Dani Bodor comments

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                                            Dani Bodor

Visualization module

blocking #241

Use actual pairing distances rather than physical distances to define potential energies

temporary code of features/contact.py, including the adjacency matrix that was created in PR #368 (at commit [835d407](https://github.com/DeepRank/deeprank-core/pull/368/commits/835d407390f0e230e5475826b6fcc29438b1de1d)), that will not be used there. There is also a test (test_intra_partners.py) present...

Use actual pairing distances rather than physical distances to define potential energies

I wonder whether we can use PDB nomenclature to define adjacency instead of using the adjacency matrix. In this way, anything that is not in the same or neighboring residues...

Use actual pairing distances rather than physical distances to define potential energies

Alternative option suggested by @LilySnow (copied from Slack): I just had a meeting with my friend who knows MD. He suggests us to move to openMM. openMM can determine 1-4...

Use actual pairing distances rather than physical distances to define potential energies

This will probably be resolved in #393

Fix hydrogens unkown to the forcefield

I believe that this will be dealt with in #393

Investigate pdb2sql v0.5.3 error

@DarioMarzella or @FarzanehParizi , can you explain what the difference is in the newest pdb2sql update and tell me if the fact that this check is failing for deeprankcore is...

Investigate pdb2sql v0.5.3 error

The change in pdb2sql that is causing problems is this one: https://github.com/DeepRank/pdb2sql/pull/82/files

Refactor duplicate code

was automatically closed, but not done. I will reopen it now

Allow for >20 types in `AminoAcid` class

Hi Daniel, I can look into this. Having a 21st for 'other' should definitely be doable, but I will check if it can be open ended. Just out of curiosity,...