chemaxon.descriptors

Class ECFPGenerator

java.lang.Object

chemaxon.descriptors.MDGenerator

chemaxon.descriptors.ECFPGenerator

All Implemented Interfaces:

chemaxon.license.Licensable

@PublicAPI
public class ECFPGenerator
extends MDGenerator
implements chemaxon.license.Licensable

The ECFPGenerator class generates ECFP fingerprints of molecular graphs.

Basic concepts
A binary string (series of 0 and 1) is constructed based on the local neighborhoods of the atoms. The length of the series is a predefined constant parameter. One further parameter specifies the diameter of the neighborhood considered for each atom.

Typical usage
For the sake of optimal memory usage, one instance of this class can generate fingerprints for a series of molecular graphs by the consecutive call to the generate() method.
In most cases, the generator is not intended to be used directly. When molecules are taken from files or databases, the corresponding MolecularDescriptors can be generated by the appropriate MDReader object. Alternatively, MolecularDescriptor.generate(final Molecule) is the simplest way to obtain a descriptor corresponding to a molecular structure.

Example of the direct use of the class within an application:

    ECFPGenerator gen = new ECFPGenerator();
    ECFP fp = new ECFP(new ECFPParameters());
    Molecule mol = getFirstMoleculeFromSomewhere();
    while (mol != null) {
        gen.generate(mol, fp);
        doSomethingWith(fp);
        mol = getNextMoleculeFromSomewhere();
    }
 

Since:

JChem 5.4

Author:

Peter Kovacs (pkovacs84)

Field Summary

Fields inherited from class chemaxon.descriptors.MDGenerator

createStatistics, density, freqCount, maxNonEmptyId, maxNonEmptyPercent, minNonEmptyId, minNonEmptyPercent, molCount, sumNonEmptyPercent

Constructor Summary

Constructors

Constructor and Description
ECFPGenerator() Creates a new instance of ECFPGenerator, which can be used to generate ECFP fingerprints for an arbitrary number of molecules.

Method Summary

Modifier and Type	Method and Description
protected int	calcFreqCount(MolecularDescriptor d) Updates statistics gathered on fingerprints generated and get the number of non-zero cells.
java.lang.String[]	generate(Molecule mol, MolecularDescriptor descr) Generates the ECFP fingerprint for the given molecule.
boolean	isLicensed() Returns information about the licensing of the product.
void	setLicenseEnvironment(java.lang.String env) Sets the license environment.

Methods inherited from class chemaxon.descriptors.MDGenerator

getAverageNonZeroRatio, getBrightestMolId, getDarkestMolId, getDensityCounts, getFrequencyCounts, getMaximumBitRatio, getMinimumBitRatio, getMoleculeCount, setCreateStatistics, updateStatistics

Methods inherited from class java.lang.Object

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

Constructor Detail

ECFPGenerator

public ECFPGenerator()

Creates a new instance of ECFPGenerator, which can be used to generate ECFP fingerprints for an arbitrary number of molecules.

Method Detail

isLicensed

public boolean isLicensed()

Returns information about the licensing of the product.

Specified by:

isLicensed in interface chemaxon.license.Licensable

Returns:

true if the product is correctly licensed

setLicenseEnvironment

public void setLicenseEnvironment(java.lang.String env)

Sets the license environment.

Specified by:

setLicenseEnvironment in interface chemaxon.license.Licensable

generate

public java.lang.String[] generate(Molecule mol,
                                   MolecularDescriptor descr)
                            throws MDGeneratorException

Generates the ECFP fingerprint for the given molecule. New instance of the ECFP object is not allocated, the ECFP provided as a method parameter is updated (and it has to be allocated and initialized by the client of this class).

Specified by:

generate in class MDGenerator

Parameters:

mol - molecule for which the fingerprint is created

descr - the ECFP fingerprint object

Returns:

names of tags (properties) set (added) during fingerprint generation, it is always null in the case of ECFP

Throws:

MDGeneratorException - in the case of any failures to generate the descriptor

calcFreqCount

protected int calcFreqCount(MolecularDescriptor d)

Updates statistics gathered on fingerprints generated and get the number of non-zero cells.

Overrides:

calcFreqCount in class MDGenerator

Parameters:

d - newly generated ECFP

Returns:

brightness of the fingerprint