.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/9-showing_custom_bonds.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_examples_9-showing_custom_bonds.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_examples_9-showing_custom_bonds.py:


Showing custom bonds using stk
==============================

This example demonstrates how to add shapes into the chemiscope output such
that custom bonds that would not automatically be assigned can be rendered.

This is done by using `stk <https://stk.readthedocs.io/en/stable/>`_ to
generate and analyse molecules, which comes with topology/bonding information
by default (using the cheminformatic software rdkit).

We use `stko <https://stko-docs.readthedocs.io/en/latest/>`_ to calculate
some rudimentary properties of `stk` molecules. `stko` can be installed with
``pip install stko``.

.. GENERATED FROM PYTHON SOURCE LINES 17-24

.. code-block:: Python


    import stk
    import stko
    from rdkit.Chem import AllChem as rdkit

    import chemiscope








.. GENERATED FROM PYTHON SOURCE LINES 25-28

Generate a list of stk BuildingBlocks (representation of a molecule) with
properties. This also includes working with rdkit, which comes installed
with stk.

.. GENERATED FROM PYTHON SOURCE LINES 29-128

.. code-block:: Python


    rdkitmol = rdkit.MolFromSmiles("Cc1ccccc1")
    rdkitmol = rdkit.AddHs(rdkitmol)
    rdkit.Kekulize(rdkitmol)
    params = rdkit.ETKDGv3()
    params.randomSeed = 0xF00D
    rdkit.EmbedMolecule(rdkitmol, params)

    structures = [
        # A building block.
        stk.BuildingBlock(smiles="NCCN"),
        # A mostly optimised cage molecule.
        stk.ConstructedMolecule(
            topology_graph=stk.cage.FourPlusSix(
                building_blocks=(
                    stk.BuildingBlock(
                        smiles="NCCN",
                        functional_groups=[stk.PrimaryAminoFactory()],
                    ),
                    stk.BuildingBlock(
                        smiles="O=CC(C=O)C=O",
                        functional_groups=[stk.AldehydeFactory()],
                    ),
                ),
                optimizer=stk.MCHammer(),
            ),
        ),
        # A metal-organic cage.
        stk.ConstructedMolecule(
            stk.cage.M2L4Lantern(
                building_blocks=(
                    stk.BuildingBlock(
                        smiles="[Pd+2]",
                        functional_groups=(
                            stk.SingleAtom(stk.Pd(0, charge=2)) for i in range(4)
                        ),
                        position_matrix=[[0.0, 0.0, 0.0]],
                    ),
                    stk.BuildingBlock(
                        smiles=("C1=NC=CC(C2=CC=CC(C3=C" "C=NC=C3)=C2)=C1"),
                        functional_groups=[
                            stk.SmartsFunctionalGroupFactory(
                                smarts="[#6]~[#7X2]~[#6]",
                                bonders=(1,),
                                deleters=(),
                            ),
                        ],
                    ),
                ),
                # Ensure that bonds between the
                # GenericFunctionalGroups of the ligand and the
                # SingleAtom functional groups of the metal are
                # dative.
                reaction_factory=stk.DativeReactionFactory(
                    stk.GenericReactionFactory(
                        bond_orders={
                            frozenset(
                                {
                                    stk.GenericFunctionalGroup,
                                    stk.SingleAtom,
                                }
                            ): 9,
                        },
                    ),
                ),
            ),
        ),
        # A host guest molecule.
        stk.ConstructedMolecule(
            topology_graph=stk.host_guest.Complex(
                host=stk.BuildingBlock.init_from_molecule(
                    stk.ConstructedMolecule(
                        topology_graph=stk.cage.FourPlusSix(
                            building_blocks=(
                                stk.BuildingBlock(
                                    smiles="NC1CCCCC1N",
                                    functional_groups=[
                                        stk.PrimaryAminoFactory(),
                                    ],
                                ),
                                stk.BuildingBlock(
                                    smiles="O=Cc1cc(C=O)cc(C=O)c1",
                                    functional_groups=[stk.AldehydeFactory()],
                                ),
                            ),
                            optimizer=stk.MCHammer(),
                        ),
                    )
                ),
                guests=stk.host_guest.Guest(
                    building_block=stk.BuildingBlock("[Br][Br]"),
                ),
            ),
        ),
        # From rdkit.
        stk.BuildingBlock.init_from_rdkit_mol(rdkitmol),
    ]









.. GENERATED FROM PYTHON SOURCE LINES 129-131

Write their properties using any method, here we show using stko:
https://stko-docs.readthedocs.io/en/latest/

.. GENERATED FROM PYTHON SOURCE LINES 132-143

.. code-block:: Python


    energy = stko.UFFEnergy()
    shape_calc = stko.ShapeCalculator()
    properties = {
        "uffenergy": [energy.get_energy(molecule) for molecule in structures],
        "aspheriticty": [
            shape_calc.get_results(molecule).get_asphericity() for molecule in structures
        ],
    }









.. GENERATED FROM PYTHON SOURCE LINES 144-145

Get the stk bonding information and convert them into shapes.

.. GENERATED FROM PYTHON SOURCE LINES 146-156

.. code-block:: Python

    shape_dict = chemiscope.convert_stk_bonds_as_shapes(
        frames=structures,
        bond_color="#fc5500",
        bond_radius=0.12,
    )

    # Write the shape string for settings to turn them on automatically.
    shape_string = ",".join(shape_dict.keys())









.. GENERATED FROM PYTHON SOURCE LINES 157-158

A chemiscope widget showing the result without the added bonding.

.. GENERATED FROM PYTHON SOURCE LINES 159-163

.. code-block:: Python


    chemiscope.show(frames=structures, properties=properties)




.. chemiscope:: _datasets/fig_9-showing_custom_bonds_015.json.gz
            :mode: default
        


.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">

    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 164-165

Writing to a json.gz file, again without added bonding.

.. GENERATED FROM PYTHON SOURCE LINES 166-176

.. code-block:: Python


    chemiscope.write_input(
        path="noshape_example.json.gz",
        frames=structures,
        properties=properties,
        meta=dict(name="Missing bonds by automation."),
        settings=chemiscope.quick_settings(x="aspheriticty", y="uffenergy", color=""),
    )









.. GENERATED FROM PYTHON SOURCE LINES 177-178

Now with added bonding information.

.. GENERATED FROM PYTHON SOURCE LINES 179-197

.. code-block:: Python


    chemiscope.show(
        frames=structures,
        properties=properties,
        shapes=shape_dict,
        settings=chemiscope.quick_settings(
            x="aspheriticty",
            y="uffenergy",
            color="",
            structure_settings={
                "shape": shape_string,
                "atoms": True,
                "bonds": False,
                "spaceFilling": False,
            },
        ),
    )



.. chemiscope:: _datasets/fig_9-showing_custom_bonds_016.json.gz
            :mode: default
        


.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">

    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 198-199

Write to json file with added shapes.

.. GENERATED FROM PYTHON SOURCE LINES 200-219

.. code-block:: Python


    chemiscope.write_input(
        path="shape_example.json.gz",
        frames=structures,
        properties=properties,
        meta=dict(name="Added all stk bonds."),
        settings=chemiscope.quick_settings(
            x="aspheriticty",
            y="uffenergy",
            color="",
            structure_settings={
                "shape": shape_string,
                "atoms": True,
                "bonds": False,
                "spaceFilling": False,
            },
        ),
        shapes=shape_dict,
    )








.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 1.001 seconds)


.. _sphx_glr_download_examples_9-showing_custom_bonds.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: 9-showing_custom_bonds.ipynb <9-showing_custom_bonds.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: 9-showing_custom_bonds.py <9-showing_custom_bonds.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: 9-showing_custom_bonds.zip <9-showing_custom_bonds.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_