Package org.openscience.cdk.fingerprint
Class SignatureFingerprinter
- java.lang.Object
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- org.openscience.cdk.fingerprint.AbstractFingerprinter
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- org.openscience.cdk.fingerprint.SignatureFingerprinter
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- All Implemented Interfaces:
IFingerprinter
public class SignatureFingerprinter extends AbstractFingerprinter implements IFingerprinter
An implementation of aAtomSignature
-based fingerprint.- Source code:
- main
- Belongs to CDK module:
- signature
- Keywords:
- fingerprint
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Constructor Summary
Constructors Constructor Description SignatureFingerprinter()
Initialize the fingerprinter with a default signature depth of 1.SignatureFingerprinter(int depth)
Initialize the fingerprinter with a certain signature depth.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description IBitFingerprint
getBitFingerprint(IAtomContainer atomContainer)
Returns the bit fingerprint for the givenIAtomContainer
.ICountFingerprint
getCountFingerprint(IAtomContainer container)
Returns the count fingerprint for the givenIAtomContainer
.protected List<Map.Entry<String,String>>
getParameters()
Base classes should override this method to report the parameters they are configured with.Map<String,Integer>
getRawFingerprint(IAtomContainer atomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.int
getSize()
Returns the size (or length) of the fingerprint.-
Methods inherited from class org.openscience.cdk.fingerprint.AbstractFingerprinter
getFingerprint, getVersionDescription
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.fingerprint.IFingerprinter
getFingerprint, getVersionDescription
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Constructor Detail
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SignatureFingerprinter
public SignatureFingerprinter()
Initialize the fingerprinter with a default signature depth of 1.
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SignatureFingerprinter
public SignatureFingerprinter(int depth)
Initialize the fingerprinter with a certain signature depth.- Parameters:
depth
- The depth of the signatures to calculate.
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Method Detail
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getParameters
protected List<Map.Entry<String,String>> getParameters()
Description copied from class:AbstractFingerprinter
Base classes should override this method to report the parameters they are configured with.- Overrides:
getParameters
in classAbstractFingerprinter
- Returns:
- The key=value pairs of configured parameters
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getBitFingerprint
public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer) throws CDKException
Description copied from interface:IFingerprinter
Returns the bit fingerprint for the givenIAtomContainer
.- Specified by:
getBitFingerprint
in interfaceIFingerprinter
- Parameters:
atomContainer
-IAtomContainer
for which the fingerprint should be calculated.- Returns:
- the bit fingerprint
- Throws:
CDKException
- may be thrown if there is an error during aromaticity detection or (for key based fingerprints) if there is a SMARTS parsing error
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getRawFingerprint
public Map<String,Integer> getRawFingerprint(IAtomContainer atomContainer) throws CDKException
Description copied from interface:IFingerprinter
Returns the raw representation of the fingerprint for the given IAtomContainer. The raw representation contains counts as well as the key strings.- Specified by:
getRawFingerprint
in interfaceIFingerprinter
- Parameters:
atomContainer
- IAtomContainer for which the fingerprint should be calculated.- Returns:
- the raw fingerprint
- Throws:
CDKException
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getSize
public int getSize()
Description copied from interface:IFingerprinter
Returns the size (or length) of the fingerprint.- Specified by:
getSize
in interfaceIFingerprinter
- Returns:
- the size of the fingerprint
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getCountFingerprint
public ICountFingerprint getCountFingerprint(IAtomContainer container) throws CDKException
Description copied from interface:IFingerprinter
Returns the count fingerprint for the givenIAtomContainer
.- Specified by:
getCountFingerprint
in interfaceIFingerprinter
- Parameters:
container
-IAtomContainer
for which the fingerprint should be calculated.- Returns:
- the count fingerprint
- Throws:
CDKException
- if there is an error during aromaticity detection or (for key based fingerprints) if there is a SMARTS parsing error.
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