Class 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
    See Also:
    PharmacophoreFingerprint, PMapper
    • 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​(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 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 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 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