Package org.openscience.cdk.smiles
Class DeduceBondSystemTool
- java.lang.Object
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- org.openscience.cdk.smiles.DeduceBondSystemTool
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@Deprecated public class DeduceBondSystemTool extends Object
Deprecated.Use the newerKekulization
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.
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Constructor Summary
Constructors Constructor Description DeduceBondSystemTool()
Deprecated.Constructor for the DeduceBondSystemTool object.DeduceBondSystemTool(AllRingsFinder ringFinder)
Deprecated.Constructor for the DeduceBondSystemTool object accepting a customAllRingsFinder
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method 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.
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Constructor Detail
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DeduceBondSystemTool
public DeduceBondSystemTool()
Deprecated.Constructor for the DeduceBondSystemTool object.
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DeduceBondSystemTool
public DeduceBondSystemTool(AllRingsFinder ringFinder)
Deprecated.Constructor for the DeduceBondSystemTool object accepting a customAllRingsFinder
.- Parameters:
ringFinder
- a customAllRingsFinder
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Method Detail
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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
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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.
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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 canceled
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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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