Class DeduceBondSystemTool


  • @Deprecated
    public class DeduceBondSystemTool
    extends Object
    Deprecated.
    Use the newer Kekulization
    Tool that tries to deduce bond orders based on connectivity and hybridization for a number of common ring systems of up to seven-membered rings. It assumes that atom types have been perceived before that class is used.

    The calculation can be interrupted with setInterrupted(boolean), but assumes that this class is not used in a threaded fashion. When a calculation is interrupted, the boolean is reset to false.

    Author:
    Todd Martin
    This class is affected by these bug(s):
    1895805 1931262
    Source code:
    main
    Belongs to CDK module:
    smiles
    Thread Safe: No
    Keywords:
    bond order
    • Constructor Detail

      • DeduceBondSystemTool

        public DeduceBondSystemTool()
        Deprecated.
        Constructor for the DeduceBondSystemTool object.
      • DeduceBondSystemTool

        public DeduceBondSystemTool​(AllRingsFinder ringFinder)
        Deprecated.
        Constructor for the DeduceBondSystemTool object accepting a custom AllRingsFinder.
        Parameters:
        ringFinder - a custom AllRingsFinder.
    • Method Detail

      • isOK

        public boolean isOK​(IAtomContainer m)
                     throws CDKException
        Deprecated.
        Determines if, according to the algorithms implemented in this class, the given AtomContainer has properly distributed double bonds.
        Parameters:
        m - IAtomContainer to check the bond orders for.
        Returns:
        true, if bond orders are properly distributed
        Throws:
        CDKException - thrown when something went wrong
      • setInterrupted

        public void setInterrupted​(boolean interrupted)
        Deprecated.
        Sets if the calculation should be interrupted.
        Parameters:
        interrupted - true, if the calculation should be canceled
      • isInterrupted

        public boolean isInterrupted()
        Deprecated.
        Returns if the next or running calculation should be interrupted.
        Returns:
        true or false