jc32173 / RISM_grids

Load, manipulate and visualise RISM data (from AMBER)

RISM grids

Some jupyter-notebooks to visualise RISM data and align RISM grids to molecules. Also includes classes to load and manipulate RISM data generated using AMBER.

• RISM_grids_usage.ipynb: Loading and manipulating RISM data using the classes in RISM_grids.py.
• RISM_3D_plots.ipynb: Examples of plotting RISM data in 3D, including interactive plots.

The html files contain working examples of the jupyter-notebooks, including the interactive plots in RISM_3D_plots.ipynb. Open them via the links below (uses https://htmlpreview.github.io/):

• RISM_grids_usage.html
• RISM_3D_plots.html

Examples:

(From RISM_3D_plots.ipynb)

• Align molecule with 2D slices through 3D RISM data.

  Code will generate VMD commands to align the view of the molecule with the corresponding 2D RISM slice.

• Interactive plot showing the RISM distribution around a molecule.

  The slider moves the 2D surface over the molecule to show how the RISM grid reflects the 3D shape of the molecule. See: interactive_fig_x, interactive_fig_y, interactive_fig_z.