Class EStateFingerprinter
- java.lang.Object
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- org.openscience.cdk.fingerprint.AbstractFingerprinter
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- org.openscience.cdk.fingerprint.EStateFingerprinter
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- All Implemented Interfaces:
IFingerprinter
public class EStateFingerprinter extends AbstractFingerprinter implements IFingerprinter
This fingerprinter generates 79 bit fingerprints using the E-State fragments.The E-State fragments are those described in [Hall, L.H. and Kier, L.B. . Journal of Chemical Information and Computer Science. 1995. 35] and the SMARTS patterns were taken from RDKit. Note that this fingerprint simply indicates the presence or occurrence of the fragments. If you need counts of the fragments take a look at
KierHallSmartsDescriptor
, which also lists the substructures corresponding to each bit position.This class assumes that aromaticity perception and atom typing have been performed prior to generating the fingerprint. Warning - ESTATE substructure keys cannot be used for substructure filtering. It is possible for some keys to match substructures and not match the superstructures. Some keys check for hydrogen counts which may not be preserved in a superstructure.
Important! this fingerprint can not be used for substructure screening.- Author:
- Rajarhi Guha
- Source code:
- main
- Belongs to CDK module:
- fingerprint
- Keywords:
- fingerprint, similarity, estate
- Created on:
- 2008-07-23
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Constructor Summary
Constructors Constructor Description EStateFingerprinter()
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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
.Map<String,Integer>
getRawFingerprint(IAtomContainer iAtomContainer)
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, getParameters, 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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Method Detail
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getBitFingerprint
public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer) throws CDKException
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 iAtomContainer) throws CDKException
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:
iAtomContainer
- IAtomContainer for which the fingerprint should be calculated.- Returns:
- the raw fingerprint
- Throws:
CDKException
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getSize
public int getSize()
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
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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