Package org.openscience.cdk.fragment
Class ExhaustiveFragmenter
- java.lang.Object
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- org.openscience.cdk.fragment.ExhaustiveFragmenter
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- All Implemented Interfaces:
IFragmenter
public class ExhaustiveFragmenter extends Object implements IFragmenter
Generate fragments exhaustively. This fragmentation scheme simply breaks single non-ring bonds. By default fragments smaller than 6 atoms in size are not considered, but this can be changed by the user. Side chains are retained.- Author:
- Rajarshi Guha
- Source code:
- main
- Belongs to CDK module:
- fragment
- Keywords:
- fragment
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Constructor Summary
Constructors Constructor Description ExhaustiveFragmenter()
Instantiate fragmenter with default minimum fragment size.ExhaustiveFragmenter(int minFragSize)
Instantiate fragmenter with user specified minimum fragment size.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
generateFragments(IAtomContainer atomContainer)
Generate fragments for the input molecule.String[]
getFragments()
Get the fragments generated as SMILES strings.IAtomContainer[]
getFragmentsAsContainers()
Get the fragments generated asIAtomContainer
objects..void
setMinimumFragmentSize(int minFragSize)
Set the minimum fragment size.
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Constructor Detail
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ExhaustiveFragmenter
public ExhaustiveFragmenter()
Instantiate fragmenter with default minimum fragment size.
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ExhaustiveFragmenter
public ExhaustiveFragmenter(int minFragSize)
Instantiate fragmenter with user specified minimum fragment size.- Parameters:
minFragSize
- the minimum fragment size desired
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Method Detail
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setMinimumFragmentSize
public void setMinimumFragmentSize(int minFragSize)
Set the minimum fragment size.- Parameters:
minFragSize
- the smallest size fragment that will be returned
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generateFragments
public void generateFragments(IAtomContainer atomContainer) throws CDKException
Generate fragments for the input molecule.- Specified by:
generateFragments
in interfaceIFragmenter
- Parameters:
atomContainer
- The input molecule.- Throws:
CDKException
- if ring detection fails
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getFragments
public String[] getFragments()
Get the fragments generated as SMILES strings.- Specified by:
getFragments
in interfaceIFragmenter
- Returns:
- a String[] of the fragments.
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getFragmentsAsContainers
public IAtomContainer[] getFragmentsAsContainers()
Get the fragments generated asIAtomContainer
objects..- Specified by:
getFragmentsAsContainers
in interfaceIFragmenter
- Returns:
- a IAtomContainer[] of the fragments.
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