Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database.
Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database.
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DOI：
10.1186/s13321-018-0279-6
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发表时间：
2018-05-18
影响因子：
8.6
通讯作者：
Vaitkus A
中科院分区：
文献类型：
--
作者：
Quirós M;Gražulis S;Girdzijauskaitė S;Merkys A;Vaitkus A
化学分子连接性的计算机描述对于搜索化学数据库和从分子结构预测化学性质是必要的。在本文中，报告了正在进行的以 SMILES 格式描述晶体学开放数据库 (COD) 中条目的化学连通性的工作。该 SMILES 集合可公开用于化学（子结构）搜索或在开放获取的基础上用于任何其他目的，就像 COD 本身一样。针对最常见的情况概述了不符合价键理论的化合物表示所遵循的惯例。从 CIF 文件中获取 SMILES 的过程首先要检查不对称单元中的原子是否是化学上可接受的化合物图像。当它们不是时（对称元素、无序、聚合物种等中的分子），在许多情况下使用先前发布的 cif_molecule 程序来获取此类图像。然后应用程序包 Open Babel 从 CIF 文件中获取 SMILES 字符串（直接从 COD 获取的字符串或在适用时由 cif_molecule 生成的字符串）。然后由人工编辑在计算机辅助任务中检查和/或修复结果，目前该任务仍然消耗大量人工时间。即使该程序仍需要改进以使其更加自动化（从而更快），但它已经产生了超过 160,000 个精心策划的化学结构，本文的目的是向化学界宣布这项工作的存在，并推广其结果的使用。本文的在线版本 (10.1186/s13321-018-0279-6) 包含补充材料，可供授权用户使用。
Computer descriptions of chemical molecular connectivity are necessary for searching chemical databases and for predicting chemical properties from molecular structure. In this article, the ongoing work to describe the chemical connectivity of entries contained in the Crystallography Open Database (COD) in SMILES format is reported. This collection of SMILES is publicly available for chemical (substructure) search or for any other purpose on an open-access basis, as is the COD itself. The conventions that have been followed for the representation of compounds that do not fit into the valence bond theory are outlined for the most frequently found cases. The procedure for getting the SMILES out of the CIF files starts with checking whether the atoms in the asymmetric unit are a chemically acceptable image of the compound. When they are not (molecule in a symmetry element, disorder, polymeric species,etc.), the previously published cif_molecule program is used to get such image in many cases. The program package Open Babel is then applied to get SMILES strings from the CIF files (either those directly taken from the COD or those produced by cif_molecule when applicable). The results are then checked and/or fixed by a human editor, in a computer-aided task that at present still consumes a great deal of human time. Even if the procedure still needs to be improved to make it more automatic (and hence faster), it has already yielded more than 160,000 curated chemical structures and the purpose of this article is to announce the existence of this work to the chemical community as well as to spread the use of its results. The online version of this article (10.1186/s13321-018-0279-6) contains supplementary material, which is available to authorized users.
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影响因子：
8.6
作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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