modelforge curated dataset: SPICE 2

Curated SPICE 2 Dataset: Full dataset restricted to elements H, C, N, O, F, Cl, S, version "full_dataset_v0_HCNOFClS": This provides a curated hdf5 file for a subset of the SPICE 2 dataset (release v2.0.1) designed to be compatible with modelforge, an infrastructure to implement and train NNPs. This subset is limited to molecules containing any of the following 7 elements: H, C, N, O, F, Cl, and S. This dataset contains 1,620,239 total conformers, for 97,280 unique molecules. When applicable, the units of properties are provided in the datafile, encoded as strings compatible with the openff-units package. For more information about the structure of the data file, please see the following: https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module This curated dataset was generated using the modelforge software at commit c5c7153: Link to the source code at this commit: https://github.com/choderalab/modelforge/tree/c5c7153e06172fe8e6f25015250ecb5db05655cc Link to the script file used to generate the dataset: https://github.com/choderalab/modelforge/blob/c5c7153e06172fe8e6f25015250ecb5db05655cc/modelforge/curation/scripts/curate_spice2.py Source Dataset: Small-molecule/Protein Interaction Chemical Energies (SPICE). The SPICE 2 dataset contains roughly 2 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 17 elements, charged and uncharged molecules, and a wide range of covalent and non-covalent interactions. SPICE 2 is an update to spice 1, roughly double the total dataset size and including 2 additional elements. It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, using Psi4 1.4.1 along with other useful quantities such as multipole moments and bond orders. Citations: Original SPICE 1 publication: Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6 Source dataset, released with CCO 1.0 Universal license: Eastman, P., Behara, P. K., Dotson, D., Galvelis, R., Herr, J., Horton, J., Mao, Y., Chodera, J., Pritchard, B., Wang, Y., De Fabritiis, G., & Markland, T. (2024). SPICE 2.0.1 (2.0.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10975225