Package chemaxon.descriptors

Class ReactionFingerprint

java.lang.Object
chemaxon.descriptors.MolecularDescriptor
chemaxon.descriptors.ReactionFingerprint
All Implemented Interfaces:
Cloneable
@PublicApi public class ReactionFingerprint extends MolecularDescriptor
ReactionFingerprint class.
Since:
JChem 3.2

  • Field Details

    • 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 plausible)

  • Constructor Details

    • ReactionFingerprint

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

    • ReactionFingerprint

      public ReactionFingerprint(RFParameters params)
      Creates a new instance of ReactionFingerprint according to the parameters given.
      Parameters:
      params - parameters used in fingerprint generation and handling

    • ReactionFingerprint

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

    • ReactionFingerprint

      public ReactionFingerprint(ReactionFingerprint rfp)
      Copy constructor. An identical copy of the reaction fingerprint passed is created. The old and the new instances share the same RFParameters object.
      Parameters:
      rfp - fingerprint to be copied

  • Method Details

    • clone

      public ReactionFingerprint clone()
      Creates a copy with identical internal state. The new instances share the same RFParameters object with the copied one.
      Specified by:
      clone in class MolecularDescriptor
      Returns:
      the newly created object

    • getName

      public String getName()
      Gets the nice name of the ReactionFingerprint descriptor object. This name is not the same as the class name: it is nicer, and more meaningful for end-users.
      Overrides:
      getName in class MolecularDescriptor
      Returns:
      the nice, external name for ReactionFingerprint descriptor class objects

    • getShortName

      public String getShortName()
      Gets the short name of the descriptor. This name appears in text outputs.
      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

    • setParameters

      public void setParameters(String parameters) throws MDParametersException
      Sets the parameters of an already created ReactionFingerprint object.
      Specified by:
      setParameters in class MolecularDescriptor
      Parameters:
      parameters - parameter settings for the descriptor
      Throws:
      MDParametersException - any XML error

    • toData

      public byte[] toData()
      Converts a reaction 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 ReactionFingerprint

    • 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

    • fromString

      public final void fromString(String cfp) throws ParseException
      Builds a fingerprint from its string representation created by toString().
      Specified by:
      fromString in class MolecularDescriptor
      Parameters:
      cfp - fingerprint string
      Throws:
      ParseException

    • 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

    • 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

    • generate

      public String[] generate(Molecule m) throws MDGeneratorException
      Creates the ReactionFingerprint descriptor for the given Molecule. Calls the generator created by the corresponding MDParameters class.
      Overrides:
      generate in class MolecularDescriptor
      Returns:
      property names set in the molecule passed during generation
      Throws:
      MDGeneratorException - when failed to generate descriptor

    • isReactionMappingIncomplete

      public boolean isReactionMappingIncomplete()
      Returns true if reaction molecule was not mapped completely during reaction fingerprint generation. Should be called after generate(Molecule).
      Returns:
      true if the reaction molecule was not mapped completely
      Since:
      JChem 5.1.2

    • getDissimilarityMetrics

      public String[] getDissimilarityMetrics()
      Gets the dissimilarity metric names
      Specified by:
      getDissimilarityMetrics in class MolecularDescriptor
      Returns:
      the metrics array

    • getDissimilarityMetricsParamNum

      public int[] getDissimilarityMetricsParamNum()
      Gets the dissimilarity metric parameter number -> no parameters.
      Returns:
      the metrics array

    • getDissimilarityMetricsParamNames

      public String[] getDissimilarityMetricsParamNames()
      Gets the dissimilarity metric parameter names -> no parameters.
      Returns:
      the metrics array

    • getDissimilarityMetricsParamRanges

      public String[] getDissimilarityMetricsParamRanges()
      Gets the dissimilarity metric parameter ranges -> no parameters.
      Returns:
      the metrics array

    • getDissimilarityMetricsParamDefault

      public String[] getDissimilarityMetricsParamDefault()
      Gets the dissimilarity metric parameter names -> no parameters.
      Returns:
      the metrics array

    • getDissimilarityMetricsParamHelp

      public String[] getDissimilarityMetricsParamHelp()
      Gets the dissimilarity metric parameter names -> no parameters.
      Returns:
      the metrics array

    • 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

    • getCommonBitCount

      public int getCommonBitCount(ReactionFingerprint f)

    • getReactantTanimoto

      public float getReactantTanimoto(ReactionFingerprint f)
      Returns the tanimoto distance of the reactant sides.
      Parameters:
      f - the distance from f is calculated
      Returns:
      the tanimoto distance (dissimilarity coefficient)

    • getProductTanimoto

      public float getProductTanimoto(ReactionFingerprint f)
      Returns the tanimoto distance of the product sides.
      Parameters:
      f - the distance from f is calculated
      Returns:
      the tanimoto distance (dissimilarity coefficient)

    • getCoarseReactionTanimoto

      public float getCoarseReactionTanimoto(ReactionFingerprint f)
      Returns the tanimoto distance of the reaction centers. The direction of the reaction is considered.
      Parameters:
      f - the distance from f is calculated
      Returns:
      the tanimoto distance (dissimilarity coefficient)

    • getMediumReactionTanimoto

      public float getMediumReactionTanimoto(ReactionFingerprint f)
      Returns the tanimoto distance of the reaction centers and their neighbouring atoms and bonds. The direction of the reaction is considered.
      Parameters:
      f - the distance from f is calculated
      Returns:
      the tanimoto distance (dissimilarity coefficient)

    • getStrictReactionTanimoto

      public float getStrictReactionTanimoto(ReactionFingerprint f)
      Returns the tanimoto distance of the reaction centers, their immediate neighbour atoms and bonds, and the neighbours' neighbouring atoms and bonds. The direction of the reaction is considered.
      Parameters:
      f - the distance from f is calculated
      Returns:
      the tanimoto distance (dissimilarity coefficient)

    • getDissimilarity

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

    • getDissimilarity

      public float getDissimilarity(MolecularDescriptor fp2, int metricIndex)
      Calculates the dissimilarity between two reaction 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 reaction fingerprint from which the distance is measured
      metricIndex - index of the metric to be used
      Returns:
      the dissimilarity ratio
      See Also:

    • getLowerBound

      public float getLowerBound(MolecularDescriptor fp2)
      Calculates the lower bound estimate of the dissimilarity from the given fingerprint. In the case of ReactionFingerprint 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.
      Overrides:
      getLowerBound in class MolecularDescriptor
      Parameters:
      fp2 - reaction fingerprint from which distance is measured
      Returns:
      estimate of the minimum distance

    • isSubSetOf

      public boolean isSubSetOf(ReactionFingerprint 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

    • getChemicalHashedFingerprint

      public static int[] getChemicalHashedFingerprint(int[] reactionFingerprint, int length)
      Creates chemical hashed fingerpint from reaction fingerprint.
      Parameters:
      reactionFingerprint - the fingeprint as was generated by ReactionFingerprint, may contain additional data (e.g. structural keys) at the end
      length - the length of the FP part in integers to consider (the remainder will be ignored, e.g. structural keys)
      Returns:
      the chemical hashed fingerprint of the total reaction

    • getAliasNames

      public List<String> getAliasNames()