FixBondOrdersTool (cdk 2.9 API)

java.lang.Object
- org.openscience.cdk.smiles.FixBondOrdersTool

```
@Deprecated
public class FixBondOrdersTool
extends Object
```
Deprecated.
use Kekulization
Class to Fix bond orders at present for Aromatic Rings only. Contains one public function: kekuliseAromaticRings(IAtomContainer molecule)
- Analyses which rings are marked aromatic/SP2/Planar3
- Splits rings into groups containing independent sets of single/fused rings
- Loops over each ring group
- Uses an adjacency matrix of bonds (rows) and atoms (columns) to represent each fused ring system
- Scans the adjacency matrix for bonds for which there is no order choice (eg - both bonds to the NH of pyrrole must be single)
- All choices made to match valency against bonds used (including implicit H atoms)
- Solves other bonds as possible - dependent on previous choices - makes free (random) choices only where necessary and possible
- Makes assumption that where there is a choice in bond order (not forced by previous choices) - either choice is consistent with correct solution
- Requires molecule with all rings to be solved being marked aromatic (SP2/Planar3 atoms). All bonds to non-ring atoms need to be fully defined (including implicit H atoms)
Author:

Kevin Lawson, Lucy Entwistle

Source code:
main

Belongs to CDK module:
smiles

Constructor Summary

Constructors
Constructor Description

FixBondOrdersTool()
Deprecated.

Constructor for the FixBondOrdersTool object.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`boolean`	`isInterrupted()`	Deprecated. Returns if the next or running calculation should be interrupted.
`IAtomContainer`	`kekuliseAromaticRings(IAtomContainer molecule)`	Deprecated. kekuliseAromaticRings - function to add double/single bond order information for molecules having rings containing all atoms marked SP2 or Planar3 hybridisation.
`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
  - FixBondOrdersTool
```
public FixBondOrdersTool()
```
    Deprecated.
    
    Constructor for the FixBondOrdersTool object.
- Method Detail
  - kekuliseAromaticRings
```
public IAtomContainer kekuliseAromaticRings(IAtomContainer molecule)
                                     throws CDKException
```
    Deprecated.
    
    kekuliseAromaticRings - function to add double/single bond order information for molecules having rings containing all atoms marked SP2 or Planar3 hybridisation.
    
    Parameters:
    
    molecule - The IAtomContainer to kekulise
    
    Returns:
    
    The IAtomContainer with kekule structure
    
    Throws:
    
    CDKException
  - setInterrupted
```
public void setInterrupted(boolean interrupted)
```
    Deprecated.
    
    Sets if the calculation should be interrupted.
    
    Parameters:
    
    interrupted - true, if the calculation should be cancelled
  - isInterrupted
```
public boolean isInterrupted()
```
    Deprecated.
    
    Returns if the next or running calculation should be interrupted.
    
    Returns:
    
    true or false