# Molecular dynamics data analysis

## Setup your environment

Clone the repository:

```bash
git clone https://github.com/MDverse/mdda.git
```

Move to the new directory:

```bash
cd mdda
```

Install [miniconda](https://docs.conda.io/en/latest/miniconda.html).

Install [mamba](https://github.com/mamba-org/mamba):

```bash
conda install mamba -n base -c conda-forge
```

Create the `mdda` conda environment:
```
mamba env create -f binder/environment.yml
```

Load the `mdda` conda environment:
```
conda activate mdda
```

Note: you can also update the conda environment with:

```bash
mamba env update -f binder/environment.yml
```

To deactivate an active environment, use

```
conda deactivate
```

## Get data

Data files should be located in the `data` directory and comply with the [data model](https://github.com/MDverse/mdws/blob/main/docs/data_model.md).

## Analyse data

Use this script to run all Jupyter notebooks in batch mode:

```bash
bash make_results.sh
```

The directory `results` contains Jupyter notebooks exported in html, figures as .png and .svg images and a couple of TSF files.