modelforge curated dataset: SPICE 2

<h1><strong>Modelforge Curated SPICE 2 Dataset:<br>- Full dataset limited to elements [H, C, N, O, F]<br>- Version: full_dataset_HCNOF_v1.1</strong></h1> <p>This provides a curated hdf5 file for a subset of the SPICE 2 dataset (release v2.0.1) designed to be compatible with <a href="https://github.com/choderalab/modelforge">modelforge</a>, an infrastructure to implement and train NNPs. This dataset contains 57037 unique records for 928073 total configurations. The dataset is limited to the elements ['H', 'C', 'N', 'O', 'F'].</p> <p>When applicable, the units of properties are provided in the datafile,&nbsp; encoded as strings compatible with the <a href="https://github.com/openforcefield/openff-units/">openff-units</a> package.&nbsp;</p> <p>This is compatible with modelforge hdf5 schema 2.</p> <p>For more information about the structure of the data file, please see the following:</p> <ul> <li><a href="https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module">https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module</a></li> </ul> <h2><strong>Source Dataset:</strong></h2> <p>Small-molecule/Protein Interaction Chemical Energies (SPICE).</p> <p>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&nbsp; uncharged molecules, and a wide range of covalent and non-covalent interactions.&nbsp; SPICE 2 is an update to spice 1, roughly double the total dataset size and including 2 additional elements.&nbsp; It provides both forces and energies calculated at the &omega;B97M-D3(BJ)/def2-TZVPPD level of theory, using Psi4 1.4.1 along with other useful quantities such as multipole moments and bond orders.</p> <div> <pre>&nbsp;</pre> </div> <h2><strong>Properties Included:</strong></h2> <ul> <li>atomic_numbers&nbsp;</li> <li>positions &nbsp; &nbsp; &nbsp; <ul> <li>"per_atom"</li> <li>"nanometer"</li> </ul> </li> <li>dft_total_force <ul> <li>"per_atom"</li> <li>"kilojoule_per_mole / nanometer"</li> </ul> </li> <li>mbis_charges &nbsp;&nbsp; <ul> <li>"per_atom"</li> <li>"elementary_charge"</li> </ul> </li> <li>mbis_dipoles &nbsp;&nbsp; <ul> <li>"per_atom"</li> <li>"elementary_charge * nanometer"</li> </ul> </li> <li>mbis_quadrupoles &nbsp; &nbsp; &nbsp;&nbsp; <ul> <li>"per_atom"</li> <li>"elementary_charge * nanometer ** 2"</li> </ul> </li> <li>mbis_octupoles&nbsp; <ul> <li>"per_atom"</li> <li>"elementary_charge * nanometer ** 3"</li> </ul> </li> <li>mayer_indices &nbsp; <ul> <li>"per_atom"</li> <li>"dimensionless"</li> </ul> </li> <li>wiberg_lowdin_indices &nbsp; <ul> <li>"per_atom"</li> <li>"dimensionless"</li> </ul> </li> <li>total_charge &nbsp;&nbsp; <ul> <li>"per_system"</li> <li>"elementary_charge"</li> </ul> </li> <li>dft_total_energy &nbsp; &nbsp; &nbsp;&nbsp; <ul> <li>"per_system"</li> <li>"kilojoule_per_mole"</li> </ul> </li> <li>formation_energy &nbsp; &nbsp; &nbsp;&nbsp; <ul> <li>"per_system"</li> <li>"kilojoule_per_mole"</li> </ul> </li> <li>scf_dipole &nbsp; &nbsp;&nbsp; <ul> <li>"per_system"</li> <li>"elementary_charge * nanometer"</li> </ul> </li> <li>scf_quadrupole&nbsp; <ul> <li>"per_system"<br>"elementary_charge * nanometer ** 2"</li> </ul> </li> <li>smiles&nbsp; <ul> <li>"meta_data"</li> </ul> </li> </ul> <p>&nbsp;</p> <h2><strong>Citations:</strong></h2> <div> <p><em>Spice 2 publication:</em></p> <ul> <li> <p>Eastman, P., Pritchard, B. P., Chodera, J. D., &amp; Markland, T. E. Nutmeg and SPICE: models and data for biomolecular machine learning. Journal of chemical theory and computation, 20(19), 8583-8593 (2024). <a href="https://doi.org/10.1021/acs.jctc.4c00794">https://doi.org/10.1021/acs.jctc.4c00794</a></p> </li> </ul> </div> <p><em>Original SPICE 1 publication:</em></p> <ul> <li>Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,&nbsp; A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). <a href="https://doi.org/10.1038/s41597-022-01882-6">https://doi.org/10.1038/s41597-022-01882-6</a></li> </ul> <p><em>Source dataset, released with CCO 1.0 Universal license:</em></p> <ul> <li> <div> <div> <div> <div> <div>Eastman, P., Behara, P. K., Dotson, D., Galvelis, R., Herr, J., Horton, J., Mao, Y., Chodera, J., Pritchard, B., Wang, Y., De Fabritiis, G., &amp; Markland, T. (2024). SPICE 2.0.1 (2.0.1) [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.10975225" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10975225</a></div> </div> </div> </div> </div> </li> </ul>