Ideas for Plugins

General Discussion
1

We already have a decent number of Python plugins, and there are threads elsewhere about improving packaging, etc.

I wanted to start a thread for requests / ideas for plugins. In other words, if you know of a package (or already use a tool) .. suggest it here. My goal is to get a bunch of these coded up this summer as examples.

I’m splitting this into categories:

Energies / Potentials

  • (Already standard force fields through Open Babel, including UFF, MMFF94 and GAFF)
  • ANI-1x
  • AIMNET-2
  • XTB (GFN-FF, GFN0, GFN1, GFN2…)
  • MACE
  • Mattersim
  • Egret
  • (I’m sure there are tons more here…)

Charge Models

  • AM1-BCC
  • ABCG2
  • CEH (from Grimme)
  • EEM
  • GFN2
  • Espaloma

Commands

  • pymatgen slab / nanoparticle construction
  • chiraltube
  • QupKake pKa model
  • AlphaFold
  • RNAFold
  • Packmol

Formats

Something to import cube / density data?

Other ideas / dreams?

2

Under the first category, possibly calling Psi4 and/or PySCF directly.

1 Like
3

I think the challenge with calling Psi4 and PySCF directly would be speed? (Since the energy calculations are used in the interactive optimizations.) But it would certainly be easy to offer.

4

You could have the default be something like HF/def2-SV(P) or HF/STO-3G. (Presumably if you wanted semiempirical you’d pick one of the XTB methods.)

1 Like
5

These would probably also be useful for charge calculations (e.g., getting single-point atomic point charges)

6

Using Chemeleon to generate crystal structures from text using Gardens looks cool:

from garden_ai import GardenClient
client = GardenClient()
my_garden = client.get_garden('10.26311/6phn-gv02')

structure_strings = my_garden.chemeleon_predict([{
    "text_input": "A crystal structure of MgB2",
    "n_samples": 1,
    "n_atoms": 3
}])

Looks like the strings are in extxyz format.