smiffer 0.3.3

Compute possible interaction with fields arround protein or RNA.

⌛️ smiffer 🦙

Contributors: Diego BARQUERO MORERA and Lucas ROUAUD

Documentation: https://smiffer.mol3d.tech/

This software is coded in python. It permits to produced grids, into a OpenDX (.dx) or MRC (.mrc) format. With those grids, it is possible to visualize multiple physical and chemical properties around a protein. This permit to see all possible area of interaction (with proteins, ligands or lipids) around a protein.

⚙️ Installation

📦 Using pipx (recommended)

• pipx link: https://github.com/pypa/pipx?tab=readme-ov-file#install-pipx

$ pipx install smiffer

# Checking the installation is done.
$ smiffer --help

🦊 From the GitLab repository:

$ git clone https://gitlab.galaxy.ibpc.fr/rouaud/smiffer.git
$ cd smiffer/
$ pipx install .

# Checking the installation is done.
$ smiffer --help

🐍 Using pip

$ python3 -m pip install smiffer

# Checking the installation is done.
$ smiffer --help

🦊 From the GitLab repository:

$ git clone https://gitlab.galaxy.ibpc.fr/rouaud/smiffer.git
$ cd smiffer/
$ python3 -m pip install .

# Checking the installation is done.
$ smiffer --help

🐋 Using docker

$ docker build -t smiffer-image .
$ docker run -it smiffer-image

# Checking the installation is done.
$ smiffer -h

🛠 From scratch (not recommended)

$ git clone https://gitlab.galaxy.ibpc.fr/rouaud/smiffer.git
$ cd smiffer

# Install globaly these packages…
$ pip install -r env/requirements.txt

# Checking the installation is done.
$ python -m src.smiffer --help

🌐 External software

The APBS server can be found at next url: https://server.poissonboltzmann.org/.

🚀 Launching the software

🎥 Example

To test the program, use the following commands in 📁 smiffer/:

$ mkdir data/output/

# Launching the software.
$ smiffer -i data/1EHE.pdb \
$         -p data/1EHE_parameter.yml \
$         -a data/1EHE_APBS.dx \
$         -o data/output/

# Visualize using VMD (or other like PyMol, Chimera, Mol*, etc.).
$ vmd data/1EHE.pdb data/output/*.mrc

🔧 parameter.yml

To see what are the options you can use, check: https://smiffer.mol3d.tech/parameter/. In this file, you can specify a lot of options to setup the software. Here is a first example to run the software on whole protein:

box:
    extra_size: 5
    area_mode: whole
other:
    macromolecule: protein

Here is a first example to run the software specific part of an RNA:

box:
    area_mode: pocket_sphere
    center:
        x: 0.7
        y: -1.8
        z: 3.6
    # Integer.
    radius: 9
other:
    macromolecule: nucleic

📝 Note :

This file is not mandatory. If not used, the software is going to fall back on default parameters. Check https://smiffer.mol3d.tech/parameter/ for more information.

🔍 Parameters description

Argument	Mandatory?	Type and usage	Description
-i or --input	Yes	--input file.pdb	The .pdb file that while be used to computed the properties.
-o or --output	Yes	--output directory	The directory to output the results.
-p or --parameter	No	--parameter file.yml	The YAML parameters file.
-a or --apbs	No	--apbs file.dx	The already computed APBS electrostatic grid.
-h or --help	No	Flag	Display the help and exit the program.
-v or --version	No	Flag	Display the version and exit the program.
--verbose	No	Flag	Activated a verbose mode, so more information are going to be displayed.

🙇‍♂️ Acknowledgement

🔍 Code reviewing: Hubert SANTUZ

✒️ Formula checking: Jules MARIEN

🔎 Citation

Statistical Molecular Interaction Fields: A Fast and Informative Tool for Characterizing RNA and Protein-Binding Pockets

Diego Barquero Morera, Giovanni Mattiotti, Alexandar Kocev, Amshuman Rousselot, Louis Meuret, Lucas Rouaud, Hubert Santuz, Marc Baaden, Antoine Taly, and Samuela Pasquali

Journal of Chemical Theory and Computation 2025 21 (18), 9120-9135

DOI: 10.1021/acs.jctc.5c00688

This work is licensed under a MIT License.