modelforge curated dataset: SPICE 1 OpenFF

Curated SPICE 1 OpenFF Dataset: Full dataset restricted to elements H, C, N, O, F, Cl, S, version "full_dataset_v1_HCNOFClS": This provides a curated hdf5 file for a subset of the SPICE 1 OpenFF dataset (Open Force Field initiative default level of theory) 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 datafile includes 996941 total conformers for 16560 unique molecules. Changes: In this version, for each record `total_charge` is stored as an array of shape (N_conformers, 1), i.e., a value for each conformer; previously this was just a single value for each record as the charge state doesn't change for each conformer. 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 <add commit number>: Link to the source code at this commit: <add link to commit> Link to the script file used to generate the dataset: <add link to commit> Source Dataset: Small-molecule/Protein Interaction Chemical Energies (SPICE). 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 uncharged molecules, and a wide range of covalent and non-covalent interactions. It provides both forces and energies calculated using B3LYP-D3BJ/DZVP level of theory, using Psi4 1.4.1.This is the default theory used for force field development by the Open Force Field Initiative. This includes the following collections from the MolSSI qcarchive (these are also included in the standard SPICE 1 dataset): "SPICE Solvated Amino Acids Single Points Dataset v1.1", "SPICE Dipeptides Single Points Dataset v1.2", "SPICE DES Monomers Single Points Dataset v1.1", "SPICE DES370K Single Points Dataset v1.0", "SPICE PubChem Set 1 Single Points Dataset v1.2", "SPICE PubChem Set 2 Single Points Dataset v1.2", "SPICE PubChem Set 3 Single Points Dataset v1.2", "SPICE PubChem Set 4 Single Points Dataset v1.2", "SPICE PubChem Set 5 Single Points Dataset v1.2", "SPICE PubChem Set 6 Single Points Dataset v1.2", This does not include the following collections (which are part of the standard SPICE 1 dataset): "SPICE Ion Pairs Single Points Dataset v1.1", "SPICE DES370K Single Points Dataset Supplement v1.0", 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精选SPICE 1 OpenFF数据集（Curated SPICE 1 OpenFF Dataset）： 本数据集限定仅包含氢（H）、碳（C）、氮（N）、氧（O）、氟（F）、氯（Cl）、硫（S）八种元素，版本为"full_dataset_v1_HCNOFClS"： 本文件为SPICE 1 OpenFF数据集的子集提供了经过精选的HDF5文件，该数据集采用开放力场倡议（Open Force Field Initiative）的默认理论级别，可与用于实现和训练神经网络势（Neural Network Potentials，NNPs）的基础设施Modelforge兼容。该子集仅包含含有以下7种元素中至少一种的分子：氢、碳、氮、氧、氟、氯及硫。此数据文件总计包含16560个独特分子的996941个构象。 更新说明：在本版本中，每条记录的「总电荷（total_charge）」将以形状为（N_conformers, 1）的数组存储，即每个构象对应一个电荷值；此前版本中每条记录仅存储单个电荷值，因电荷状态不会随构象变化。在适用情况下，数据文件中会以与openff-units包兼容的字符串形式提供各属性的单位。如需了解数据文件的更多结构信息，请参阅以下链接： https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module 本精选数据集通过Modelforge软件的指定提交（commit）版本生成：<add commit number> 该提交版本的源代码链接：<add link to commit> 用于生成本数据集的脚本文件链接：<add link to commit> 源数据集： SPICE（Small-molecule/Protein Interaction Chemical Energies，小分子/蛋白质相互作用化学能数据集）。 SPICE数据集包含110万个构象，涵盖多样化的小分子、二聚体、二肽以及溶剂化氨基酸。该数据集包含15种元素，涵盖带电与中性分子，并包含广泛的共价与非共价相互作用。其提供了使用Psi4 1.4.1软件、基于B3LYP-D3BJ/DZVP理论级别计算得到的力与能量数据。该理论级别是开放力场倡议用于力场开发的默认理论级别。 本数据集包含以下来自MolSSI QCArchive的数据集子集（这些子集也包含于标准SPICE 1数据集中）： "SPICE Solvated Amino Acids Single Points Dataset v1.1", "SPICE Dipeptides Single Points Dataset v1.2", "SPICE DES Monomers Single Points Dataset v1.1", "SPICE DES370K Single Points Dataset v1.0", "SPICE PubChem Set 1 Single Points Dataset v1.2", "SPICE PubChem Set 2 Single Points Dataset v1.2", "SPICE PubChem Set 3 Single Points Dataset v1.2", "SPICE PubChem Set 4 Single Points Dataset v1.2", "SPICE PubChem Set 5 Single Points Dataset v1.2", "SPICE PubChem Set 6 Single Points Dataset v1.2", 本数据集未包含以下属于标准SPICE 1数据集的子集： "SPICE Ion Pairs Single Points Dataset v1.1", "SPICE DES370K Single Points Dataset Supplement v1.0", 引用信息： SPICE 1原始论文： Eastman, P., Behara, P.K., Dotson, D.L. 等. SPICE：用于训练机器学习势的类药物分子与肽数据集. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6