smiffer 0.2.1

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 format (.dx). 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

$ 

🛠 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 data1EHE.pdb \
$         -p data1EHE_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/*.dx

🔍 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

This work is licensed under a MIT License.