.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/2D_simulation(crystalline)/plot_6_PASS_itraconazole_drug.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_examples_2D_simulation(crystalline)_plot_6_PASS_itraconazole_drug.py>`
        to download the full example code

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

.. _sphx_glr_examples_2D_simulation(crystalline)_plot_6_PASS_itraconazole_drug.py:


Itraconazole, ¹³C (I=1/2) PASS
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

¹³C (I=1/2) 2D Phase-adjusted spinning sideband (PASS) simulation.

.. GENERATED FROM PYTHON SOURCE LINES 9-13

The following is a simulation of a 2D PASS spectrum of itraconazole, a triazole
containing drug prescribed for the prevention and treatment of fungal infection.
The 2D PASS spectrum is a correlation of finite speed MAS to an infinite speed MAS
spectrum. The parameters for the simulation are obtained from Dey `et al.` [#f1]_.

.. GENERATED FROM PYTHON SOURCE LINES 13-21

.. code-block:: Python

    import matplotlib.pyplot as plt

    from mrsimulator import Simulator
    from mrsimulator.method.lib import SSB2D
    from mrsimulator import signal_processor as sp
    from mrsimulator.method import SpectralDimension









.. GENERATED FROM PYTHON SOURCE LINES 23-26

There are 41 :math:`^{13}\text{C}` single-site spin systems partially describing the
NMR parameters of itraconazole. We will import the directly import the spin systems
to the Simulator object using the `load_spin_systems` method.

.. GENERATED FROM PYTHON SOURCE LINES 26-32

.. code-block:: Python


    sim = Simulator()

    filename = "https://ssnmr.org/sites/default/files/mrsimulator/itraconazole_13C.mrsys"
    sim.load_spin_systems(filename)








.. GENERATED FROM PYTHON SOURCE LINES 33-35

Use the ``SSB2D`` method to simulate a PASS, MAT, QPASS, QMAT, or any equivalent
sideband separation spectrum. Here, we use the method to generate a PASS spectrum.

.. GENERATED FROM PYTHON SOURCE LINES 35-60

.. code-block:: Python

    PASS = SSB2D(
        channels=["13C"],
        magnetic_flux_density=11.74,
        rotor_frequency=2000,
        spectral_dimensions=[
            SpectralDimension(
                count=20 * 4,
                spectral_width=2000 * 20,  # value in Hz
                label="Anisotropic dimension",
            ),
            SpectralDimension(
                count=1024,
                spectral_width=3e4,  # value in Hz
                reference_offset=1.1e4,  # value in Hz
                label="Isotropic dimension",
            ),
        ],
    )
    sim.methods = [PASS]  # add the method.

    # A graphical representation of the method object.
    plt.figure(figsize=(5, 2.5))
    PASS.plot()
    plt.show()




.. image-sg:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_6_PASS_itraconazole_drug_001.png
   :alt: SSB2D
   :srcset: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_6_PASS_itraconazole_drug_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 61-64

For 2D spinning sideband simulation, set the number of spinning sidebands in the
Simulator.config object to `spectral_width/rotor_frequency` along the sideband
dimension.

.. GENERATED FROM PYTHON SOURCE LINES 64-69

.. code-block:: Python

    sim.config.number_of_sidebands = 20

    # run the simulation.
    sim.run()








.. GENERATED FROM PYTHON SOURCE LINES 70-72

Apply post-simulation processing. Here, we apply a Lorentzian line broadening to the
isotropic dimension.

.. GENERATED FROM PYTHON SOURCE LINES 72-83

.. code-block:: Python

    dataset = sim.methods[0].simulation
    processor = sp.SignalProcessor(
        operations=[
            sp.IFFT(dim_index=0),
            sp.apodization.Exponential(FWHM="100 Hz", dim_index=0),
            sp.FFT(dim_index=0),
        ]
    )
    processed_dataset = processor.apply_operations(dataset=dataset).real
    processed_dataset /= processed_dataset.max()








.. GENERATED FROM PYTHON SOURCE LINES 84-85

The plot of the simulation.

.. GENERATED FROM PYTHON SOURCE LINES 85-94

.. code-block:: Python

    plt.figure(figsize=(4.25, 3.0))
    ax = plt.subplot(projection="csdm")
    cb = ax.imshow(processed_dataset, aspect="auto", cmap="gist_ncar_r", vmax=0.5)
    plt.colorbar(cb)
    ax.invert_xaxis()
    ax.invert_yaxis()
    plt.tight_layout()
    plt.show()




.. image-sg:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_6_PASS_itraconazole_drug_002.png
   :alt: plot 6 PASS itraconazole drug
   :srcset: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_6_PASS_itraconazole_drug_002.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 95-99

.. [#f1] Dey, K .K, Gayen, S., Ghosh, M., Investigation of the Detailed Internal
      Structure and Dynamics of Itraconazole by Solid-State NMR Measurements,
      ACS Omega (2019) **4**, 21627.
      `DOI:10.1021/acsomega.9b03558 <https://doi.org/10.1021/acsomega.9b03558>`_


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

   **Total running time of the script:** (0 minutes 1.101 seconds)


.. _sphx_glr_download_examples_2D_simulation(crystalline)_plot_6_PASS_itraconazole_drug.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: plot_6_PASS_itraconazole_drug.ipynb <plot_6_PASS_itraconazole_drug.ipynb>`

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

      :download:`Download Python source code: plot_6_PASS_itraconazole_drug.py <plot_6_PASS_itraconazole_drug.py>`


.. only:: html

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

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