Discrete Feature Representations of CHO Reaction Mechanisms as Quasireaction Subgraphs

This data set contains 194778 quasireaction subgraphs extracted from CHO transition networks with 2-6 non-hydrogen atoms (CxHyOz, 2 &lt;= x + z &lt;= 6). The complete table of subgraphs (including file locations) is in CHO-6-atoms-subgraphs.csv file. The subgraphs are in GraphML format (http://graphml.graphdrawing.org) and are compressed using bzip2. All subgraphs are undirected and unweighted. The reactant and product nodes (initial and final) are labeled in the "type" node attribute. The nodes are represented as multi-molecule SMILES strings. The edges are labeled by the reaction rules in SMARTS representation. The forward and backward reading of the SMARTS string should be considered equivalent. The generation and analysis of this data set is described in<br> D. Rappoport, Statistics and Bias-Free Sampling of Reaction Mechanisms from Reaction Network Models, 2023, submitted. Preprint at ChemrXiv, DOI: 10.26434/chemrxiv-2023-wltcr Simulation parameters<br> - CHO networks constructed using polar bond break/bond formation rule set for CHO.<br> - High-energy nodes were excluded using the following rules:<br> (i) more than 3 rings, (ii) triple and allene bonds in rings, (iii) double bonds at<br> bridge atoms,(iv) double bonds in fused 3-membered rings.<br> - Neutral nodes were defined as containing only neutral molecules.<br> - Shortest path lengths were determined for all pairs of neutral nodes.<br> - Pairs of neutral nodes with shortest-path length &gt; 8 were excluded.<br> - Additionally, pairs of neutral nodes connected only by shortest paths passing through<br> additional neutral nodes (reducible paths) were excluded. For background and additional details, see paper above.本数据集包含194778个准反应子图，这些子图从包含2至6个非氢原子（分子式为CₓHᵧO_z，其中2 ≤ x + z ≤6）的CHO过渡网络中提取得到。完整的子图表（包含文件存储路径）存于CHO-6-atoms-subgraphs.csv文件中。子图采用GraphML（GraphML）格式（http://graphml.graphdrawing.org），并通过bzip2（bzip2）进行压缩。所有子图均为无向、无加权图。反应物与产物节点（即初始与终态节点）通过"type"节点属性进行标注。节点以多分子SMILES（SMILES）字符串形式表示，边则通过SMARTS（SMARTS）表示的反应规则进行标注。SMARTS字符串的正向与反向读取视为等价。本数据集的构建与分析详见论文：D. Rappoport, 《反应机制的统计与无偏采样：基于反应网络模型》，2023年，已投稿。预印本发布于ChemrXiv，DOI: 10.26434/chemrxiv-2023-wltcr。 仿真参数 - CHO网络基于针对CHO体系的极性键断裂/键形成规则集构建。 - 采用以下规则剔除高能节点：(i) 环数超过3个；(ii) 环内存在三键与累积双键；(iii) 桥原子上的双键；(iv) 稠合三元环内的双键。 - 中性节点定义为仅包含中性分子的节点。 - 计算所有中性节点对的最短路径长度。 - 剔除最短路径长度大于8的中性节点对。 - 此外，剔除仅通过经过额外中性节点的最短路径（可约简路径）连接的中性节点对。更多背景与细节请参见上述论文。