Docs:	https://aitomic.readthedocs.io/en/stable/
EPSRC Grant:	EP/Y028775/1

aitomic

aitomic is a Python library developed by the AIchemy Hub for making AI in chemistry simple. As a chemical researcher, you likely do not want to spend your time thinking about how to organize your data or collect it from various sources. Most likely, you want to write simple function call and get access to all your data in a data frame. Well, thats what aitomic does for you. Currently, the library provides tools for accessing your NMR data stored in a NOMAD NMR server. For example:

from aitomic import bruker, nomad_nmr

client = nomad_nmr.Client.login(
    "http://demo.nomad-nmr.uk",
    username="demo",
    password="dem0User",
)
experiments = client.auto_experiments()
peak_df = bruker.nmr_peaks_df_1d(experiments.download())
peak_df = nomad_nmr.add_metadata(client, peak_df)

┌─────────────────────────────────┬──────────┬──────────────┬────────────────────────────────┬───┬──────────────┬──────────┬──────────────────────────┬─────────────┐
│ spectrum                        ┆ ppm      ┆ integral     ┆ auto_experiment_id             ┆ … ┆ submitted_at ┆ username ┆ group_id_right           ┆ group_name  │
│ ---                             ┆ ---      ┆ ---          ┆ ---                            ┆   ┆ ---          ┆ ---      ┆ ---                      ┆ ---         │
│ str                             ┆ f64      ┆ f64          ┆ str                            ┆   ┆ null         ┆ str      ┆ str                      ┆ str         │
╞═════════════════════════════════╪══════════╪══════════════╪════════════════════════════════╪═══╪══════════════╪══════════╪══════════════════════════╪═════════════╡
│ 2410081201-0-1-lukasturcani/10… ┆ 8.344768 ┆ 20680.796875 ┆ 2410081201-0-1-lukasturcani-10 ┆ … ┆ null         ┆ test3    ┆ 672fdae0eb3b1c3c17062fee ┆ test-admins │
│ 2410081201-0-1-lukasturcani/10… ┆ 8.339878 ┆ 31792.195312 ┆ 2410081201-0-1-lukasturcani-10 ┆ … ┆ null         ┆ test3    ┆ 672fdae0eb3b1c3c17062fee ┆ test-admins │
│ 2410081201-0-1-lukasturcani/10… ┆ 8.338044 ┆ 20503.757812 ┆ 2410081201-0-1-lukasturcani-10 ┆ … ┆ null         ┆ test3    ┆ 672fdae0eb3b1c3c17062fee ┆ test-admins │
│ 2410081201-0-1-lukasturcani/10… ┆ 8.336821 ┆ 10042.96875  ┆ 2410081201-0-1-lukasturcani-10 ┆ … ┆ null         ┆ test3    ┆ 672fdae0eb3b1c3c17062fee ┆ test-admins │
│ 2410081201-0-1-lukasturcani/10… ┆ 8.323985 ┆ 10558.703125 ┆ 2410081201-0-1-lukasturcani-10 ┆ … ┆ null         ┆ test3    ┆ 672fdae0eb3b1c3c17062fee ┆ test-admins │
│ …                               ┆ …        ┆ …            ┆ …                              ┆ … ┆ …            ┆ …        ┆ …                        ┆ …           │
│ 2410161546-0-1-admin/10/pdata/… ┆ 1.398485 ┆ 10062.0      ┆ 2410161546-0-1-admin-10        ┆ … ┆ null         ┆ test1    ┆ 672fdae0eb3b1c3c17062fed ┆ group-1     │
│ 2410161546-0-1-admin/10/pdata/… ┆ 1.238337 ┆ 4.8948e7     ┆ 2410161546-0-1-admin-10        ┆ … ┆ null         ┆ test1    ┆ 672fdae0eb3b1c3c17062fed ┆ group-1     │
│ 2410161546-0-1-admin/10/pdata/… ┆ 1.051905 ┆ 31991.0      ┆ 2410161546-0-1-admin-10        ┆ … ┆ null         ┆ test1    ┆ 672fdae0eb3b1c3c17062fed ┆ group-1     │
│ 2410161546-0-1-admin/10/pdata/… ┆ 1.048848 ┆ 41602.6875   ┆ 2410161546-0-1-admin-10        ┆ … ┆ null         ┆ test1    ┆ 672fdae0eb3b1c3c17062fed ┆ group-1     │
│ 2410161546-0-1-admin/10/pdata/… ┆ 0.858137 ┆ 146085.9375  ┆ 2410161546-0-1-admin-10        ┆ … ┆ null         ┆ test1    ┆ 672fdae0eb3b1c3c17062fed ┆ group-1     │
└─────────────────────────────────┴──────────┴──────────────┴────────────────────────────────┴───┴──────────────┴──────────┴──────────────────────────┴─────────────┘

For more documentation make sure to check out our docs. There's lots of examples and it's easy to get started.

Installation

You can install aitomic via pip:

$ pip install aitomic

Development Notes

UV

This repository uses uv to manage the development environment. You can install uv by running the following command:

$ pip install uv

Once you have uv installed, you can set up the development environment by running the following command:

$ uv sync --all-extras --dev

From then on, you can run any command using uv with uv run.

See the uv documentation for more information.

Git LFS

This repository uses Git LFS to store large files. If you are cloning the repository, make sure to have Git LFS installed. You can find more information about Git LFS in the official documentation.

Unit Tests

The unit tests are written using pytest. To run the tests, you must have a local NOMAD NMR server running. You can install the server by following the instructions in the NOMAD NMR repository.

Once you have the server running, you must initialize the test database by running the following command:

$ uv run dev/init_nomad_nmr_test_db.py mongodb://localhost:27017 <PARENT_PATH>/nomad-server/datastore dev/nmr-data

Where <PARENT_PATH> is the path to the NOMAD NMR server repository.

You can then run the tests by running the following command:

$ uv run pytest --cov=src --cov-report term-missing

Documentation

The documentation is built using Sphinx.