org.openscience.cdk.smiles

Class DeduceBondSystemTool

java.lang.Object

org.openscience.cdk.smiles.DeduceBondSystemTool

Deprecated.

Use the newer Kekulization

@Deprecated
public class DeduceBondSystemTool
extends Object

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:

master

Belongs to CDK module:

smiles

Thread Safe: No

Keywords:

bond order

Constructor Summary

Constructors

Constructor and Description
DeduceBondSystemTool() Deprecated. Constructor for the DeduceBondSystemTool object.
DeduceBondSystemTool(AllRingsFinder ringFinder) Deprecated. Constructor for the DeduceBondSystemTool object accepting a custom AllRingsFinder.

Method Summary

Methods

Modifier and Type	Method and Description
IAtomContainer	fixAromaticBondOrders(IAtomContainer atomContainer) Deprecated. Added missing bond orders based on atom type information.
boolean	isInterrupted() Deprecated. Returns if the next or running calculation should be interrupted.
boolean	isOK(IAtomContainer m) Deprecated. Determines if, according to the algorithms implemented in this class, the given AtomContainer has properly distributed double bonds.
void	setInterrupted(boolean interrupted) Deprecated. Sets if the calculation should be interrupted.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

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