modelforge curated dataset: SPICE 1

<h1><strong>Modelforge Curated SPICE 1 Dataset:</strong><br><strong>-full dataset, limited to [H, C, N, O, F, Cl, S]</strong><br><strong>-Version: <span>full_dataset_HCNOFClS_v1.1</span></strong></h1> <p>This provides a curated hdf5 file for the SPICE 1 dataset (release v1.1.4) designed to be compatible with&nbsp;<a href="https://github.com/choderalab/modelforge">modelforge</a>, an infrastructure to implement and train NNPs.&nbsp; <span>This dataset contains 16565 unique records for 976408&nbsp;</span><span>total configurations.</span>&nbsp;The dataset is limited to the elements that are compatible with the ANI2x NNP: [H, C, N, O, F, Cl, S].</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.&nbsp;</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>Properties Included:</strong></h2> <ul> <li>atomic_numbers&nbsp;</li> <li>positions &nbsp; &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; <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>&nbsp;"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"</li> <li>"elementary_charge * nanometer ** 2"</li> </ul> </li> <li>smiles&nbsp; <ul> <li>"meta_data"<strong><br></strong></li> </ul> </li> </ul> <h2><strong>Source Dataset:</strong></h2> <p>Small-molecule/Protein Interaction Chemical Energies (SPICE).</p> <p>The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and&nbsp; uncharged molecules, and a wide range of covalent and non-covalent interactions.&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> <p>&nbsp;</p> <h3>Citations:</h3> <p><em>Original 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. (2022). SPICE 1.1.4 (1.1.4) [Data set]. Zenodo.&nbsp;<a href="https://doi.org/10.5281/zenodo.8222043" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.8222043</a></div> </div> </div> </div> </div> </li> </ul>