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A question came up recently on the OpenBabel mailing list regarding generation of 2D structures. This is an area of interest for me as well, but I'm more interested in the algorithmic details. I understand there are rule-based methods, distance geometry, and a substantial graph drawing literature (GraphViz comes to mind), but I've not found anything that provides a good algorithmic analysis of the techniques. If anyone has good links or references, please post them. -Kirk DeLisle |
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I haven;t seen a review of the various techniques. Rather there's a number of papers on individual techniques. http://dx.doi.org/10.1021/ci050550m comes to mind. There's also the MCDL paper (but I don't remmeber the reference). Agrafiotis' SPE based depiction method was nice (but I don't recall seeing a paper on that). |
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There is a really good review by Harold Helson from CambridgeSoft in "Reviews in Computational Chemistry - Volume 13" http://www3.interscience.wiley.com/cgi-bin/summary/114034693/SUMMARY There's also a nice article by Alex Clark in the CCG Journal http://www.chemcomp.com/journal/depictor.htm My all time favorite is this paper by Ray Carhart from 1976 A Model-Based Approach to the Teletype Printing of Chemical Structures http://pubs.acs.org/doi/abs/10.1021/ci60006a011 Carhart was rendering chemical structures in ASCII! Kids these days, they don't know how easy they have it :-) |
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The first paper that I'm aware of on the subject of structure diagram generation is this one from CAS dating back to 1977. |
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