode​(int order)
      • getAtropismNode

        public static Node getAtropismNode​(int order,
                                           Node a1,
                                           boolean isFirst)
      • isAtropism

        public static boolean isAtropism​(int order)
      • isOrderH

        public static boolean isOrderH​(int order)
      • getPartialBondDotted

        public static final int getPartialBondDotted​(int order)
      • getPartialBondOrder

        public static final int getPartialBondOrder​(int order)
      • getCovalentBondOrder

        protected static final int getCovalentBondOrder​(int order)
      • getBondOrderFromFloat

        public static final int getBondOrderFromFloat​(float fOrder)
      • getBondOrderFromString

        public static int getBondOrderFromString​(java.lang.String name)
      • getBondType

        public int getBondType()
        Description copied from interface: SimpleEdge
        Get the order of the bond. This could be covalent order, but also could be NEAR, FAR, etc.
        Specified by:
        getBondType in interface SimpleEdge
        Returns:
        order
      • setCIPChirality

        public void setCIPChirality​(int c)
        Parameters:
        c -
      • getCIPChirality

        public java.lang.String getCIPChirality​(boolean doCalculate)
        Parameters:
        doCalculate -
        Returns:
        CIP chirality label