Molecular Query Language (MQL)-A Context-Free Grammar for Substructure Matching

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• 作者：Ewgenij Proschak ; Jö ; rg K. Wegner ; Andreas Sch&uuml ; ller ; Gisbert Schneider ; Uli Fechner
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2007
• 出版时间：March 2007
• 年：2007
• 卷：47
• 期：2
• 页码：295 - 301
• 全文大小：171K
• 年卷期：v.47,no.2(March 2007)
• ISSN：1549-960X

文摘

We have developed a Java library for substructure matching that features easy-to-read syntax and extensibility.This molecular query language (MQL) is grounded on a context-free grammar, which allows forstraightforward modification and extension. The formal description of MQL is provided in this paper. Moleculeprimitives are atoms, bonds, properties, branching, and rings. User-defined features can be added via a Javainterface. In MQL, molecules are represented as graphs. Substructure matching was implemented using theUllmann algorithm because of favorable run-time performance. The Ullmann algorithm carries out a fastsubgraph isomorphism search by combining backtracking with effective forward checking. MQL softwaredesign was driven by the aim to facilitate the use of various cheminformatics toolkits. Two Java interfacesprovide a bridge from our MQL package to an external toolkit: the first one provides the matching rules forevery feature of a particular toolkit; the second one converts the found match from the internal format ofMQL to the format of the external toolkit. We already implemented these interfaces for the ChemistryDevelopment Toolkit.