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Open Access Methodology

A rule-based algorithm for automatic bond type perception

Qian Zhang1, Wei Zhang3, Youyong Li1, Junmei Wang3, Liling Zhang1 and Tingjun Hou12*

Author Affiliations

1 Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China

2 College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China

3 Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390, USA

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Journal of Cheminformatics 2012, 4:26  doi:10.1186/1758-2946-4-26

Published: 31 October 2012

Abstract

Assigning bond orders is a necessary and essential step for characterizing a chemical structure correctly in force field based simulations. Several methods have been developed to do this. They all have advantages but with limitations too. Here, an automatic algorithm for assigning chemical connectivity and bond order regardless of hydrogen for organic molecules is provided, and only three dimensional coordinates and element identities are needed for our algorithm. The algorithm uses hard rules, length rules and conjugation rules to fix the structures. The hard rules determine bond orders based on the basic chemical rules; the length rules determine bond order by the length between two atoms based on a set of predefined values for different bond types; the conjugation rules determine bond orders by using the length information derived from the previous rule, the bond angles and some small structural patterns. The algorithm is extensively evaluated in three datasets, and achieves good accuracy of predictions for all the datasets. Finally, the limitation and future improvement of the algorithm are discussed.

Keywords:
Bond type perception; Bond order; Chemical bond; Molecular modeling

Graphical abstract