Rodrigo Vargas Honorato

`pdb_tidy` removes the `TER` record between chains and removes last `ENDMDL` in a multi-model PDB

8

**Describe the bug** `pdb_tidy` removes the `TER` record between chains and removes last `ENDMDL` in a multi-model PDB. **To Reproduce** 1. test.pdb ```text MODEL 1 ATOM 1 N THR A...

cif conversion causes unexpected renumbering of residues

1

While using `create_cif.py`, the resulting `.cif` has a different numbering than the input `.pdb`, Green: input .pdb Cyan: output .cif 

Add a `saxsscore` module.

3

With it we can score chi2, Rg, or Dmax, and combine it with the haddock-score.

This PR does some minor simplification on the return types of some functions. This is not a comprehensive change since there are several functions that have very complex returns and...

Currently the API endpoints are spread troughout the code; ```python from arctic3d.modules.pdb import BESTPDB_URL, PDBE_URL from arctic3d.cli_localise import UNIPROT_API_URL from arctic3d.modules.interface import LIGAND_URL ``` It would be easier to maintain...

Some functions might return a `None` type that is not handled downstream, we should add checks for those; - `get_cif_dict` - `fetch_updated_cif` - `validate_api_hit`, argument `fetch_list` - `get_maxint_pdb` - `get_best_pdb`

Customize `StrictnessLevel`

9

I'm using pdbtbx to validate input PDBs in our [new frontend](https://wenmr.science.uu.nl) via wasm. While implementing it I've came acrross the `StrictnessLevel` which is a nice way to be more or...

You are about to submit a new Pull Request. Before continuing make sure you read the [contributing guidelines](CONTRIBUTING.md) and that you comply with the following criteria: - [x] You have...

There is currently support for 3 execution modes: - `batch`: via `HPCScheduler`, a mode in which the application becomes a daemon directly interacting with the system's scheduler via system calls...