.. _example_protein: Protein example -------------------------------------------------------------------- Visualize a protein graph structure downloaded from the protein database in standard pdb format. We parse the pdb file, but extract only a very small amount of information: the type of atoms, their positions, and the links between them. Most of the complexity of this example comes from the code turning the PDB information into a list of 3D positions, with associated scalar and connection information. We assign a scalar value for the atoms to differenciate the different types of atoms, but it does not correspond to the atomic mass. The size and the color of the atom on the visualization is therefore not chemicaly-significant. The atoms are plotted using mlab.points3d, and connections between atoms are added to the dataset, and visualized using a surface module. The graph is created by adding connection information to points. For this, each point is designated by its number (in the order of the array passed to mlab.points3d), and the connection array, made of pairs of these numbers, is constructed. There is some slightly tedious data manipulation to go from the named-node graph representation as stored in the pdb file, to the index-based connection pairs. A similar technique to plot the graph is done in the :ref:`example_flight_graph`. Another example of graph plotting, showing a different technique to plot the graph, can be seen on :ref:`example_delaunay_graph`. To visualize the local atomic density, we use a gaussian splatter filter that builds a kernel density estimation of the continuous density field: each point is convoluted by a Gaussian kernel, and the sum of these Gaussians form the resulting density field. We visualize this field using volume rendering. Reference for the pdb file standard: http://mmcif.pdb.org/dictionaries/pdb-correspondence/pdb2mmcif.html .. image:: ../generated_images/example_protein.jpg :align: center **Python source code:** :download:`protein.py` .. literalinclude:: protein.py :lines: 39-