.. _hello-water:

Hello Water
===========

Starting with an empty database::

    $ bee molecule list
    | id | canonical_smiles | multiplicity | charge | molecular_formula | recipe_ids | identifiers | tags |
    +----+------------------+--------------+--------+-------------------+------------+-------------+------+

.. note::
   Tip: All ``bee`` sub-commands may be abbreviated as long as it is unique.
   E.g. above command can be abbreviated as ``bee mol l``.


Add Water to the Database
-------------------------

Single molecules can be added to the database using ``bee mol create`` and
specifying the SMILES string. The following adds water as a **Molecule** with
``id=1``::

    $ bee mol create --smiles O
    1
    $ bee mol list
    | id | canonical_smiles | multiplicity | charge | molecular_formula | recipe_ids | identifiers | tags |
    +----+------------------+--------------+--------+-------------------+------------+-------------+------+
    | 1  |        O         |      1       |   0    |        H2O        |            |             |      |

Alternatively, we could use the REST-API:

.. code-block:: sh

    $ curl -X 'POST' \
        'http://localhost:8000/api/v1/molecule' \
        -H 'accept: application/json' \
        -H 'Content-Type: application/json' \
        -d '{
        "smiles": "O"
        }'
.. code-block:: json

    {
      "id": 1,
      "canonical_smiles": "O",
      "original_smiles": "O",
      "inchi": "InChI=1S/H2O/h1H2",
      "multiplicity": 1,
      "ambiguous_input": false,
      "charge": 0,
      "mass": 18.015,
      "molecular_formula": "H2O",
      "number_of_atoms": 3,
      "atoms": [
        "H",
        "H",
        "O"
      ],
      "bonds": [
        {
          "atom_indices": [
            0,
            2
          ],
          "type": "SINGLE"
        },
        {
          "atom_indices": [
            1,
            2
          ],
          "type": "SINGLE"
        }
      ],
      "identifiers": [],
      "tags": [],
      "initial_conformers": [
        {
          "id": 1,
          "coordinates": [
            [
              0.7903084630389962,
              -0.19728968119872656,
              0
            ],
            [
              -0.7870020412828991,
              -0.1999835515539665,
              -0
            ],
            [
              -0.0033064217560969445,
              0.3972732327526928,
              -0
            ]
          ],
          "trajectory_step": 0,
          "tags": null,
          "properties": [],
          "conformer_generations": [],
          "optimisations": [],
          "nms": []
        }
      ],
      "recipes": []
    }




Run Weasel confSearch workflow on water
---------------------------------------

Running Weasel manually can be quite cumbersome because it requires to add a
**Workflow** by hand, but we would like to present it nevertheless once for
easier understanding. In the next subsection we present an easier method using
**Recipes**.

.. asciinema:: water_confsearch.cast
   :preload: 1

..
    PS1='/tmp $ '
    bee workflow create -h
    bee workflow create --name 'aiqu_confSearch' --command 'weasel -W aiqu_confSearch -bee-conf 1 -bee-workflow {id}' --software 'WEASEL'
    bee workflow get 1
    weasel -W aiqu_confSearch -bee-conf 1 -bee-workflow 1
    bee workflow overview 1


.. _browsing:

Browsing the results
--------------------

As shown above, we now have the following simulations from this Weasel run:

.. code-block::

    $ bee workflow overview 1
    Workflow 1 (aiqu_confsearch) has FINISHED on 2022-06-21 10:37:23
        [     18s]   1  #1 CONFORMER_GENERATION (CREST-RDKIT) on Conformer 1 generating Conformers 3, 2
        [      0s]   2  #1 SIMULATION (XTB) on Conformer 3
        [      0s]   3  #1 SIMULATION (XTB) on Conformer 2
        [      0s]   4  #2 OPTIMISATION (XTB) on Conformer 2 generating Conformers 4@0
        [      1s]   5  #3 OPTIMISATION (r2SCAN-3c) on Conformer 4 generating Conformers 5@3
        [     10s]   6  #4 OPTIMISATION (wB97M-V) on Conformer 5 generating Conformers 9@5, 8@4, 7@2, 6@0

Starting with the **Molecule's** initial conformer, **Bee** stores the origin of
each **Conformer** in a tree of alternating **Conformers** and **Simulations**.
The CLI allows to print it::

    $ bee mol tree --show-methods 1
    Molecule 1: O
    └── Conformer 1
        └── Conformer Generation (CREST-RDKIT) 1
            ├── Conformer 2
            │   ├── Simulation (XTB) 3
            │   └── Optimisation (XTB) 4
            │       └── Conformer 4
            │           └── Optimisation (r2SCAN-3c) 5
            │               └── Conformer 5
            │                   └── Optimisation (wB97M-V) 6
            │                       ├── Conformer 6
            │                       ├── Conformer 7
            │                       ├── Conformer 8
            │                       └── Conformer 9
            └── Conformer 3
                └── Simulation (XTB) 2

..
    code-block:: yaml

    Molecule:
      id: 1
      smiles: O
      initial_conformers:
        - Conformer:
            id: 1
            coordinates: ...
            conformer_generations:
              - Simulation:
                  id: 1
                  type: CONFORMER_GENERATION
                  generated_conformers:
                    - Conformer:
                        id: 2
                        coordinates: ...
                        properties: [ ... ]
                        conformer_generations: []
                        optimisations:
                          - Simulation:
                              id: 4
                              type: OPTIMISATION
                              generated_conformers:
                                - Conformer:
                                    id: 4
                                    coordinates: []
                                    properties: [ ... ]
                                    ...
                    - Conformer:
                        id: 3
                        coordinates: ...
                        properties: [ ... ]
                        conformer_generations: []
                        optimisations:
                          - Simulation:
                              id: 136
                              type: OPTIMISATION
                              generated_conformers:
                                - Conformer:
                                    id: 23
                                    coordinates: []
                                    properties: [ ... ]
                                    ...
            optimisations: []


Here is the original JSON dump from the Weasel run which can be obtained
via ``bee mol get --depth=-1 1`` or directly in a browser:
`http://localhost:8000/api/v1/molecule/1?depth=-1 <http://localhost:8000/api/v1/molecule/1?depth=-1>`_ (:download:`json <water_confsearch.json>`):

.. literalinclude:: water_confsearch.json
    :language: json