Cleaning up the test functionalities

[JohannesKarwou]

Description

We should clean up, our tests, and make sure, that all of them run on every system

Todos

• [x] Loeffler Systems not there
• [x] maybe change the working directory (/tmp) is sometimes not big enough
• [x] support CI test also for lone pairs
• [x] modify CI so it can run at least one complete free energy calculation
• [ ] we should have at least one test where CHARMM is used locally (currently one has to set a lot of variable for doing so)
• [ ] Creating a notebook for rbfe

To Check

Think about a better solution here:

is there a reason why this is preferred to atom.GetSymbol() == 'H? It would also be true for He, right?

one solution might be the use of a if else function

_Originally posted by @wiederm in https://github.com/wiederm/transformato/pull/48#discussion_r885247348_

Questions

• [x] is it possible to install a python package in the conda environment from a forked github page? -> won't be necessary if parmed is updated

Status

• [ ] Ready to go

[codecov-commenter]

Codecov Report

Merging #54 (3a061e7) into master (852ff5d) will not change coverage. The diff coverage is n/a.

[JohannesKarwou]

First suggestion on how we could structure the repository:

│   README.md
│
└───data
│   │   **toppar**
│   │   system1
│   └───ligand
│   └───complex
│   │   system2
│   │   ...
│   │
└───transformato
│   │   mutate.py
│   │   ...
│   └───tests
│   │  │   test_misc.py
│   │  │   ...
└───docs

[JohannesKarwou]

For 2-Methylindol and 2-Methylfuran there is no folder in the data folder

[wiederm]

superceeded by #77