modelforge curated dataset: SPICE 1 OpenFF

Curated SPICE 1 OpenFF Dataset: 1000 conformer test set restricted to elements H, C, N, O, F, Cl, S, version "nc_1000_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 1000 total conformers for 100 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： 1000构象测试集，限定元素为H、C、N、O、F、Cl、S，版本为"nc_1000_v1_HCNOFClS"： 本数据集为SPICE 1 OpenFF数据集（开放力场倡议（Open Force Field Initiative）默认理论水平）的子集，经整理后的HDF5文件，适配用于实现和训练神经网络势（Neural Network Potentials, NNPs）的基础设施modelforge。该子集仅包含含以下7种元素的分子：H、C、N、O、F、Cl及S。本数据文件总计包含100个独特分子的1000个构象。 版本更新说明：在此版本中，每条记录的`total_charge`（总电荷）以形状为(N_conformers, 1)的数组存储，即每个构象对应一个电荷值；此前该字段仅为每条记录存储单个固定值，因同一分子的不同构象电荷状态不会改变。若适用，数据文件中会以字符串形式存储各属性的单位，兼容openff-units工具包。如需了解数据文件的结构详情，请参阅： https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module 本整理后的数据集基于特定提交版本的modelforge软件生成： 该提交版本的源代码链接：<添加提交链接> 用于生成本数据集的脚本文件链接：<添加提交链接> 源数据集：小分子/蛋白质相互作用化学能（SPICE, Small-molecule/Protein Interaction Chemical Energies）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。其包含15种元素，带电与不带电分子，以及广泛的共价与非共价相互作用。该数据集提供了基于B3LYP-D3BJ/DZVP理论水平、使用Psi4 1.4.1计算得到的作用力与能量数据，这也是开放力场倡议（Open Force Field Initiative）用于力场开发的默认理论方法。 本数据集包含以下来自MolSSI qcarchive的数据集子集（这些子集同样收录于标准SPICE 1数据集中）： "SPICE 溶剂化氨基酸单点数据集v1.1"， "SPICE 二肽单点数据集v1.2"， "SPICE DES 单体单点数据集v1.1"， "SPICE DES370K 单点数据集v1.0"， "SPICE PubChem 集合1 单点数据集v1.2"， "SPICE PubChem 集合2 单点数据集v1.2"， "SPICE PubChem 集合3 单点数据集v1.2"， "SPICE PubChem 集合4 单点数据集v1.2"， "SPICE PubChem 集合5 单点数据集v1.2"， "SPICE PubChem 集合6 单点数据集v1.2"， 本数据集未包含以下属于标准SPICE 1数据集的子集： "SPICE 离子对单点数据集v1.1"， "SPICE DES370K 单点数据集补充版v1.0"， 引用信息：SPICE 1原始出版物： 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. 科学数据(Sci Data) 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6