Package org.jmol.util

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 Detail

      • 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 aotm
      • 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

        javajs.util.P3 getXYZ()
        Returns:
        the position of this atom