On 9/24/07, Geoffrey Hutchison <[EMAIL PROTECTED]> wrote: > > description that it used SPE, I'm going to assume that it was building > > a distance bounds matrix using a set of rules and then embedding that > > matrix into 3D. The key to this type of approach is, I think, the > > quality of the bounds matrix that one generates first.[1,2] > > I'm curious on following up on your comment here Greg. Do you have a > reference for the algorithm you use in RDKit? I'm a novice here, so > any references would be greatly appreciated.
The best "getting started" reference I found is the review article from Jeff Blaney and Scott Dixon: Blaney, J.M., and J.S. Dixon, 1994, Distance geometry in molecular modeling, in Reviews in Computational Chemistry, vol. 5, K.B. Lipkowitz and D.B. Boyd, eds., VCH Publishers, New York, pp. 299-335. (http://www3.interscience.wiley.com/cgi-bin/summary/114034562/SUMMARY) They have references to some other papers as well that contain important details, but this is a good place to start for an overview of the algorithm. -greg ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Blueobelisk-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
