GALP Validation Set for Binding Site Identification in Metal Organic Frameworks

This dataset contains the binding site outputs generated with the in house GALP code for the validation of the algorithm across several molecular guests. For every experimental MOF and guest in the validation set, the dataset includes the folded adsorption density profiles, the volumetric overlap data used during fitting, and the final processed binding site results. The guests included are C2H2.T298.P1, C3H6.T373.P1, C3H8.T373.P1, CH4.T298.P1, CH4.T298.P65, CO2.T298.P1, Kr.T298.P1, Xe.T298.P1, and N2.T298.P0.75. These files correspond to the data used in the validation of the GALP algorithm described in the paper titled “A robust and automated tool for localizing binding sites from adsorbate probability distributions generated from molecular simulation of metal organic frameworks.” A separate overview PDF summarizes which MOFs appear in the validation set for each guest. Note that for N2.T298.P0.75, ten additional MOFs were included beyond the core set of one hundred used for the other guests. Each guest also has a companion CSV file containing information relevant to that specific guest and MOF. These CSV files report the optimized fitting parameters used for that MOF guest combination (Sigma, Radius, Cutoff, OV_Tol, RMSD), a boolean localization flag from manual assessment, Tanimoto and Entropy values for each ADPs, and general adsorption metrics such as uptake and heat of absorption. Each compressed archive (C2H2.T298.P1.tar.gz, C3H6.T373.P1.tar.gz, C3H8.T373.P1.tar.gz, CH4.T298.P1.tar.gz, CO2.T298.P1.tar.gz, Kr.T298.P1.tar.gz, Xe.T298.P1.tar.gz, N2.T298.P0.75.tar.gz) contains one directory per MOF, with the following contents. Note 1: The code used to generate this dataset is referred to as GALP throughout the associated publication. Earlier development versions of the code were named GALA. As a result, file names within this archive, such as GALA.inp, gala.log and gala.err, retain the original naming convention but correspond to outputs generated using the GALP code. Notes 2: The label “O” refers to the methane adsorbate, which is treated as a single site. This is an internal naming choice and does not represent oxygen.For C3H6, the labels Cx, Cy, and Cz refer to a coarse-grain model. Cx corresponds to CH2, Cy corresponds to CH, and Cz corresponds to CH3.For C3H8, Cx corresponds to CH2 and Cy corresponds to the two CH3 groups.The labels Xex and Krx refer to xenon and krypton, respectively. Files FIELD -- A file in DLPOLY FIELD format defining the force field and interaction parameters used for guest–host binding energy calculations. CONTROL -- DLPOLY CONTROL file defining the GCMC simulation. It is not required by GALP but is parsed when present, which reduces the number of parameters needed in GALA.inp. GALA.inp -- Input file specifying the parameters used by the GALP code for binding-site extraction. gala.log -- Log file recording all operations and diagnostics from the GALA run. Tanimoto.txt -- Text file containing the Tanimoto values for each of the ADPs in the system. Entropy.txt -- Text file containing the Entropy values for each of the ADPs in the system. gala.err -- Error file recording any warning or errors that would be printed to the command line. Prob_Guest_<guest>_Site_<site>_folded.cube -- Raw folded adsorbate probability distributions for each site in guest molecule. Subdirectories DL_poly_BS/ -- Directory generated by GALA to compute guest–host interaction energies for each binding site. Each subdirectory within DL_poly_BS contains DLPOLY input/output files for the framework and for each binding-site configuration. The <framework>_<guest> subdirectory contains the framework with a randomly placed guest configuration, used to calculate the framework’s electrostatic reference energy. This energy is subtracted from each binding-site configuration energy in GALA. In this configuration, any guest charges are zeroed out. (See the GALP documentation for more details on the energy decomposition and binding energy calculation procedure.) GALA_Output/ -- Directory generated by GALA containing the processed binding-site information <guest>_binding_sites.cif -- Binding sites in CIF format, listed in order of decreasing occupancy <guest>_binding_sites_fractional.xyz -- Fractional coordinates of all binding sites within the MOF unit cell *.vesta -- Visualization files that combine the fitted binding sites with the corresponding volumetric ADPs. <guest>_gala_binding_sites.xyz -- Cartesian coordinates of each binding site, ordered by decreasing occupancy. This file also reports: Total binding energy (Ebind) Electrostatic contribution percentage (esp%) van der Waals energy (Evdw) Electrostatic energy (Eesp) Relative occupancy (%) (occ) <guest>_guest_information.xyz -- Contains guest information and binding sites listed in order of increasing occupancy, including absolute occupancy values and both fractional and Cartesian coordinates <guest>_gala_local_maxima.cif -- Raw local maxima extracted from the probability map prior to any pruning or molecular fitting. Directory Naming Convention Each guest directory follows the format: <Guest>.<Temperature in K>.<Pressure in bar> This naming scheme identifies the exact simulation conditions associated with the files.本数据集包含使用自研GALP代码生成的结合位点输出结果，用于验证算法在多种分子吸附质上的性能。针对验证集中的每一种实验型金属有机框架（Metal-Organic Framework，MOF）与吸附质，本数据集均提供了折叠后的吸附密度分布、拟合过程中所用的体积重叠数据，以及最终经处理的结合位点结果。本数据集涵盖的吸附质包括：C2H2.T298.P1、C3H6.T373.P1、C3H8.T373.P1、CH4.T298.P1、CH4.T298.P65、CO2.T298.P1、Kr.T298.P1、Xe.T298.P1以及N2.T298.P0.75。 这些文件对应于发表在题为《一种用于从金属有机框架分子模拟得到的吸附质概率分布中定位结合位点的稳健自动化工具》的论文中用于验证GALP算法的数据。另有一份独立的概述PDF文件，汇总了每个吸附质对应的验证集所包含的MOF种类。需注意的是，针对N2.T298.P0.75，相较于其他吸附质所用的100种核心MOF集合，额外纳入了10种MOF。 每种吸附质均配有一份配套CSV文件，包含与该特定吸附质-MOF组合相关的信息。这些CSV文件会记录该组合所用的优化拟合参数（Sigma、Radius、Cutoff、OV_Tol、RMSD）、人工评估得到的布尔型定位标记、每个吸附质概率分布（Adsorbate Probability Distribution，ADP）的Tanimoto值与熵值，以及吸附量、吸附热等通用吸附性能指标。 每个压缩归档文件（C2H2.T298.P1.tar.gz、C3H6.T373.P1.tar.gz、C3H8.T373.P1.tar.gz、CH4.T298.P1.tar.gz、CO2.T298.P1.tar.gz、Kr.T298.P1.tar.gz、Xe.T298.P1.tar.gz、N2.T298.P0.75.tar.gz）均包含一个对应MOF的目录，目录内包含以下内容： ### 注释1 本数据集所用的生成代码在相关论文中统一称为GALP，该代码的早期开发版本名为GALA。因此，本归档文件内的部分文件名（如GALA.inp、gala.log和gala.err）保留了原始命名规范，但实际对应使用GALP代码生成的输出结果。 ### 注释2 标签「O」指代单中心模型下的甲烷吸附质，此为内部命名选择，并非指代氧元素。对于C3H6，标签Cx、Cy、Cz对应粗粒化模型：Cx代表CH2基团，Cy代表CH基团，Cz代表CH3基团。对于C3H8，Cx代表CH2基团，Cy代表两个CH3基团。标签Xex与Krx分别指代氙与氪。 ### 文件列表 - **FIELD**：采用DLPOLY FIELD格式的文件，用于定义主客结合能计算所用的力场与相互作用参数。 - **CONTROL**：DLPOLY CONTROL文件，用于定义巨正则蒙特卡洛（Grand Canonical Monte Carlo，GCMC）模拟的配置。该文件并非GALP运行所必需，但如果存在则会被解析，可减少GALA.inp中所需的参数数量。 - **GALA.inp**：输入文件，用于指定GALP代码执行结合位点提取所用的参数。 - **gala.log**：日志文件，记录GALA运行过程中的所有操作与诊断信息。 - **Tanimoto.txt**：文本文件，包含体系中每个ADP的Tanimoto值。 - **Entropy.txt**：文本文件，包含体系中每个ADP的熵值。 - **gala.err**：错误文件，记录所有将被打印至命令行的警告与错误信息。 - **Prob_Guest_<guest>_Site_<site>_folded.cube**：吸附质分子每个位点的折叠吸附质概率分布原始文件。 ### 子目录 - **DL_poly_BS/**：由GALA生成的目录，用于计算每个结合位点的主客相互作用能。该目录下的每个子目录均包含对应框架与每个结合位点构型的DLPOLY输入/输出文件。 - **<framework>_<guest>**：包含随机放置吸附质的MOF框架的子目录，用于计算框架的静电参考能。该能量会在GALP中被从每个结合位点构型的能量中扣除。在此构型中，所有吸附质的电荷均被置零。更多关于能量分解与结合能计算流程的细节，请参阅GALP官方文档。 - **GALA_Output/**：由GALA生成的目录，包含经处理的结合位点信息： - **<guest>_binding_sites.cif**：采用CIF格式的结合位点文件，按占有率降序排列。 - **<guest>_binding_sites_fractional.xyz**：MOF晶胞内所有结合位点的分数坐标文件。 - ***.vesta**：可视化文件，将拟合得到的结合位点与对应的体积ADP相结合。 - **<guest>_gala_binding_sites.xyz**：每个结合位点的笛卡尔坐标文件，按占有率降序排列。该文件同时会报告以下信息：总结合能（Ebind）、静电贡献百分比（esp%）、范德华能（Evdw）、静电能（Eesp）、相对占有率（%，occ）。 - **<guest>_guest_information.xyz**：包含吸附质信息与结合位点的文件，按占有率升序排列，其中包含绝对占有率值、分数坐标与笛卡尔坐标。 - **<guest>_gala_local_maxima.cif**：未经修剪与分子拟合的、从概率图中提取的原始局部极大值文件。 ### 目录命名规范 每个吸附质目录均遵循以下格式：<Guest>.<Temperature in K>.<Pressure in bar>，该命名方案用于标识与文件对应的精确模拟条件。