Package chemaxon.descriptors

Class MDGenerator

java.lang.Object
chemaxon.descriptors.MDGenerator
Direct Known Subclasses:
BCUTGenerator, CFGenerator, ECFPGenerator, PFGenerator, RFGenerator, ShapeGenerator
@PublicApi public abstract class MDGenerator extends Object
Base class for all kinds of MolecularDescriptor generators. Its main purpose is two-fold: (1) defines an interface for all generator classes (that is, what methods should be implemented), (2) implements function for gather statistical data on descriptor generated and retrieval functions for these statistics.
Since:
JChem 2.1

  • Field Details Link icon

    • createStatistics Link icon

      protected boolean createStatistics
      indicates if statistical data has to be gathered during generation

    • molCount Link icon

      protected int molCount
      variables to collect statistical data in

    • minNonEmptyPercent Link icon

      protected float minNonEmptyPercent

    • minNonEmptyId Link icon

      protected int minNonEmptyId

    • maxNonEmptyPercent Link icon

      protected float maxNonEmptyPercent

    • maxNonEmptyId Link icon

      protected int maxNonEmptyId

    • sumNonEmptyPercent Link icon

      protected float sumNonEmptyPercent

    • freqCount Link icon

      protected int[] freqCount

    • density Link icon

      protected int[] density

  • Constructor Details Link icon

    • MDGenerator Link icon

      protected MDGenerator()
      Created an object.

  • Method Details Link icon

    • generate Link icon

      public abstract String[] generate(Molecule m, MolecularDescriptor d) throws MDGeneratorException
      Generates the molecular descriptor for the given molecule. The MolecularDescriptor provided is updated (thus it has to be allocated and initialized by the client of this class).
      Parameters:
      m - molecule for which the descriptor is created
      d - the generated descriptor
      Returns:
      names of tags (properties) added
      Throws:
      MDGeneratorException - in the case of any failures to generate the descriptor

    • setCreateStatistics Link icon

      public void setCreateStatistics(boolean createStatistics)
      Toggles the create statistics flag.
      Parameters:
      createStatistics - new value for the create statistics flag
      Since:
      JChem 2.1

    • updateStatistics Link icon

      protected void updateStatistics(MolecularDescriptor d)
      Updates statistics gathered on fingerprints generated.
      Parameters:
      d - newly generated MolecularDescriptor
      Since:
      JChem 2.1

    • calcFreqCount Link icon

      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.
      Parameters:
      d - descriptor in which non-zero cells should be counted
      Returns:
      number of non-zero cells

    • getMoleculeCount Link icon

      public int getMoleculeCount()
      Gets the number of molecules processed (that is, the number of descriptors generated) since the initialization of the object.
      Returns:
      number of molecules processed

    • getAverageNonZeroRatio Link icon

      public float getAverageNonZeroRatio()
      Gets the average percentage of cells that have non-zero value taken all descriptors generated since the initialization of the generator into account.
      Returns:
      relative number of bits set in descriptors

    • getMaximumBitRatio Link icon

      public float getMaximumBitRatio()
      Gets the maximum percentage of non-zero cells in descriptors generated.
      Returns:
      maximum bits set, relative to descriptor length

    • getBrightestMolId Link icon

      public int getBrightestMolId()
      Gets the id of that molecule which had the maximum number of non-zero cells among all descriptors generated since the initialization of the generator object.
      Returns:
      unique molecule identifier (a consequtive index from zero)

    • getMinimumBitRatio Link icon

      public float getMinimumBitRatio()
      Gets the minimum percentage of non-zero cells in descriptors generated.
      Returns:
      minimum bits set, relative to descriptor length

    • getDarkestMolId Link icon

      public int getDarkestMolId()
      Gets the id of that molecule which had the minimum number of non-zero cells among all descriptors generated since the initialization of the generator object.
      Returns:
      unique molecule identifier (a consequtive index from zero)

    • getDensityCounts Link icon

      public int[] getDensityCounts()
      Gets the array of bit density. The array can be indexed from 0 to 10. Index i returns the number of descriptors in which the ratio non-zero cells is between 10 * i and 10 * i + 10 .
      Returns:
      array of density counts

    • getFrequencyCounts Link icon

      public int[] getFrequencyCounts()
      Gets the absolute frequence count array for all descriptors generated. Each element of the array stores the number of descriptors in which the corresponding cell had non-zero value.
      Returns:
      per-cell frequency count array