Recombination output: text instead of pickle

[dominiquesydow]

Description

Currently, the recombination output is a pickle file. This file can only be read with the kinase_focused_fragement_library code. In this PR, we want to make the data independent from the code, i.e. we want to save the data as text file (e.g. in json format)

Todos

• [ ] Save data in Combination (and Result object) as dict.
• [ ] Save the dict in json format to file (find out if one can write recombined ligands one by one to file)
• [ ] Keep also pickle output

Questions

Status

• [ ] Ready to go

[dominiquesydow]

This PR is deprecated. We still use the pickle format during recombination - but use json as output during ligand_analysis.