pyKinML database

This is a set of SQL databases with information about molecules and radicals with the following database conventions and content. Each database is named as “CnHm”, where n and m range from 1 to 5 and indicate the number of carbon (C) and hydrogen (H) atoms in the structures in the database. Each database contains entries of a large number of “CnHm” geometries. Within each database are frous tables. Table “meta”Contains the name of the database and the date it was created.Table “xyz”The columns of the “xyz” database are the following: “id”: a numerical identification number, integer “calc_params”: metadata describing the level of theory and other details of the quantum chemical calculations to generate the Hessian used for generating this structure, numpy array stored as a blob. “calc”: software used to for the calculation, string “temp”: the temperature used during the normal mode sampling process to generate the structure in K, outliers are assigned negative temperature, float “name”: a unique name describing the anchor point the structure was generated from, string “dist”: the normalized unitless distance of the structure from its anchor point at the temperature given in “temp”, float “geometry”: atomic coordinates in angstroms, (n+m) by 3 numpy array of floats stored as a blob. Note that the atomic positions are listed with carbons first followed by hydrogens. “created_at”: date the structure was generated Table “energy”The columns of the “energy” database are the following: “id”: a numerical identification number, not linked to the “id” in “xyz”, integer “fidelity”: the fidelity level the energy was calculated at, integer 0 = B3LYP/6-31+G(d) 1 = wB97X-D/6-311++G(d,p) 2 = HF/6-31G 3 = B3LYP/6-31G 4 = B2PLYPD3/6-311++G(d,p) “E”: molecular energy in eV, float “xyz_id”: the “id” of the geometry in the “xyz” table this energy calculated for, integer “hessian”: empty “forces”: atomic forces in eV/angstrom, (n+m) by 3 numpy array of floats stored as a blob. Note that the atomic forces are listed in the same order as the atoms in the “geometry” in the “xyz” table “calc_params”: metadata describing the level of theory and other details of the energy and force calculations of this entry, numpy array stored as a blob “calc”: software used to for the energy and force calculation “created_at”: date the energy and forces were calculated “sample_set_id”: empty Table “aev”: currently empty (edited)本数据集为包含分子与自由基信息的SQL数据库集合，遵循以下数据库规范与内容组织形式。 每个数据库的命名格式为"CnHm"，其中n与m的取值范围均为1至5，分别代表该数据库内结构所含碳（C）与氢（H）原子的数量。 每个数据库包含大量"CnHm"构型条目，且内置四张数据表。 ### 表"meta" 用于存储数据库名称与创建日期。 ### 表"xyz" 该表的字段如下： - "id"：整型数值识别编号 - "calc_params"：用于描述生成该构型所用Hessian矩阵（Hessian）的量子化学计算理论级别与其他细节的元数据，为以二进制大对象（BLOB）存储的numpy数组（numpy array） - "calc"：计算所用软件，字符串类型 - "temp"：生成该构型时采用正则模式采样的温度，单位为开尔文（K），异常值将被赋予负温度值，浮点类型 - "name"：用于描述该构型生成所基于的锚点的唯一名称，字符串类型 - "dist"：该构型相对于"temp"字段指定温度下锚点的归一化无量纲距离，浮点类型 - "geometry"：以埃（angstrom）为单位的原子坐标，为(n+m)行3列的浮点型numpy数组（numpy array），以二进制大对象（BLOB）存储。需注意原子排列顺序为先所有碳原子，再依次排列氢原子 - "created_at"：该构型的生成日期 ### 表"energy" 该表的字段如下： - "id"：整型数值识别编号，与"xyz"表中的"id"无关联 - "fidelity"：能量计算所使用的精度级别，整型，对应关系如下： 0 = B3LYP/6-31+G(d) 1 = wB97X-D/6-311++G(d,p) 2 = HF/6-31G 3 = B3LYP/6-31G 4 = B2PLYPD3/6-311++G(d,p) - "E"：以电子伏特（eV）为单位的分子能量，浮点类型 - "xyz_id"：该能量计算所对应的"xyz"表中构型的"id"值，整型 - "hessian"：空字段 - "forces"：原子受力，单位为电子伏特/埃（eV/angstrom），为(n+m)行3列的浮点型numpy数组（numpy array），以二进制大对象（BLOB）存储。需注意原子顺序与"xyz"表"geometry"字段中的原子顺序一致 - "calc_params"：用于描述本条目能量与受力计算的理论级别及其他细节的元数据，为以二进制大对象（BLOB）存储的numpy数组（numpy array） - "calc"：用于能量与受力计算的软件 - "created_at"：能量与受力的计算日期 - "sample_set_id"：空字段 ### 表"aev" 当前为空（已编辑）