<div align="center">
# ⌛️ smiffer 🦙
[](https://www.python.org/downloads/release/python-350/)
[](https://opensource.org/licenses/MIT)
<img src="https://smiffer.mol3d.tech/ressources/img/logo_compress.png" width="40%">
Contributors: **Diego BARQUERO MORERA** and **Lucas ROUAUD**
**Documentation:** https://smiffer.mol3d.tech/
</div align="center">
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](https://github.com/pypa/pipx?tab=readme-ov-file#install-pipx)
```bash
$ pipx install smiffer
# Checking the installation is done.
$ smiffer --help
```
> **🦊 From the GitLab repository:**
>
> ```bash
> $ git clone https://gitlab.galaxy.ibpc.fr/rouaud/smiffer.git
> $ cd smiffer/
> $ pipx install .
>
> # Checking the installation is done.
> $ smiffer --help
> ```
### 🐍 Using pip
```bash
$ python3 -m pip install smiffer
# Checking the installation is done.
$ smiffer --help
```
> **🦊 From the GitLab repository:**
>
> ```bash
> $ 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
```bash
$ docker build -t smiffer-image .
$ docker run -it smiffer-image
# Checking the installation is done.
$ smiffer -h
```
### 🛠 From scratch (not recommended)
```bash
$ 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/`:
```sh
$ 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**:
```yml
box:
extra_size: 5
area_mode: whole
other:
macromolecule: protein
```
Here is a first example to run the software specific part of an **RNA**:
```yml
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<br/>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<br/>electrostatic grid. |
| **`-h` or `--help`** | No | Flag | Display the help and exit the<br/>program. |
| **`-v` or `--version`** | No | Flag | Display the version and exit the<br/>program. |
| **`--verbose`** | No | Flag | Activated a verbose mode, so more<br/>information are going to be displayed. |
## 🙇♂️ Acknowledgement
🔍 Code reviewing: **Hubert SANTUZ**
✒️ Formula checking: **Jules MARIEN**
_This work is licensed under a [MIT License](https://opensource.org/licenses/MIT)._
[](https://opensource.org/licenses/MIT)
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"description": "<div align=\"center\">\n\n# \u231b\ufe0f smiffer \ud83e\udd99\n\n[](https://www.python.org/downloads/release/python-350/)\n[](https://opensource.org/licenses/MIT)\n\n<img src=\"https://smiffer.mol3d.tech/ressources/img/logo_compress.png\" width=\"40%\">\n\nContributors: **Diego BARQUERO MORERA** and **Lucas ROUAUD**\n\n**Documentation:** https://smiffer.mol3d.tech/\n\n</div align=\"center\">\n\nThis 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.\n\n## \u2699\ufe0f Installation\n\n### \ud83d\udce6 Using pipx (recommended)\n\n- pipx link: [https://github.com/pypa/pipx?tab=readme-ov-file#install-pipx](https://github.com/pypa/pipx?tab=readme-ov-file#install-pipx)\n\n```bash\n$ pipx install smiffer\n\n# Checking the installation is done.\n$ smiffer --help\n```\n\n> **\ud83e\udd8a From the GitLab repository:**\n>\n> ```bash\n> $ git clone https://gitlab.galaxy.ibpc.fr/rouaud/smiffer.git\n> $ cd smiffer/\n> $ pipx install .\n>\n> # Checking the installation is done.\n> $ smiffer --help\n> ```\n\n### \ud83d\udc0d Using pip\n\n```bash\n$ python3 -m pip install smiffer\n\n# Checking the installation is done.\n$ smiffer --help\n```\n\n> **\ud83e\udd8a From the GitLab repository:**\n>\n> ```bash\n> $ git clone https://gitlab.galaxy.ibpc.fr/rouaud/smiffer.git\n> $ cd smiffer/\n> $ python3 -m pip install .\n>\n> # Checking the installation is done.\n> $ smiffer --help\n> ```\n\n### \ud83d\udc0b Using docker\n\n```bash\n$ docker build -t smiffer-image .\n$ docker run -it smiffer-image\n\n# Checking the installation is done.\n$ smiffer -h\n```\n\n### \ud83d\udee0 From scratch (not recommended)\n\n```bash\n$ git clone https://gitlab.galaxy.ibpc.fr/rouaud/smiffer.git\n$ cd smiffer\n\n# Install globaly these packages\u2026\n$ pip install -r env/requirements.txt\n\n# Checking the installation is done.\n$ python -m src.smiffer --help\n```\n\n## \ud83c\udf10 External software\n\nThe APBS server can be found at next url: https://server.poissonboltzmann.org/.\n\n## \ud83d\ude80 Launching the software\n\n### \ud83c\udfa5 Example\n\nTo test the program, use the following commands in `\ud83d\udcc1 smiffer/`:\n\n```sh\n$ mkdir data/output/\n\n# Launching the software.\n$ smiffer -i data/1EHE.pdb \\\n$ -p data/1EHE_parameter.yml \\\n$ -a data/1EHE_APBS.dx \\\n$ -o data/output/\n\n# Visualize using VMD (or other like PyMol, Chimera, Mol*, etc.).\n$ vmd data/1EHE.pdb data/output/*.mrc\n```\n\n### \ud83d\udd27 `parameter.yml`\n\nTo see what are the options you can use, check: https://smiffer.mol3d.tech/parameter/.\nIn this file, you can specify a lot of options to setup the software.\nHere is a first example to run the software on whole **protein**:\n\n```yml\nbox:\n extra_size: 5\n area_mode: whole\nother:\n macromolecule: protein\n```\n\nHere is a first example to run the software specific part of an **RNA**:\n\n```yml\nbox:\n area_mode: pocket_sphere\n center:\n x: 0.7\n y: -1.8\n z: 3.6\n # Integer.\n radius: 9\nother:\n macromolecule: nucleic\n```\n\n> **\ud83d\udcdd Note :**\n>\n> This file is not mandatory. If not used, the software is going to fall back on default parameters.\n> Check https://smiffer.mol3d.tech/parameter/ for more information.\n\n### \ud83d\udd0d Parameters description\n\n| **Argument** | **Mandatory?** | **Type and usage** | **Description** |\n| :------------------------ | :------------: | :--------------------- | :--------------------------------------------------------------------------- |\n| **`-i` or `--input`** | Yes | `--input file.pdb` | The `.pdb` file that while be used<br/>to computed the properties. |\n| **`-o` or `--output`** | Yes | `--output directory` | The directory to output the results. |\n| **`-p` or `--parameter`** | No | `--parameter file.yml` | The YAML parameters file. |\n| **`-a` or `--apbs`** | No | `--apbs file.dx` | The already computed APBS<br/>electrostatic grid. |\n| **`-h` or `--help`** | No | Flag | Display the help and exit the<br/>program. |\n| **`-v` or `--version`** | No | Flag | Display the version and exit the<br/>program. |\n| **`--verbose`** | No | Flag | Activated a verbose mode, so more<br/>information are going to be displayed. |\n\n## \ud83d\ude47\u200d\u2642\ufe0f Acknowledgement\n\n\ud83d\udd0d Code reviewing: **Hubert SANTUZ**\n\n\u2712\ufe0f Formula checking: **Jules MARIEN**\n\n_This work is licensed under a [MIT License](https://opensource.org/licenses/MIT)._\n\n[](https://opensource.org/licenses/MIT)\n",
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