org.openscience.cdk.smiles

Class FixBondOrdersTool

java.lang.Object

org.openscience.cdk.smiles.FixBondOrdersTool

Deprecated.

use Kekulization

@Deprecated
public class FixBondOrdersTool
extends Object

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:

master

Belongs to CDK module:

smiles

Constructor Summary

Constructors

Constructor and Description
FixBondOrdersTool() Deprecated. Constructor for the FixBondOrdersTool object.

Method Summary

Modifier and Type	Method and 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