chemaxon.descriptors

Class PFGenerator

java.lang.Object

chemaxon.descriptors.MDGenerator

chemaxon.descriptors.PFGenerator

@PublicAPI
public class PFGenerator
extends MDGenerator

The PFGenerator class generates 2-dimensional pharmacophore fingerprints for molecular graphs.

Basic concepts
The pharmacophore fingerprint is based on and created from atom centre based pharmacophoric point types that are identified and assigned by the PMapper class. All possible point pairs are recorded in the fingerprint and are represented in a histogram. Bins of such histogram are associated with topological distances (that is, length of shortest path) between pharmacophore point pairs. (See PharmacophoreFingerprint class for an elaborate description.)

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

      PMapper m = new PMapper( "pharmacophore_config.xml" );
      PFGenerator gen = new PFGenerator( m );
      gen.setUsePMAP( false ); // do not use existing PMAP tag in molecules
      PharmacophoreFingerprint pfp = new PharmacophoreFingerprint();
      pfp.setParameters(new PFParameters());
      String[] newTags = null;
      Molecule mol = getFirstMoleculeFromSomewhere();
      while ( mol != null ) {
          gen.generate( mol, p );
          doSomethingWith( p );
          mol = getNextMoleculeFromSomewhere();
      }
 

Since:

JChem 2.0

Author:

Miklos Vargyas

See Also:

PharmacophoreFingerprint, PMapper

Field Summary

Fields inherited from class chemaxon.descriptors.MDGenerator

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

Constructor Summary

Constructors

Constructor and Description
PFGenerator(PMapper pmapper) Creates a new instance of PFGenerator which can be used to generate fingerprints for an arbitrary number of molecules.

Method Summary

Modifier and Type	Method and Description
protected int	calcFreqCount(MolecularDescriptor d) Calculate and store in freqCount[] absolute frequency counts per cells.
java.lang.String[]	generate(Molecule m, MolecularDescriptor d) Generates the pharmacophore fingerprint of the given molecule.
java.lang.String	getPMap(Molecule m, PSymbols pSym) Gets pharmacophore map of the input molecule.
java.lang.String	getPMAPTagName() Gets the name of the SDfile tag (Molecule property) which stores the pharmacophore map data.
void	setPMAPTagName(java.lang.String tagName) Sets the name of the SDfile tag (Molecule property) which stores the pharmacophore map data.
void	setUsePMAP(boolean use) Omit or use pharmacophore map data optionally available in molecular structure.

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

PFGenerator

public PFGenerator(PMapper pmapper)

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

Parameters:

pmapper - assign pharmacophore type labels to atoms

Method Detail

setUsePMAP

public void setUsePMAP(boolean use)

Omit or use pharmacophore map data optionally available in molecular structure. If not to be used, the pharmacophore point map is generated, even in the case when the input molecule has already been assigned this data to.

Parameters:

use - indicates whether or not existing pmap data should be used

setPMAPTagName

public void setPMAPTagName(java.lang.String tagName)

Sets the name of the SDfile tag (Molecule property) which stores the pharmacophore map data.

Parameters:

tagName - name of the SDfile tag (Molecule property)

getPMAPTagName

public java.lang.String getPMAPTagName()

Gets the name of the SDfile tag (Molecule property) which stores the pharmacophore map data.

Returns:

name of the SDfile tag (Molecule property)

generate

public java.lang.String[] generate(Molecule m,
                                   MolecularDescriptor d)
                            throws MDGeneratorException

Generates the pharmacophore fingerprint of the given molecule. New instance of the PFp object is not allocated, the provided MolecularDescriptor is updated (and it has to be allocated and initialized by the client of this class).

Specified by:

generate in class MDGenerator

Parameters:

m - molecule for which the fingerprint is created

d - the 2d pharmacophore fingerprint generated

Returns:

names of tags (properties) set (added) (eg. "PMAP")

Throws:

MDGeneratorException - when perception or mapping cannot be completed for any reason

getPMap

public java.lang.String getPMap(Molecule m,
                                PSymbols pSym)
                         throws MDGeneratorException

Gets pharmacophore map of the input molecule. If the map is not yet calculated and stored as a property in the molecule, this method generates then returns it. The input molecule has to be standardized.

Parameters:

m - a molecule

pSym - pharmacophore type symbols

Returns:

pharmacophore point map of the input molecule

Throws:

MDGeneratorException - when perception or mapping cannot be completed for any reason

Since:

JChem 2.2

calcFreqCount

protected int calcFreqCount(MolecularDescriptor d)

Calculate and store in freqCount[] absolute frequency counts per cells. Also gets number of non-zero cells in the descriptor.

Overrides:

calcFreqCount in class MDGenerator

Parameters:

d - descriptor in which non-zero cells should be counted

Returns:

number of non-zero cells