Interface SimpleNode

All Known Subinterfaces:
Node
All Known Implementing Classes:
Atom, SmilesAtom
public interface SimpleNode
Just the bare minimum for CIP, and non-BioSMILES

  • Method Details

    • setCIPChirality

      void setCIPChirality(int rs)

    • getIsotopeNumber

      int getIsotopeNumber()

    • getAtomName

      String getAtomName()

    • getBondCount

      int getBondCount()
      Get the total number of bonds, including hydrogen bonds.
      Returns:
      number of bonds

    • getCovalentBondCount

      int getCovalentBondCount()
      Get the total number of covalent bonds, thus not including hydrogen bonds.
      Returns:
      number of bonds

    • getEdges

      SimpleEdge[] getEdges()
      Get the bond array, including hydrogen bonds.
      Returns:
      number of bonds

    • getElementNumber

      int getElementNumber()
      Returns:
      the atomic number for this atom

    • getFormalCharge

      int getFormalCharge()
      Returns:
      the formal charge for this atom

    • getIndex

      int getIndex()
      Returns:
      the unique ID number associated with this atom (which in Jmol is its position in the atoms[] array

    • getMass

      float getMass()
      Returns:
      the mass or, if specified, the mass number

    • getValence

      int getValence()
      Returns:
      the sum of the bond orders for this atom

    • getXYZ

      P3 getXYZ()
      Returns:
      the position of this atom