Parsing molecules

[dominiquesydow]

I am wondering if we want to set up a module that allows us to parse structural data (proteins, ligands, ...) from different file formats (mol2, pdb, ...) to different output formats (mdanalysis universes, biopandas DataFrames, rdkit molecules, ...).

What we currently have:

https://github.com/volkamerlab/opencadd/blob/master/opencadd/structure/core.py
mdanalysis universes from a plethora of input formats (super powerful).

https://github.com/volkamerlab/opencadd/blob/databases_klifs_api/opencadd/databases/klifs/parser.py
biopandas DataFrames and rdkit molecules from mol2 files or from mol2 text (mol2 file content, e.g. when queried from a database).
I use this data structure for the opencadd.databases.klifs and opencadd.structure.subpocket modules as well as in the kissim and ratar projects.

Such a module could live at the top level, e.g. opencadd.parser.

@jaimergp - have you thought of something like this already?
Definitely something we could discuss with a whole group to collect everybody's needs.

[jaimergp]

Yep, we will need opencadd.io eventually. We could explicitly load with the parsers there in, or subtly delegate the calls from the main core objects (structure, compound, dataset, etc). Ideally, we don't need to use many different objects so we can all converge in a single object model that works across the different levels. More realistically, we will have to set-up exporters to deal with the different package needs...

We can schedule this as part of the discussion, possibly roping in the members of @openkinome/kinoml as well.

[dominiquesydow]

That sounds fantastic!

I am unsure how to proceed until we have the envisioned quite powerful opencadd.io module.

I was planning on using the classes Mol2ToDataFrame and lateron PdbToDataFrame from here quite a lot now in the modules opencadd.databases.klifs, opencadd.structure.subpocket, kissim, and ratar.

Shall I already set up an opencadd.io module with that minimum set of classes, which will be refactored/generalized as soon as we get started with the real deal?

[jaimergp]

Yes, please add them there so at least they are in the same place. Something like opencadd/io/dataframes.py should work to contain those functions!