Package org.openscience.cdk.smiles
Class FixBondOrdersTool
java.lang.Object
org.openscience.cdk.smiles.FixBondOrdersTool
Deprecated.
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
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Constructor Summary
ConstructorsConstructorDescriptionDeprecated.Constructor for the FixBondOrdersTool object. -
Method Summary
Modifier and TypeMethodDescriptionboolean
Deprecated.Returns if the next or running calculation should be interrupted.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.
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Constructor Details
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FixBondOrdersTool
public FixBondOrdersTool()Deprecated.Constructor for the FixBondOrdersTool object.
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Method Details
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kekuliseAromaticRings
Deprecated.kekuliseAromaticRings - function to add double/single bond order information for molecules having rings containing all atoms marked SP2 or Planar3 hybridisation.- Parameters:
molecule
- TheIAtomContainer
to kekulise- Returns:
- The
IAtomContainer
with kekule structure - Throws:
CDKException
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setInterrupted
public void setInterrupted(boolean interrupted) Deprecated.Sets if the calculation should be interrupted.- Parameters:
interrupted
- true, if the calculation should be cancelled
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isInterrupted
public boolean isInterrupted()Deprecated.Returns if the next or running calculation should be interrupted.- Returns:
- true or false
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Kekulization