rdkit.Chem.Fingerprints.SimilarityScreener module — The RDKit 2016.09.1 documentation

# rdkit.Chem.Fingerprints.SimilarityScreener module

class definitions for similarity screening

See _SimilarityScreener_ for overview of required API

class `rdkit.Chem.Fingerprints.SimilarityScreener.` `SimilarityScreener`(probe=None, metric=None, dataSource=None, fingerprinter=None)

  Bases: `object`

  base class

  important attributes:

    > probe: the probe fingerprint against which we screen.

    > metric: a function that takes two arguments and returns a similarity
    >   measure between them
    > dataSource: the source pool from which to draw, needs to support
    >   a next() method
    > fingerprinter: a function that takes a molecule and returns a
    >   fingerprint of the appropriate format

    Notes
      subclasses must support either an iterator interface or __len__ and __getitem__
  `GetSingleFingerprint`(probe)

    returns a fingerprint for a single probe object

    This is potentially useful in initializing our internal probe object.

  `Reset`()

    used to reset screeners that behave as iterators

  `SetProbe`(probeFingerprint)

    sets our probe fingerprint

class `rdkit.Chem.Fingerprints.SimilarityScreener.` `ThresholdScreener`(threshold, **kwargs)

  Bases: `rdkit.Chem.Fingerprints.SimilarityScreener.SimilarityScreener`

  Used to return all compounds that have a similarity
    to the probe beyond a threshold value

  Notes:

  > - This is as lazy as possible, so the data source isn’t queried until the client asks for a hit.
  > - In addition to being lazy, this class is as thin as possible. (Who’d have thought it was possible!) Hits are not stored locally, so if a client resets the iteration and starts over, the same amount of work must be done to retrieve the hits.
  > - The thinness and laziness forces us to support only forward iteration (not random access)

  `Reset`()

    used to reset our internal state so that iteration starts again from the beginning

  `next`()

    required part of iterator interface

class `rdkit.Chem.Fingerprints.SimilarityScreener.` `TopNScreener`(num, **kwargs)

  Bases: `rdkit.Chem.Fingerprints.SimilarityScreener.SimilarityScreener`

  A screener that only returns the top N hits found

  Notes

  > - supports forward iteration and getitem

  `Reset`()
  `next`()