strange-mol 0.2.0

Compute possible interaction between molecules.

strange

A python software used to computed interaction between two molecules, from their pharmacophore.

Contributors: Lucas ROUAUD

Documentation: https://strange.mol3d.tech/

Installation

[!INFO]

We recommand either pipx or uv as installation method.

pipx

pipx install strange-mol
strange --help

uv

uv pip install strange-mol
strange --help

pip

pip install strange-mol
strange --help

Running through nix

If you have nix, you can run this software without installing it like:

nix --extra-experimental-features "nix-command flakes" run \
    git+https://gitlab.galaxy.ibpc.fr/rouaud/strange -- \
    --help

The first two lines are for the nix command. After the --, you can give strange argument. For instance:

nix --extra-experimental-features "nix-command flakes" run \
    git+https://gitlab.galaxy.ibpc.fr/rouaud/strange -- \
    --input ... --output ...

Command line interface

--help and parameters explained

To get the program help, you can run:

strange --help

Here, is a table giving parameters details:

• Bold parameters are mandatory.
• [option in brackets] must be given together. So [opt1 opt2] for parameter -x will be translated to -x opt1 opt2 in the CLI.

Parameter	Value type	Explaination	Values example
--input or -i	One or two files with molecules.	This is where you input the molecules to compute pharmacophore and interaction from.	[protein.pdb ligand.sdf] [protein.pdb]
--output or -o	A .csv files to store compute interaction.	This files is going to contain which pharmacophores are interacting, and some other parameters.	[interaction.csv]
--help or -h
--version or -v
--selection or -s	Selection to apply to the molecule. Work only for files parsed by MDAnalysis (not .sdf, .mol, .mol2, xyz). For more details, check MDAnalysis selection algebra.	This parameter will let you select subparts of your molecule to make the computation.	["protein" "resid CEL"] ["chainID A" "chainID B"]
--parameter or -p	Parameter file to configure the software. Check the associated section.	The parameter file that you will input here is going to change the software behaviour.	[parameters.yml] [parameters.json] [parameters.toml]
--pharmacophore	Two .csv files to store compute pharmacophore.	The computed pharmacophore. If you gave two molecules, the first file correspond to the first molecule, the second one to the second molecule. If one molecule is given, first and second files will respectfully correspond to the first and second selection.	[protein.csv ligand.csv]
--feature_file	A .fdef file that is going to be used by RDKit to identify pharmacophore.	This file contained SMART that are used to define certain type of pharmacophore with RDKit.	[feature_file.fdef]
--visualization	You can either give a .pml file or a .mvsj file to visualize using PyMOL or MolStar.	Use this to visualize the pharmacophore using PyMOL (pymol visualization.pml) or MolStar (open first the visualization.mvsj, then load it, then your molecules).	[interaction.pml] [interaction.mvsj]
--add_hydrogen or -a	If you want to add hydrogens to your input molecules.	You can choose, with this option, to add hydrogen to the first input molecule only, the second input molecule only, both or none. If one file is given, it will correspond to the selection (first selection only, second only, both or none).	[0] ["both"]

🙇‍♂️ Acknowledgement

• Original idea: Etienne REBOUL
• Formula checking: Charles ROBERT
• Beta testing: Isleme KHALFAOUI, Malek MELLITI

License

This works is under:

• A MIT license (software).
• A CC-BY license (documentation).