.. only:: html

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

        Click :ref:`here <sphx_glr_download_examples_2D_simulation(crystalline)_plot_6_PASS_itraconazole_drug.py>`     to download the full example code or to run this example in your browser via Binder
    .. 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.

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]_.


.. code-block:: python

    import matplotlib as mpl
    import matplotlib.pyplot as plt
    import mrsimulator.signal_processing as sp
    import mrsimulator.signal_processing.apodization as apo
    from mrsimulator import Simulator
    from mrsimulator.methods import SSB2D

    # global plot configuration
    font = {"size": 9}
    mpl.rc("font", **font)
    mpl.rcParams["figure.figsize"] = [4.5, 3.0]








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.


.. code-block:: python


    sim = Simulator()

    filename = "https://sandbox.zenodo.org/record/687656/files/itraconazole_13C.mrsys"
    sim.load_spin_systems(filename)









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.


.. code-block:: python

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

    # 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.
    sim.config.number_of_sidebands = 20

    # run the simulation.
    sim.run()








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


.. code-block:: python

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








The plot of the simulation.


.. code-block:: python

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




.. image:: /examples/2D_simulation(crystalline)/images/sphx_glr_plot_6_PASS_itraconazole_drug_001.png
    :alt: plot 6 PASS itraconazole drug
    :class: sphx-glr-single-img





.. [#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  1.452 seconds)


.. _sphx_glr_download_examples_2D_simulation(crystalline)_plot_6_PASS_itraconazole_drug.py:


.. only :: html

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


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