.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/1D_simulation(macro_amorphous)/plot_0_protein_GB1.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_examples_1D_simulation(macro_amorphous)_plot_0_protein_GB1.py>`
        to download the full example code

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

.. _sphx_glr_examples_1D_simulation(macro_amorphous)_plot_0_protein_GB1.py:


Protein GB1, ¹³C and ¹⁵N (I=1/2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

¹³C/¹⁵N (I=1/2) spinning sideband simulation.

.. GENERATED FROM PYTHON SOURCE LINES 9-15

The following is the spinning sideband simulation of a macromolecule, protein GB1. The
:math:`^{13}\text{C}` and :math:`^{15}\text{N}` CSA tensor parameters were obtained
from Hung `et al.` [#f1]_, which consists of 42 :math:`^{13}\text{C}\alpha`,
44 :math:`^{13}\text{CO}`, and 44 :math:`^{15}\text{NH}` tensors. In the following
example, instead of creating 130 spin systems, we download the spin systems from
a remote file and load it directly to the Simulator object.

.. GENERATED FROM PYTHON SOURCE LINES 15-23

.. code-block:: Python

    import matplotlib.pyplot as plt

    from mrsimulator import Simulator
    from mrsimulator.method.lib import BlochDecaySpectrum
    from mrsimulator.method import SpectralDimension
    from mrsimulator import signal_processor as sp









.. GENERATED FROM PYTHON SOURCE LINES 25-26

Create the Simulator object and load the spin systems from an external file.

.. GENERATED FROM PYTHON SOURCE LINES 26-33

.. code-block:: Python

    sim = Simulator()

    host = "https://ssnmr.org/sites/default/files/mrsimulator/"
    filename = "protein_GB1_15N_13CA_13CO.mrsys"
    sim.load_spin_systems(host + filename)  # load the spin systems.
    print(f"number of spin systems = {len(sim.spin_systems)}")





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    number of spin systems = 130




.. GENERATED FROM PYTHON SOURCE LINES 34-37

.. code-block:: Python

    all_sites = sim.sites().to_pd()
    all_sites.head()






.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">
    <div>
    <style scoped>
        .dataframe tbody tr th:only-of-type {
            vertical-align: middle;
        }

        .dataframe tbody tr th {
            vertical-align: top;
        }

        .dataframe thead th {
            text-align: right;
        }
    </style>
    <table border="1" class="dataframe">
      <thead>
        <tr style="text-align: right;">
          <th></th>
          <th>isotope</th>
          <th>isotropic_chemical_shift</th>
          <th>shielding_symmetric.zeta</th>
          <th>shielding_symmetric.eta</th>
        </tr>
      </thead>
      <tbody>
        <tr>
          <th>0</th>
          <td>15N</td>
          <td>123.33333333333333 ppm</td>
          <td>-118.66666666666667 ppm</td>
          <td>0.101124</td>
        </tr>
        <tr>
          <th>1</th>
          <td>15N</td>
          <td>121.66666666666667 ppm</td>
          <td>-115.33333333333333 ppm</td>
          <td>0.225434</td>
        </tr>
        <tr>
          <th>2</th>
          <td>15N</td>
          <td>125.33333333333333 ppm</td>
          <td>-110.66666666666667 ppm</td>
          <td>0.000000</td>
        </tr>
        <tr>
          <th>3</th>
          <td>15N</td>
          <td>125.33333333333333 ppm</td>
          <td>-110.66666666666667 ppm</td>
          <td>0.126506</td>
        </tr>
        <tr>
          <th>4</th>
          <td>15N</td>
          <td>126.0 ppm</td>
          <td>-114.0 ppm</td>
          <td>0.192982</td>
        </tr>
      </tbody>
    </table>
    </div>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 38-39

Create a :math:`^{13}\text{C}` Bloch decay spectrum method.

.. GENERATED FROM PYTHON SOURCE LINES 39-53

.. code-block:: Python

    method_13C = BlochDecaySpectrum(
        channels=["13C"],
        magnetic_flux_density=11.74,  # in T
        rotor_frequency=3000,  # in Hz
        spectral_dimensions=[
            SpectralDimension(
                count=8192,
                spectral_width=5e4,  # in Hz
                reference_offset=2e4,  # in Hz
                label=r"$^{13}$C resonances",
            )
        ],
    )








.. GENERATED FROM PYTHON SOURCE LINES 54-56

Since the spin systems contain both :math:`^{13}\text{C}` and :math:`^{15}\text{N}`
sites, let's also create a :math:`^{15}\text{N}` Bloch decay spectrum method.

.. GENERATED FROM PYTHON SOURCE LINES 56-70

.. code-block:: Python

    method_15N = BlochDecaySpectrum(
        channels=["15N"],
        magnetic_flux_density=11.74,  # in T
        rotor_frequency=3000,  # in Hz
        spectral_dimensions=[
            SpectralDimension(
                count=8192,
                spectral_width=4e4,  # in Hz
                reference_offset=7e3,  # in Hz
                label=r"$^{15}$N resonances",
            )
        ],
    )








.. GENERATED FROM PYTHON SOURCE LINES 71-72

Add the methods to the Simulator object and run the simulation

.. GENERATED FROM PYTHON SOURCE LINES 72-83

.. code-block:: Python


    # Add the methods.
    sim.methods = [method_13C, method_15N]

    # Run the simulation.
    sim.run()

    # Get the simulation dataset from the respective methods.
    dataset_13C = sim.methods[0].simulation  # method at index 0 is 13C Bloch decay method.
    dataset_15N = sim.methods[1].simulation  # method at index 1 is 15N Bloch decay method.








.. GENERATED FROM PYTHON SOURCE LINES 84-85

Add post-simulation signal processing.

.. GENERATED FROM PYTHON SOURCE LINES 85-94

.. code-block:: Python

    processor = sp.SignalProcessor(
        operations=[sp.IFFT(), sp.apodization.Exponential(FWHM="10 Hz"), sp.FFT()]
    )
    # apply post-simulation processing to dataset_13C
    processed_dataset_13C = processor.apply_operations(dataset=dataset_13C).real

    # apply post-simulation processing to dataset_15N
    processed_dataset_15N = processor.apply_operations(dataset=dataset_15N).real








.. GENERATED FROM PYTHON SOURCE LINES 95-96

The plot of the simulation after signal processing.

.. GENERATED FROM PYTHON SOURCE LINES 96-110

.. code-block:: Python

    fig, ax = plt.subplots(
        1, 2, subplot_kw={"projection": "csdm"}, sharey=True, figsize=(9, 4)
    )

    ax[0].plot(processed_dataset_13C, color="black", linewidth=0.5)
    ax[0].invert_xaxis()

    ax[1].plot(processed_dataset_15N, color="black", linewidth=0.5)
    ax[1].set_ylabel(None)
    ax[1].invert_xaxis()

    plt.tight_layout()
    plt.show()




.. image-sg:: /examples/1D_simulation(macro_amorphous)/images/sphx_glr_plot_0_protein_GB1_001.png
   :alt: plot 0 protein GB1
   :srcset: /examples/1D_simulation(macro_amorphous)/images/sphx_glr_plot_0_protein_GB1_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 111-116

.. [#f1] Hung I., Ge Y., Liu X., Liu M., Li C., Gan Z., Measuring
    :math:`^{13}\text{C}`/:math:`^{15}\text{N}` chemical shift anisotropy in
    [:math:`^{13}\text{C}`, :math:`^{15}\text{N}`] uniformly enriched proteins using
    CSA amplification, Solid State Nuclear Magnetic Resonance. 2015, **72**, 96-103.
    `DOI: 10.1016/j.ssnmr.2015.09.002 <https://doi.org/10.1016/j.ssnmr.2015.09.002>`_


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

   **Total running time of the script:** (0 minutes 2.530 seconds)


.. _sphx_glr_download_examples_1D_simulation(macro_amorphous)_plot_0_protein_GB1.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: plot_0_protein_GB1.ipynb <plot_0_protein_GB1.ipynb>`

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

      :download:`Download Python source code: plot_0_protein_GB1.py <plot_0_protein_GB1.py>`


.. only:: html

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

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