Package org.openscience.cdk.smiles

Class DeduceBondSystemTool

java.lang.Object
org.openscience.cdk.smiles.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 Details

    • 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 Details

    • 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

    • fixAromaticBondOrders

      public IAtomContainer fixAromaticBondOrders(IAtomContainer atomContainer) throws CDKException
      Deprecated.
      Added missing bond orders based on atom type information.
      Parameters:
      atomContainer - IAtomContainer for which to distribute double bond orders
      Returns:
      a IAtomContainer with assigned double bonds.
      Throws:
      CDKException - if 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