gt4sd.algorithms.generation.paccmann_vae.implementation module

Implementation of PaccMann^RL conditional generators.

Summary

Classes:

PaccMannVaeDefaultGenerator

Molecular generator as implemented in https://doi.org/10.1016/j.isci.2021.102269

Reference

class PaccMannVaeDefaultGenerator(temperature=1.4, batch_size=32, algorithm_version='v0', generated_length=100)

Bases: object

Molecular generator as implemented in https://doi.org/10.1016/j.isci.2021.102269

__init__(temperature=1.4, batch_size=32, algorithm_version='v0', generated_length=100)

Initialize the generator.

Parameters

• batch_size (int) – batch size used for generation.

• algorithm_version (str) – algorithm version for the PaccMannRLProteinBasedGenerator. NOTE: Only the decoder of that model is used here.

• temperature (float) – temperature for the sampling. Defaults to 1.4.

• generated_length (int) – maximum length of the generated molecules. Defaults to 100.

generate()

Generate a given number of samples (molecules) from a given protein.

Parameters

number_of_molecules – number of molecules to sample.

Return type

List[str]

Returns

list of SMILES generated.

__dict__ = mappingproxy({'__module__': 'gt4sd.algorithms.generation.paccmann_vae.implementation', '__doc__': '\n    Molecular generator as implemented in https://doi.org/10.1016/j.isci.2021.102269\n    ', '__init__': <function PaccMannVaeDefaultGenerator.__init__>, 'generate': <function PaccMannVaeDefaultGenerator.generate>, '__dict__': <attribute '__dict__' of 'PaccMannVaeDefaultGenerator' objects>, '__weakref__': <attribute '__weakref__' of 'PaccMannVaeDefaultGenerator' objects>, '__annotations__': {}})

__doc__ = '\n    Molecular generator as implemented in https://doi.org/10.1016/j.isci.2021.102269\n    '

__module__ = 'gt4sd.algorithms.generation.paccmann_vae.implementation'

__weakref__

list of weak references to the object (if defined)