In a recent post I wrote about Integrating Jupyter Notebook into Flare as a new Python extension dedicated to Python developers and enthusiasts. The Python extension that makes this possible is now released (Figure 1).
Figure 1. The button which enables the Python Notebook extension.
As discussed in my previous post, the feature that personally I enjoy most is the fact that the Flare Python Notebook has direct access to the Flare main_window() object, and hence allows you to work on the project currently loaded in the main viewport, i.e., interact with ligands and proteins, visualize molecular and field surfaces, etc. As this involves running the Python code in the main GUI thread, only a single Python Notebook may have access to the GUI at any given time.
However, I thought it would be useful to be able to run other concurrent, separate pyflare processes within the same Python Notebook while the main GUI process is busy doing a computation, e.g., preparing a protein (Figure 2):
Figure 2. Download a PDB complex in the GUI, then run Protein Preparation.
Figure 3. Open another tab and carry out some other task in a separate process.
To provide better integration with the Flare GUI, I have moved the familiar ‘Kernel’ notebook menu controls to the bottom of the window (Figure 4):
Figure 4. Restart/Stop commands can be accessed from bottom left buttons.
Figure 5. Load/Save notebooks through a standard file dialog.