开源软件在化学数据库分子结构检索中的应用

分子结构检索是化学数据库必备的检索手段,利用开源化学软件是实现分子结构检索的有效途径.不同于商业软件的解决方案,开源本身就体现了经济性和可重复开发的特点.本文利用Java开源化学软件开发工具包如Chemistry Development Kit(CDK)、JOELib的基本构件,基于JSP Servlet Bean MySQL技术搭建了一个网络化学数据库结构检索平台.其中包括分子全结构和子结构检索,并实现了在线提交分子和化合物结构的三维显示等.对包含12万化合物结构信息的数据库的测试表明,该系统在经过预处理和一系列优化措施下,实现了较好的检索性能.

Using open-source software in the structure searching of chemical database

Using open-source software is an effective and cheaper implementation of chemical structure searching in a chemical data- base.Unlike commercial solutions,open source itself also represents extensibility.By integrating modules in open-source software, such as Chemistry Development Kit (CDK) and JOELib,based on JSP Servlet Bean MySQL technology,we build up a web- based,searchable molecular structure database,including the full structure and substructure search.Online chemical structure query and 3D display of chemical structure in hit list are also provided.Much faster searching speed can be obtained for a database of approx- imately 120 000 structures by pretreatments and optimization algorithms.