org.openscience.cdk.fingerprint

Class PubchemFingerprinter

java.lang.Object

org.openscience.cdk.fingerprint.AbstractFingerprinter

org.openscience.cdk.fingerprint.PubchemFingerprinter

All Implemented Interfaces:

IFingerprinter

public class PubchemFingerprinter
extends AbstractFingerprinter
implements IFingerprinter

Generates a Pubchem fingerprint for a molecule. These fingerprints are described here and are of the structural key type, of length 881. See Fingerprinter for a more detailed description of fingerprints in general. This implementation is based on the public domain code made available by the NCGC here A fingerprint is generated for an AtomContainer with this code:

   Molecule molecule = new Molecule();
   PubchemFingerprinter fprinter = new PubchemFingerprinter();
   BitSet fingerprint = fprinter.getBitFingerprint(molecule);
   fprinter.getSize(); // returns 881
   fingerprint.length(); // returns the highest set bit
 

Note that the fingerprinter assumes that you have detected aromaticity and atom types before evaluating the fingerprint. Also the fingerprinter expects that explicit H's are present Note that this fingerprint is not particularly fast, as it will perform ring detection using AllRingsFinder as well as multiple SMARTS queries. Some SMARTS patterns have been modified from the original code, since they were based on explicit H matching. As a result, we replace the explicit H's with a query of the #<N>&!H0 where <N> is the atomic number. Thus bit 344 was originally [#6](~[#6])([H]) but is written here as [#6&!H0]~[#6]. In some cases, where the H count can be reduced to single possibility we directly use that H count. An example is bit 35, which was [#6](~[#6])(~[#6])(~[#6])([H]) and is rewritten as [#6H1](~[#6])(~[#6])(~[#6]). Warning - this class is not thread-safe and uses stores intermediate steps internally. Please use a seperate instance of the class for each thread.

Author:

Rajarshi Guha

Source code:

master

Belongs to CDK module:

fingerprint

Thread Safe: No

Keywords:

fingerprint, similarity

Field Summary

Fields

Modifier and Type	Field and Description
static int	FP_SIZE Number of bits in this fingerprint.

Constructor Summary

Constructors

Constructor and Description
PubchemFingerprinter(IChemObjectBuilder builder)

Method Summary

Methods

Modifier and Type	Method and Description
static BitSet	decode(String enc) Returns a fingerprint from a Base64 encoded Pubchem fingerprint.
IBitFingerprint	getBitFingerprint(IAtomContainer atomContainer) Calculate 881 bit Pubchem fingerprint for a molecule.
ICountFingerprint	getCountFingerprint(IAtomContainer container) Returns the count fingerprint for the given IAtomContainer.
byte[]	getFingerprintAsBytes() Returns the fingerprint generated for a molecule as a byte[].
Map<String,Integer>	getRawFingerprint(IAtomContainer iAtomContainer) Returns the raw representation of the fingerprint for the given IAtomContainer.
int	getSize() Get the size of the fingerprint.

Methods inherited from class org.openscience.cdk.fingerprint.AbstractFingerprinter

getFingerprint, getParameters, getVersionDescription

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.openscience.cdk.fingerprint.IFingerprinter

getFingerprint, getVersionDescription

Field Detail

FP_SIZE

public static final int FP_SIZE

Number of bits in this fingerprint.

See Also:

Constant Field Values

Constructor Detail

PubchemFingerprinter

public PubchemFingerprinter(IChemObjectBuilder builder)

Method Detail

getBitFingerprint

public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer)
                                  throws CDKException

Calculate 881 bit Pubchem fingerprint for a molecule. See here for a description of each bit position.

Specified by:

getBitFingerprint in interface IFingerprinter

Parameters:

atomContainer - the molecule to consider

Returns:

the fingerprint

Throws:

CDKException - if there is an error during substructure searching or atom typing

See Also:

getFingerprintAsBytes()

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 interface IFingerprinter

Parameters:

iAtomContainer - IAtomContainer for which the fingerprint should be calculated.

Returns:

the raw fingerprint

Throws:

CDKException

getSize

public int getSize()

Get the size of the fingerprint.

Specified by:

getSize in interface IFingerprinter

Returns:

The bit length of the fingerprint

getFingerprintAsBytes

public byte[] getFingerprintAsBytes()

Returns the fingerprint generated for a molecule as a byte[]. Note that this should be immediately called after calling getBitFingerprint(org.openscience.cdk.interfaces.IAtomContainer)

Returns:

The fingerprint as a byte array

See Also:

getBitFingerprint(org.openscience.cdk.interfaces.IAtomContainer)

decode

public static BitSet decode(String enc)

Returns a fingerprint from a Base64 encoded Pubchem fingerprint.

Parameters:

enc - The Base64 encoded fingerprint

Returns:

A BitSet corresponding to the input fingerprint

getCountFingerprint

public ICountFingerprint getCountFingerprint(IAtomContainer container)
                                      throws CDKException

Returns the count fingerprint for the given IAtomContainer.

Specified by:

getCountFingerprint in interface IFingerprinter

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.