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View Code? Open in Web Editor NEWObject-oriented Representation for Chemical Spaces
License: MIT License
Object-oriented Representation for Chemical Spaces
License: MIT License
ChemicalSpace.__init__
takes in a featurizer function and a distance metric.
Allow passing args
and kwargs
to from_smi
and from_sdf
to allow setting the needed __init__
parameters from there as well
Title
Optionally allow to hash molecules by their InChI Key and index
Title
Clustering methods that support or not a n_clusters
argument are not handled in a very elegant way
To reduce dependency on local environment
Title
Returning a ChemicalSpace layer object with factory
and passing hardcoded arguments is likely to cause issues if a derived layer takes in other attributes that were not specificed. Find a way to relax this
Consider parallelizing molecule hashing
Title
Title
Title
Implement Sphere Exclusion Clustering as clustering method
Investigate
Consider adding functionality to align the representation of the molecules of a chemical space to a 2D template
indexing via __getitem__
should return a ChemicalSpace
object, and not unpack the result as a tuple of mols, indices and scores
As things are now, features are cached.
But if one were to split a ChemicalSpace by slicing/clustering/etc, then features would need to be recalculated each time
Title
Add a ChemicalSpace.draw
option, or equivalent, to render the molecules in the space
Or even 3.6
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