Dani Bodor comments

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                                            Dani Bodor

ValueErrors raised in Variant tutorials

I wonder whether this is related to #520

Create feature classes

This will probably be useful once we start making new features for new data types (such as nucleic acids, etc).

Add performances comparisons with previous packages

I don't have a great idea about this, apart from just doing a "not fair" comparison and being open about it and explaining the differences.

evaluate whether we want to stop suppressing errors by default in `_process_one_query` method of `QueryCollection`

The decision is to by default throw an error if a faulty PDB file is encountered, meaning the code will stop executing at this point. We will also implement a...

evaluate whether we want to stop suppressing errors by default in `_process_one_query` method of `QueryCollection`

We still suppress the errors, but provide better feedback of what is going on. No option was added to enforce hard fails.

Variant queries requesting redudant inputs

In response to [this](https://github.com/DeepRank/deeprank2/pull/459#discussion_r1291179282): I actually believe it is the wt and not the variant that is listed in the pdb. At least that seems to be the case in...

Variant queries requesting redudant inputs

Come to think of it, currently, the user can input both a wt and a variant aa, neither of which is the one listed in the pdb (and it doesn't...

Variant queries requesting redudant inputs

See further the points raised here. This is all related to each other: https://github.com/DeepRank/deeprank2/pull/492#issuecomment-1732423764

calculate atom pairwise energies (combination between LJ and Coulomb) using OpenMM

Currently the definition of the interface is a bit of a mess (see #460), as we don't differentiate between the distance cutoff between graph nodes to create an edge and...