ambit2.descriptors.fingerprints

Class PubChemFingerprinter

java.lang.Object

ambit2.descriptors.fingerprints.PubChemFingerprinter

public class PubChemFingerprinter
extends Object

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 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

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()

Method Summary

Modifier and Type	Method and Description
static BitSet	decode(String enc) Returns a fingerprint from a Base64 encoded Pubchem fingerprint.
BitSet	getFingerprint(org.openscience.cdk.interfaces.IAtomContainer atomContainer) Calculate 881 bit Pubchem fingerprint for a molecule.
byte[]	getFingerprintAsBytes() Returns the fingerprint generated for a molecule as a byte[].
int	getSize()

Methods inherited from class java.lang.Object

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

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()

Method Detail

getFingerprint

public BitSet getFingerprint(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
                      throws org.openscience.cdk.exception.CDKException

Calculate 881 bit Pubchem fingerprint for a molecule.

See here for a description of each bit position.

Parameters:

atomContainer - the molecule to consider

Returns:

the fingerprint

Throws:

org.openscience.cdk.exception.CDKException - if there is an error during substructure searching or atom typing

See Also:

getFingerprintAsBytes()

getSize

public int getSize()

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