.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "examples/gallery/structure/molecule/molecular_visualization.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code .. rst-class:: sphx-glr-example-title .. _sphx_glr_examples_gallery_structure_molecule_molecular_visualization.py: Molecular visualization of a small molecule using Matplotlib ============================================================ .. currentmodule:: biotite.structure.graphics *Biotite* provides simple interactive molecular visualization via :func:`plot_atoms()`. Although it does not produce publication-suitable images, this function can be a convenient tool for a quick visual analysis of a structure. This example displays the small molecule caffeine. .. GENERATED FROM PYTHON SOURCE LINES 15-71 .. container:: sphx-glr-animation .. raw:: html

.. code-block:: Python # Code source: Patrick Kunzmann # License: BSD 3 clause import matplotlib.pyplot as plt import numpy as np from matplotlib.animation import FuncAnimation import biotite.structure as struc import biotite.structure.graphics as graphics import biotite.structure.info as info # Get an atom array for caffeine # Caffeine has the PDB reside name 'CFF' caffeine = info.residue("CFF") # For cosmetic purposes align central rings to x-y plane n1 = caffeine[caffeine.atom_name == "N1"][0] n3 = caffeine[caffeine.atom_name == "N3"][0] n7 = caffeine[caffeine.atom_name == "N7"][0] # Normal vector of ring plane normal = np.cross(n1.coord - n3.coord, n1.coord - n7.coord) # Align ring plane normal to z-axis caffeine = struc.align_vectors(caffeine, normal, np.array([0, 0, 1])) # Caffeine should be colored by element colors = np.zeros((caffeine.array_length(), 3)) colors[caffeine.element == "H"] = (0.8, 0.8, 0.8) # gray colors[caffeine.element == "C"] = (0.0, 0.8, 0.0) # green colors[caffeine.element == "N"] = (0.0, 0.0, 0.8) # blue colors[caffeine.element == "O"] = (0.8, 0.0, 0.0) # red fig = plt.figure(figsize=(8.0, 8.0)) ax = fig.add_subplot(111, projection="3d") graphics.plot_atoms( ax, caffeine, colors, line_width=5, background_color="white", zoom=1.5 ) fig.tight_layout() # Create an animation that rotates the molecule about the x-axis def update(angle): ax.elev = angle FPS = 50 DURATION = 4 angles = np.linspace(-180, 180, DURATION * FPS) # Start at 90 degrees angles = np.concatenate( [ np.linspace(90, 180, int(DURATION * FPS * 1 / 4)), np.linspace(-180, 90, int(DURATION * FPS * 3 / 4)), ] ) animation = FuncAnimation(fig, update, angles, interval=int(1000 / FPS)) plt.show() .. _sphx_glr_download_examples_gallery_structure_molecule_molecular_visualization.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: molecular_visualization.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: molecular_visualization.py ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_