Package org.jmol.modelset

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

      public boolean isPartial()
      Specified by:
      isPartial in class Edge

    • 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

    • isCovalentNotPartial0

      public boolean isCovalentNotPartial0()