ambit2.descriptors.fingerprints

Class PubChemFingerprinterAmbitSmarts

java.lang.Object

ambit2.descriptors.fingerprints.PubChemFingerprinterAmbitSmarts

All Implemented Interfaces:

org.openscience.cdk.fingerprint.IFingerprinter

public class PubChemFingerprinterAmbitSmarts
extends Object
implements org.openscience.cdk.fingerprint.IFingerprinter

Reimplemented org.openscience.cdk.fingerprint.PubchemFingerprinter for performance reasons

Author:

Nikolay Kochev nick@uni-plovdiv.bg

Field Summary

Fields

Modifier and Type	Field and Description
static int	FP_SIZE

Constructor Summary

Constructors

Constructor and Description
PubChemFingerprinterAmbitSmarts()

Method Summary

Modifier and Type	Method and Description
static BitSet	decode(String enc) Returns a fingerprint from a Base64 encoded Pubchem fingerprint.
org.openscience.cdk.fingerprint.IBitFingerprint	getBitFingerprint(org.openscience.cdk.interfaces.IAtomContainer arg0)
org.openscience.cdk.fingerprint.ICountFingerprint	getCountFingerprint(org.openscience.cdk.interfaces.IAtomContainer arg0)
BitSet	getFingerprint(org.openscience.cdk.interfaces.IAtomContainer atomContainer) CDK 1.5.15
byte[]	getFingerprintAsBytes() Returns the fingerprint generated for a molecule as a byte[].
Map<String,Integer>	getRawFingerprint(org.openscience.cdk.interfaces.IAtomContainer arg0)
int	getSize() Get the size of the fingerprint.
String	getVersionDescription()

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

See Also:

Constant Field Values

Constructor Detail

PubChemFingerprinterAmbitSmarts

public PubChemFingerprinterAmbitSmarts()

Method Detail

getBitFingerprint

public org.openscience.cdk.fingerprint.IBitFingerprint getBitFingerprint(org.openscience.cdk.interfaces.IAtomContainer arg0)
                                                                  throws org.openscience.cdk.exception.CDKException

Specified by:

getBitFingerprint in interface org.openscience.cdk.fingerprint.IFingerprinter

Throws:

org.openscience.cdk.exception.CDKException

getCountFingerprint

public org.openscience.cdk.fingerprint.ICountFingerprint getCountFingerprint(org.openscience.cdk.interfaces.IAtomContainer arg0)
                                                                      throws org.openscience.cdk.exception.CDKException

Specified by:

getCountFingerprint in interface org.openscience.cdk.fingerprint.IFingerprinter

Throws:

org.openscience.cdk.exception.CDKException

getRawFingerprint

public Map<String,Integer> getRawFingerprint(org.openscience.cdk.interfaces.IAtomContainer arg0)
                                      throws org.openscience.cdk.exception.CDKException

Specified by:

getRawFingerprint in interface org.openscience.cdk.fingerprint.IFingerprinter

Throws:

org.openscience.cdk.exception.CDKException

getFingerprint

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

CDK 1.5.15

Specified by:

getFingerprint in interface org.openscience.cdk.fingerprint.IFingerprinter

Throws:

org.openscience.cdk.exception.CDKException

getSize

public int getSize()

Get the size of the fingerprint.

Specified by:

getSize in interface org.openscience.cdk.fingerprint.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 getFingerprint(org.openscience.cdk.interfaces.IAtomContainer)

Returns:

The fingerprint as a byte array

See Also:

getFingerprint(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

getVersionDescription

public String getVersionDescription()

Specified by:

getVersionDescription in interface org.openscience.cdk.fingerprint.IFingerprinter