MDverse database schema

Setup environment

We use uv to manage dependencies and the project environment.

Clone the GitHub repository:

git clone git@github.com:MDverse/mdverse_data_schema.git
cd mdverse_data_schema

Sync dependencies:

uv sync

Retrieve data

Download parquet files from Zenodo to build the database:

uv run src/download_data.py

Files will be downloaded to data/parquet_files:

data
└── parquet_files
    ├── datasets.parquet
    ├── files.parquet
    ├── gromacs_gro_files.parquet
    ├── gromacs_mdp_files.parquet
    ├── gromacs_xtc_files.parquet

Build the database

Create the empty database:

uv run src/create_database.py

Populate the tables with the data from parquet files:

uv run src/ingest_data.py

Information on the database

Report on the number of rows and columns of the table of the database:

uv run report.py

This will create the file report.log with the information.

Re-ingesting simulation data

If you wish to re-ingest data from any of the following tables:

• TopologyFile
• ParameterFile
• TrajectoryFile

You can run these commands:

uv run src/ingest_topol_files.py

or

uv run src/ingest_param_files.py

or

uv run src/ingest_traj_files.py