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
pipxoruvas 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-xwill be translated to-x opt1 opt2in 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
MITlicense (software). - A
CC-BYlicense (documentation).
1 maintainer
Metadata
1 maintainer
Release files for strange-mol 0.2.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| strange_mol-0.2.0.tar.gz | 42.5 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| strange_mol-0.2.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 84.9 kB
Release files / strange_mol-0.2.0.tar.gz
| Download URL | strange_mol-0.2.0.tar.gz |
|---|---|
| Size | 42.5 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
a822127ff84c34c043a05262e40bcfbbe26ac2668e135acc3eaae05e3332b8ba
|
|
BLAKE2b-256 checksum How to use checksums |
3a23f06e8a8c17ec27ce388e516ef36bd7c5b9cc4ef40e52e548b667f3546ebd
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
uv/0.10.4 {"installer":{"name":"uv","version":"0.10.4","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":null}
|
Release files / strange_mol-0.2.0-py3-none-any.whl
| Download URL | strange_mol-0.2.0-py3-none-any.whl |
|---|---|
| Size | 42.4 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
e6dacbb5836c892b2a904b787b9f0efa81a5d365110f8bfad4b315ae8208c08f
|
|
BLAKE2b-256 checksum How to use checksums |
d3f222caa6948e7df0ad91e2a17abe438607ea4dfc6a49038df639e74230bd5e
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
uv/0.10.4 {"installer":{"name":"uv","version":"0.10.4","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":null}
|
