Class Bond

java.lang.Object
org.jmol.util.Edge
org.jmol.modelset.Bond
All Implemented Interfaces:
SimpleEdge
Direct Known Subclasses:
HBond

public class Bond extends Edge
  • Field Details

    • 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 Details

    • Bond

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

    • setMad

      public void setMad(short mad)
    • setShapeVisibility

      void setShapeVisibility(boolean isVisible)
    • getIdentity

      public String getIdentity()
    • isCovalent

      public boolean isCovalent()
      Specified by:
      isCovalent in interface SimpleEdge
      Specified by:
      isCovalent in class Edge
    • 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
    • getCovalentOrder

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

      public Atom getOtherAtom(Atom thisAtom)
    • is

      public boolean is(int bondType)
    • getOtherNode

      public SimpleNode getOtherNode(SimpleNode thisAtom)
    • setAtropisomerOptions

      public void setAtropisomerOptions()
    • getCIPChirality

      public 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 String toString()
      Overrides:
      toString in class Object
    • getAtom

      public SimpleNode getAtom(int i)
      Description copied from interface: SimpleEdge
      Get the respective atom, 0 or 1
      Returns:
      SimpleNode