Class Bond

  • All Implemented Interfaces:
    SimpleEdge
    Direct Known Subclasses:
    HBond

    public class Bond
    extends Edge
    • Field Detail

      • myVisibilityFlag

        public static final int myVisibilityFlag
      • atom1

        public Atom atom1
      • atom2

        public Atom atom2
      • mad

        public short mad
      • colix

        public short colix
      • shapeVisibilityFlags

        public int shapeVisibilityFlags
    • Constructor Detail

      • Bond

        public Bond​(Atom atom1,
                    Atom atom2,
                    int order,
                    short mad,
                    short colix)
        Parameters:
        atom1 -
        atom2 -
        order -
        mad -
        colix -
    • Method Detail

      • setMad

        public void setMad​(short mad)
      • setShapeVisibility

        void setShapeVisibility​(boolean isVisible)
      • getIdentity

        public java.lang.String getIdentity()
      • isHydrogen

        public boolean isHydrogen()
        Specified by:
        isHydrogen in class Edge
      • isStereo

        boolean isStereo()
      • isPartial

        boolean isPartial()
      • isAromatic

        boolean isAromatic()
      • getEnergy

        public float getEnergy()
      • getValence

        public int getValence()
      • deleteAtomReferences

        void deleteAtomReferences()
      • setTranslucent

        public void setTranslucent​(boolean isTranslucent,
                                   float translucentLevel)
      • setOrder

        public void setOrder​(int order)
      • getAtomIndex1

        public int getAtomIndex1()
        Specified by:
        getAtomIndex1 in class Edge
      • getAtomIndex2

        public int getAtomIndex2()
        Specified by:
        getAtomIndex2 in class Edge
      • getOtherAtom

        public Atom getOtherAtom​(Atom thisAtom)
      • is

        public boolean is​(int bondType)
      • setAtropisomerOptions

        public void setAtropisomerOptions​(javajs.util.BS bsA,
                                          javajs.util.BS bsB)
      • getCIPChirality

        public java.lang.String getCIPChirality​(boolean doCalculate)
        Not implemented.
        Overrides:
        getCIPChirality in class Edge
        Parameters:
        doCalculate -
        Returns:
        "" or "Z" or "E"
      • setCIPChirality

        public void setCIPChirality​(int c)
        Not implemented.
        Overrides:
        setCIPChirality in class Edge
        Parameters:
        c - [0:unknown; 1: Z; 2: E; 3: none]
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object