Automatically download public examples to run in nanoDFT.py

[AlexanderMath]

To quickly experiment with different molecules, we want --mol_str tryptofan to automatically download/run simulation for tryptofan. We don't want to host molecule data, instead, download data on the fly and then do the simulation.

Useful small datasets

• https://github.com/openmm/spice-dataset/tree/main/solvated-amino-acids (~1mb)
• https://github.com/openmm/spice-dataset/blob/main/dipeptides/dipeptides.hdf5 (~18mb)

Download on the fly from pubchem:
Example: search for cyclodextrin on pubchem, click the entryalpha-cyclodextrin, copy SMILES string then create RDKit object and use their force field to optimize 3d atom positions (we can then run DFT).

Pointers

• import pandas as pd; pd.read_hdf5("..")
• import wget; wget.download(url)

Suggestion

• Rename gdb to utils/. Write the code to download molecules in utils/download.py and then import that from nanoDFT.py