This repository contains supplementary data and code for the manuscript
"Teaching a neural network to attach and detach electrons from molecules" by Roman Zubatyuk, Justin S. Smith, Benjamin T. Nebgen, Sergei Tretiak, Olexandr Isayev https://www.nature.com/articles/s41467-021-24904-0
The models directory contains JIT-compiled Pytorch AIMNet-NSE trained models . Five models were trained on 80/20 cross-validation splits of the training dataset. It is advised to use average prediction of these 5 models to get the most accurate results. The model was trained for neutral and ion-radical states of non-equilibrium conformations of organic molecules containing {H, C, N, O, F, Si, P, S, Cl} elements. Given molecular conformation and charge state, it predicts PBE0/ma-def2-SVP energies and NBO spin-polarized partial charges, as well as derived properties, such as ionization potential, electron affinity, Fukui functions, electronegativity, hardness, etc.
The models could be loaded with the torch.jit.load function. As an input, they accept dingle argument of type Dict[str, Tensor] with following data:
coords: shape (m, n, 3) - atomic coordinates in Angstrom
numbers: shape (m, n) - atomic numbers
charge: shape (m, 2) - total alpha and beta molecular charges
For the convenience, eval.py script has a function to convert charge and multiplicity to the total alpha and beta molecular charges as: ab_charges = 0.5 * torch.stack([charge - mult + 1, charge + mult - 1])
The Ions-16 and ChEMBL-20 datasets are available at http://doi.org/10.5281/zenodo.5007980
The datasets contain PBE0/ma-Def2-SVP energies and NBO atomic charges for the non-equilibrium conformers of neutral organic molecules randomly sampled from PubChem database (Ions-16) and B97-3c optimized conformations of neutral organic molecules randomly sampled from ChEMBL database (ChEMBL-20). The number in the dataset name corresponds to the maximum number of non-hydrogen atoms in the molecules. The dataset which was used for training the AIMNet-NSE model contains molecules up to 12 non-H atoms, whereis ons-16 and ChEMBL-20 contain the molecules with 13 non-hydrogen atoms or more.
The datasets formatted as HDF5 files. Data group names have format as _???, where ??? corresponds to the number of atoms in molecules. Each group contain data for M molecules, each having N atoms. The groups contain following datasets:
| Name | Data type | Shape | Description |
|---|---|---|---|
| mol_id | S24 | M | Molecule ID |
| coord | float32 | M, N, 3 | Cartesian coordinates, Å |
| numbers | uint8 | M, N | Atomic numbers |
| charge | int8 | M | Molecular charge |
| mult | uint8 | M | Spin multiplicity |
| energy | float64 | M | PBE0/ma-def2-SVP energy, eV |
| charges | float32 | M, N, 2 | α and β NBO charges |
The molecule ID is a hash of molecular conformation. In each group, there are up to 3 entries with the same mol_id value, but with different charge. Those correspond to neutral, cation-radical and anion-radical states.
Test datasets could be evaluated with AIMNet-NSE model wth eval.py script:
python eval.py test_datasets/chembl20.h5 models/aimnet-nse-cv?.jpt
usage: eval_mols.py [-h] [--models MODELS [MODELS ...]] [--in-file [IN_FILE]]
[--out OUT] [--allow-charged]
optional arguments:
-h, --help show this help message and exit
--models MODELS [MODELS ...]
--in-file [IN_FILE] Multi-molecule input file. Extension should be an
acceptable to OpenBabel file type.
--out OUT Output multi-line JSON file with computed properties.
--allow-charged Skip check for molecule neutral charge. Useful for
reading XYZ files, e.g. when OpenBabel guess for
molecular charge is wrong.
The script reads several files with compiled models and constructs an ensembled AIMNet-NSE model. For each molecule in the in-file it calculates a set of properties and writes a json-formatted dict to the out file (stdout by default). The output keys are the following:
energy, charges, ip, ea, f_el, f_nuc, f_rad, chi, eta, omega, omega_el, omega_nuc, omega_rad.
The units are eV and e.