FoldX in ibex

---

Installation

1. (Skip if you're using the version in ibex) Register at the FoldX website, download and extract the program wherever you want to save it.

2. Clone this repository and go into the directory that was created

git clone https://github.com/strubelab/FoldX_ibex.git

cd FoldX_ibex

2. Create a virtual environment with the provided environment.yml file, and activate

conda env create --file environment.yml --prefix ./env
conda activate ./env

3. Install the FoldX_ibex package

pip install -e .

4. Download and install the Executor library (from a different directory)

# Go to your home directory, or wherever you want to install the Executor library
cd

# Clone the repository
git clone https://github.com/guzmanfj/Executor.git

# Install the library. Make sure the venv cretaed in step 2 is still activated
pip install -e ./Executor

Usage

Command line program

You can run the wrapper from the command line, but only for a single PDB file at a time:

$ foldx_wrapper --help
usage: foldx_wrapper [-h] --input INPUT [--mutations MUTATIONS [MUTATIONS ...]] [-d DESTINATION]

Takes a PDB file and one or more amino acid mutations

options:
  -h, --help            show this help message and exit
  --input INPUT         PDB file to model the mutation.
  --mutations MUTATIONS [MUTATIONS ...]
                        Mutations to model on the given PDB file, in the format [from_aa][chain][number][to_aa], e.g. LA675P
  -d DESTINATION, --destination DESTINATION
                        Path for saving the resulting energies in pickle format.
``

## Python class

You can also run the wrapper from a python session. In this example we will model mutations on the `2oun` PDB structure. It has two identical chains, so we have to indicate them both in the `mutations` and `chains` arguments:

```python
from pathlib import Path
from FoldX.FoldX_ibex import FoldXIbex

# These have to be inside lists. You can give more than 1 pdb to model 
# many mutations in many PDBs
pdbs = [Path('./test/test_outputs/2oun.pdb')]
# One PDB, one mutation for chain A, and one for chain B
mutations = [[['L675W'], ['L675P']]]
# One PDB, chain A and chain B
chains = [['A','B']]

out_dir = Path('./output')

exe = FoldXIbex(pdbs, mutations, chains, out_dir=out_dir)
exe.run()

It will save in the output_dir a pickle file with the name of the pdb and the modeled mutations in the format [from_aa][chain][number][to_aa]. E.g. for the example the name will be ./output/2oun_LA675W_LB675P.pkl.