org.openscience.cdk.fingerprint

Class HybridizationFingerprinter

java.lang.Object

org.openscience.cdk.fingerprint.AbstractFingerprinter

org.openscience.cdk.fingerprint.Fingerprinter

org.openscience.cdk.fingerprint.HybridizationFingerprinter

All Implemented Interfaces:

IFingerprinter

public class HybridizationFingerprinter
extends Fingerprinter
implements IFingerprinter

Generates a fingerprint for a given IAtomContainer. Fingerprints are one-dimensional bit arrays, where bits are set according to a the occurrence of a particular structural feature (See for example the Daylight inc. theory manual for more information). Fingerprints allow for a fast screening step to exclude candidates for a substructure search in a database. They are also a means for determining the similarity of chemical structures.

A fingerprint is generated for an AtomContainer with this code:

   Molecule molecule = new Molecule();
   IFingerprinter fingerprinter =
     new HybridizationFingerprinter();
   BitSet fingerprint = fingerprinter.getFingerprint(molecule);
   fingerprint.size(); // returns 1024 by default
   fingerprint.length(); // returns the highest set bit
 

The FingerPrinter assumes that hydrogens are explicitly given! Furthermore, if pseudo atoms or atoms with malformed symbols are present, their atomic number is taken as one more than the last element currently supported in PeriodicTable.

Unlike the Fingerprinter, this fingerprinter does not take into account aromaticity. Instead, it takes into account SP2 IAtomType.Hybridization.

Source code:

master

Belongs to CDK module:

standard

Keywords:

fingerprint, similarity

Field Summary

Fields inherited from class org.openscience.cdk.fingerprint.Fingerprinter

DEFAULT_SEARCH_DEPTH, DEFAULT_SIZE

Constructor Summary

Constructors

Constructor and Description
HybridizationFingerprinter() Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.
HybridizationFingerprinter(int size)
HybridizationFingerprinter(int size, int searchDepth) Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.

Method Summary

Modifier and Type	Method and Description
protected String	getBondSymbol(IBond bond) Gets the bond Symbol attribute of the Fingerprinter class.

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

encodePaths, findPathes, getBitFingerprint, getBitFingerprint, getCountFingerprint, getParameters, getRawFingerprint, getSearchDepth, getSize, setHashPseudoAtoms, setPathLimit

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

getFingerprint, 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

getBitFingerprint, getCountFingerprint, getFingerprint, getRawFingerprint, getSize, getVersionDescription

Constructor Detail

HybridizationFingerprinter

public HybridizationFingerprinter()

Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.

HybridizationFingerprinter

public HybridizationFingerprinter(int size)

HybridizationFingerprinter

public HybridizationFingerprinter(int size,
                                  int searchDepth)

Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.

Parameters:

size - The desired size of the fingerprint

searchDepth - The desired depth of search

Method Detail

getBondSymbol

protected String getBondSymbol(IBond bond)

Gets the bond Symbol attribute of the Fingerprinter class.

Overrides:

getBondSymbol in class Fingerprinter

Parameters:

bond - Description of the Parameter

Returns:

The bondSymbol value