Class ChemicalFingerprint

  • All Implemented Interfaces:
    Cloneable

    @PublicAPI
    public class ChemicalFingerprint
    extends MolecularDescriptor
    The ChemicalFingerprint class implements topological fingerprints as a type of MolecularDescriptors. Such fingerprints encode the topological connection between atoms of the chemical graph. Though such encoding loses information, still it preserves enough to allow fast comparisons of chemical structures without their direct structural comparison but instead involving their topological fingerprints.
    This class provides two metrics for dissimilarity calculations: Tanimoto and Euclidean. Many varieties of the base metrics are supported, for instance scaling, directing, weighting. Euclidean has a normalized form too in order to upper bound the otherwise unbounded Euclidean metric.

    Typical usage:


    Generating fingerprints
          CFParameters params = new CFParameters( "config.xml" );
          CF fp = new CF( params );
    
          // always use an MDSet object, even if it has one component only 
          MDSet ds = new MDSet();
          ds.addDescriptor( pfp );
    
          // create an input source reader that takes molecules from a smiles file
          MDFileReader src = new MDFileReader( "input.smiles" );
          src.setIdTagName( "CGX_ID" ); // just an example
    
          // process input: get the fingerprints from the input source and do sg
    
          while ( src.next( ds ) ) {  // scr generates the descriptor!
              do_something( ds );
          }
          src.close();
     
    Since:
    JChem 2.0
    • Field Detail

      • fp

        protected int[] fp
        storage for the fingerprint
      • brightness

        protected int brightness
        number of bits set in the fingerprint (sometimes this is called the darkness, but that seems to be less pausible)
    • Constructor Detail

      • ChemicalFingerprint

        public ChemicalFingerprint()
        Creates a new, empty instance of ChemicalFingerprint without allocating internal storage.
      • ChemicalFingerprint

        public ChemicalFingerprint​(CFParameters params)
        Creates a new instance of ChemicalFingerprint according to the parameters given.
        Parameters:
        params - parameters used in fingerprint generation and handling
        Since:
        JChem 2.2
      • ChemicalFingerprint

        public ChemicalFingerprint​(String params)
        Creates a new instance of ChemicalFingerprint according to the parameters given.
        Parameters:
        params - parameter settings
      • ChemicalFingerprint

        public ChemicalFingerprint​(ChemicalFingerprint cfp)
        Copy constructor. An identical copy of the chemical fingerprint passed is created. The old and the new instances share the same CFParameters object.
        Parameters:
        cfp - fingerprint to be copied
    • Method Detail

      • getName

        public String getName()
        Gets the name of the ChemicalFingerprint object. The name is not the same as the class name, it is nicer, more readable and meaningful for end-users too.
        Overrides:
        getName in class MolecularDescriptor
        Returns:
        the nice, external name for ChemicalFingerprint class objects
      • getShortName

        public String getShortName()
        Gets the short name of the descriptor.
        Overrides:
        getShortName in class MolecularDescriptor
        Returns:
        the short name used in text outputs (tables etc.)
      • getParametersClassName

        public String getParametersClassName()
        Gets the name of the parameters class corresponding to the descriptor.
        Overrides:
        getParametersClassName in class MolecularDescriptor
        Returns:
        the name of the parameters class
      • getBrightness

        public int getBrightness()
        Gets the brightness of the fingerprint. Actually, sometimes this is called the darkness. To be precise, this methods gets the numbers of 1 (one) bits in the fingerprint.
        Returns:
        number of bits set to 1
      • setParameters

        public void setParameters​(MDParameters parameters)
        Sets parameters, allocates internal storage if needed and cleans the descriptor.
        Overrides:
        setParameters in class MolecularDescriptor
        Parameters:
        parameters - fingerprint parameters
      • toData

        public byte[] toData()
        Converts a chemical fingerprint object into a byte array. This format can be reffered to as an "external representation" since it servers as the data format for storing fingerprints in databases.
        Use the fromData() method to build the fingerprint from this "external" representation.
        Specified by:
        toData in class MolecularDescriptor
        Returns:
        byte array representation of the fingerprint object
      • fromData

        public void fromData​(byte[] dbRepr)
        Builds a fingerprint from an external data format, created by a previous call to toData().
        Specified by:
        fromData in class MolecularDescriptor
        Parameters:
        dbRepr - "external" representation of ChemicalFingerprint
      • clear

        public final void clear()
        Clears the fingerprint: sets all bins to store zero value.
      • toString

        public final String toString()
        Converts the fingerprint into a readable string. This is the default external text format of the fingerprint, which can also be stored into an SDfile.
        Specified by:
        toString in class MolecularDescriptor
        Returns:
        string representation of the fingerprint
      • toDecimalString

        public final String toDecimalString()
        Converts the fingerprint into a tab separated string.
        Specified by:
        toDecimalString in class MolecularDescriptor
        Returns:
        string representation of the fingerprint
      • toBinaryString

        public String toBinaryString()
        Converts the fingerprint into a 0,1 string.
        Overrides:
        toBinaryString in class MolecularDescriptor
        Returns:
        binary string representation of the fingerprint
        Since:
        JChem 2.3
      • toFloatArray

        public final float[] toFloatArray()
        Creates the float array representation of the fingerprint. This array contains all values of the fingerprint (including all zeros) in the elements of the array.
        Specified by:
        toFloatArray in class MolecularDescriptor
        Returns:
        a float array representation of the fingerprint
        Since:
        JChem 2.0.1
      • fromFloatArray

        public void fromFloatArray​(float[] descr)
                            throws RuntimeException
        Builds fingerprint from its float array representation. Typically used when a hypothesis is created.
        Specified by:
        fromFloatArray in class MolecularDescriptor
        Parameters:
        descr - fingerprint represented in a float array (e.g. generated by toFloatArray())
        Throws:
        RuntimeException
        Since:
        JChem 2.0.1
      • getDefaultDissimilarityMetricThresholds

        public float[] getDefaultDissimilarityMetricThresholds()
        Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
        Specified by:
        getDefaultDissimilarityMetricThresholds in class MolecularDescriptor
        Returns:
        array of dissimilarity threshold values
      • getDefaultMetricIndex

        public int getDefaultMetricIndex()
        Gets the index of the default metric. In the case of this class this is Tanimoto.
        Overrides:
        getDefaultMetricIndex in class MolecularDescriptor
        Returns:
        metric index of the default metric
      • getDefaultThreshold

        public float getDefaultThreshold​(int metricIndex)
        Gets a metric dependent default threshold value. Ideally, this value should be based on statistics, though the actual value is not too critical, since these are only used in user interfaces to simplify the use of applications for beginners.
        Overrides:
        getDefaultThreshold in class MolecularDescriptor
        Parameters:
        metricIndex - index of a parameterized metric
      • getTanimoto

        public float getTanimoto​(ChemicalFingerprint f)
        Calculates the Tanimoto metric.
        Parameters:
        f - the distance from f is calculated
        Returns:
        the tanimoto distance (dissimilarity coefficient)
      • getTversky

        public float getTversky​(ChemicalFingerprint f)
        Calculates the Tversky !!DISSIMILARITY!! index: (1-(commonly used tversky))
        Parameters:
        f - the distance from f is calculated
        Returns:
        the Tversky dissmilarity index as float
      • getEuclidean

        public float getEuclidean​(ChemicalFingerprint f)
        Calculates the Euclidean distance. This is the same as the Euclidean distance for bit string.
        Parameters:
        f - the distance from f is calculated
        Returns:
        the dissimilarity coefficient
      • getWeightedEuclidean

        public float getWeightedEuclidean​(ChemicalFingerprint f)
        Calculates the weighted Euclidean distance. This is the same as the weighted Euclidean distance for bit strings.
        Parameters:
        f - the distance from f is calculated
        Returns:
        the dissimilarity coefficient
      • getAsymmetricEuclidean

        public float getAsymmetricEuclidean​(ChemicalFingerprint f)
        Calculates the asymmetric Euclidean distance. This is the same as the asymmetric Euclidean distance for bit strings.
        Parameters:
        f - the distance from f is calculated
        Returns:
        the dissimilarity coefficient
      • getWeightedAsymmetricEuclidean

        public float getWeightedAsymmetricEuclidean​(ChemicalFingerprint f)
        Calculates the weighted asymmetric Euclidean distance. This is the same as the asymmetric Euclidean distance for bit strings.
        Parameters:
        f - the distance from f is calculated
        Returns:
        the dissimilarity coefficient
      • getDissimilarity

        public float getDissimilarity​(MolecularDescriptor fp2)
        Calculates the dissimilarity between two chemical fingerprints using the default distance measure.
        Specified by:
        getDissimilarity in class MolecularDescriptor
        Parameters:
        fp2 - the other pahrmacophore fingerprint
        Returns:
        dissimilarity ratio
      • getDissimilarity

        public float getDissimilarity​(MolecularDescriptor fp2,
                                      int metricIndex)
        Calculates the dissimilarity between two chemical fingerprints using the specified distance metric. The index of the required metric can be obtained by calling getMetricIndex( String metricName ) .
        New metrics implemented by this class have to be added at the end of the existing ones.
        Specified by:
        getDissimilarity in class MolecularDescriptor
        Parameters:
        fp2 - the chemical fingerprint from which the distance is measured
        metricIndex - index of the metric to be used
        Returns:
        the dissimilarity ratio
        See Also:
        MDParameters, PFParameters
      • getLowerBound

        public float getLowerBound​(Object fp2)
        Calculates the lower bound estimate of the dissimilarity from the given fingerprint. In the case of ChemicalFingerprint a good estimate for the minimum distance cannot be obtained efficiently (that is, significantly faster than calculating the proper distance) therefore 0 is returned. This trivial distance bound estimation will lead to calling getDistance.
        Parameters:
        fp2 - chemical fingerprint from which distance is measured
        Returns:
        estimate of the minimum distance
      • isSubSetOf

        public boolean isSubSetOf​(ChemicalFingerprint f)
        Checks if this fingerprint is a subset of another fingerprint that is passed as method parameter. A binary fingerprint is considered to be a subset of another if none of its bits is larger than that of the other's.
        Parameters:
        f - a descriptor which is supposed to be a superset
        Returns:
        true if this descriptor is a subset of the parameter
      • getAliasNames

        public List<String> getAliasNames()
        Simple test function for engineering purposes, comment it out from released version.