Compute possible interaction with fields arround protein or RNA.
Project description
⌛️ 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 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 usedto 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. |
🙇♂️ Aknowledgement
🔍 Code reviewing: Hubert SANTUZ
✒️ Formula checking: Jules MARIEN
This work is licensed under a MIT License.
Project details
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