Load precomputed fingerprints

[davide-grheco]

Thank you for the useful package, it takes away a lot of the hustle about writing plotting code all the time.

When working on large datasets I generally precompute fingerprints / descriptors and then use them as I see fit.
Would it be possible to add an option to load data directly as a matrix to retain the plotting capabilities but without having to go through the FP computation all the time?

[JacksonBurns]

This isn't directly possible with the current API, but you can code it for yourself - here's an idea of how to get started.

When you setup chemplot with a method like from_smiles it just runs:

ChemPlot/chemplot/chemplot.py

Lines 159 to 175 in 6acf926

	def from_smiles(cls, smiles_list, target=[], target_type=None, sim_type=None):
	"""
	Class method to construct a Plotter object from a list of SMILES.
	:param smile_list: List of the SMILES representation of the molecules to plot.
	:param target: target values
	:param target_type: target type R (regression) or C (classificatino)
	:param sim_type: similarity type structural or tailored
	:type smile_list: list
	:type target: list
	:type target_type: string
	:type sim_type: string
	:returns: A Plotter object for the molecules given as input.
	:rtype: Plotter
	"""
	return cls(smiles_list, target, target_type, sim_type, desc.get_mordred_descriptors, desc.get_ecfp)

Calling the constructor with function pointing towards the mrodred descriptor and fingerprint functions. You can write a function like get_precomputed that takes in a SMILES and looks up the corresponding precomputed descriptors, then call __init__.

[davide-grheco]

Thank you, I'll take a look at this and see whether it makes sense for me to implement the feature.
In case I do, I'll open a PR as I'd imagine this could be useful for other people as well.

[jonwzheng]

I think that including other common/easily computable fingerprints with the current modules (like Morgan/topological fingerprints) would be really helpful.

[JacksonBurns]

@jonwzheng this was partially implemented here: #21

If you'd be willing to pick it back up!