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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.<\/jats:p>","DOI":"10.1186\/1758-2946-4-26","type":"journal-article","created":{"date-parts":[[2012,10,31]],"date-time":"2012-10-31T19:13:55Z","timestamp":1351710835000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["A rule-based algorithm for automatic bond type perception"],"prefix":"10.1186","volume":"4","author":[{"given":"Qian","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Youyong","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junmei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liling","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tingjun","family":"Hou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,10,31]]},"reference":[{"key":"364_CR1","doi-asserted-by":"publisher","first-page":"D301","DOI":"10.1093\/nar\/gkl971","volume":"35","author":"H Berman","year":"2007","unstructured":"Berman H, Henrick K, Nakamura H, Markley JL: The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. 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