Package chemaxon.descriptors

Class ScalarDescriptor

java.lang.Object
chemaxon.descriptors.MolecularDescriptor
chemaxon.descriptors.ScalarDescriptor
All Implemented Interfaces:
Cloneable
Direct Known Subclasses:
HAcc, HDon, Heavy, LogD, LogP, Mass, TPSA
@PublicAPI public class ScalarDescriptor extends MolecularDescriptor
Base class for all scalar descriptors. All scalar descriptors should be derived from this class.
Since:
JChem 2.2

  • Field Details

    • descrValue

      protected float descrValue
      descriptor value

  • Constructor Details

    • ScalarDescriptor

      public ScalarDescriptor()
      Creates a new, empty instance of ScalarDescriptor.

    • ScalarDescriptor

      public ScalarDescriptor(SDParameters params)
      Creates a new instance of ScalarDescriptor according to the parameters given.
      Parameters:
      params - parameters settings

    • ScalarDescriptor

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

    • ScalarDescriptor

      public ScalarDescriptor(ScalarDescriptor sd)
      Copy constructor. An identical copy of the descriptor passed is created. The old and the new instances share the same SDParameters object.
      Parameters:
      sd - a ScalarDescriptor to be copied

  • Method Details

    • clone

      public MolecularDescriptor clone()
      Creates a new instance with identical internal state.
      Specified by:
      clone in class MolecularDescriptor
      Returns:
      the newly copied object

    • getName

      public String getName()
      Gets the name of the ScalarDescriptor object. The name is not the same as the class name, but a nicer, readable and more meaningful for end-users.
      Overrides:
      getName in class MolecularDescriptor
      Returns:
      the nice external name for ScalarDescriptor 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

    • 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 ScalarDescriptor 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 ScalarDescriptor object into an array of bytes. This format can be reffered to as an "external representation" since it servers as the data format for storing scalar descriptors in databases.
      Use the fromData() method to build the scalar descriptor from this "external" representation.
      Specified by:
      toData in class MolecularDescriptor
      Returns:
      byte array representation of the descriptor object

    • fromData

      public void fromData(byte[] dbRepr)
      Builds a descriptor from an external data format, created by a previous call to toData().
      Specified by:
      fromData in class MolecularDescriptor
      Parameters:
      dbRepr - "external" representation of the ScalarDescriptor object

    • toFloatArray

      public final float[] toFloatArray()
      Creates the float array representation of the descriptor.
      Specified by:
      toFloatArray in class MolecularDescriptor
      Returns:
      a float array of one element

    • fromFloatArray

      public void fromFloatArray(float[] descr) throws RuntimeException
      Builds the descriptor from a float array of one element.
      Specified by:
      fromFloatArray in class MolecularDescriptor
      Parameters:
      descr - descriptor stored in a (one element) float array
      Throws:
      RuntimeException

    • clear

      public void clear()
      Clears the descritor: sets its value to zero value.

    • toString

      public final String toString()
      Converts the descriptor value into a readable string. This is the default external text format.
      Specified by:
      toString in class MolecularDescriptor
      Returns:
      string representation of the descriptor value

    • toDecimalString

      public String toDecimalString()
      Converts the descriptor value into a readable string. This is the default external text format.
      Specified by:
      toDecimalString in class MolecularDescriptor
      Returns:
      string representation of the descriptor value

    • fromString

      public final void fromString(String sd) throws ParseException
      Builds a descriptpr from its string representation created by toString().
      Specified by:
      fromString in class MolecularDescriptor
      Parameters:
      sd - descriptor value as string
      Throws:
      ParseException

    • set

      public void set(float newValue)
      Set the value of the descriptor.
      Parameters:
      newValue - the value to be set

    • generate

      public String[] generate(Molecule m) throws MDGeneratorException
      Creates the ScalarDescriptor descriptor for the given Molecule. Side-effect!!!!!! Standardizes the input molecule (as defined in MDParameters).
      Overrides:
      generate in class MolecularDescriptor
      Returns:
      property names set in the molecule passed during generation
      Throws:
      MDGeneratorException - when failed to generate descriptor

    • getDissimilarityMetrics

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

    • getDefaultThreshold

      public float getDefaultThreshold(int metricIndex)
      Gets a metric dependent default threshold value.
      Overrides:
      getDefaultThreshold in class MolecularDescriptor
      Parameters:
      metricIndex - index of a parameterized metric

    • getDissimilarity

      public float getDissimilarity(MolecularDescriptor sd)
      Calculates the dissimilarity between two scalar descriptor using the default metrics In the present implementation it is always the absolute difference between them.
      Specified by:
      getDissimilarity in class MolecularDescriptor
      Parameters:
      sd - a scalar descriptor value
      Returns:
      dissimilarity value

    • getDissimilarity

      public float getDissimilarity(MolecularDescriptor sd, int metricIndex)
      Calculates the dissimilarity between two scalar descriptor using the specified metric.
      Specified by:
      getDissimilarity in class MolecularDescriptor
      Parameters:
      sd - a scalar descriptor
      metricIndex - index of the metric to be used
      Returns:
      the dissimilarity ratio
      See Also:

    • getLowerBound

      public float getLowerBound(MolecularDescriptor sd)
      Calculates the lower bound estimate of the dissimilarity from the given descriptor.
      Overrides:
      getLowerBound in class MolecularDescriptor
      Parameters:
      sd - a descriptor value
      Returns:
      always returns 0