Dear JP, On Tue, Jan 22, 2013 at 1:20 PM, JP <[email protected]> wrote: > > Is there a way how to do a molecular volume overlap in RDKit? I cannot seem > to find it and the only related discussion I can find is here. But the > fourth slide here, clearly states that RDKit is able to do this.
Noel's deck indicates that the RDKit can do shape similarity, which is correct, but doesn't mention actually aligning the molecules using shape/volume. This is, of course, more difficult. The RDKit has a "functional, but not great" implementation of the subshape alignment algorithm published by Santosh Putta and some other former colleagues (http://pubs.acs.org/doi/abs/10.1021/ci0256384) in rdkit.Chem.Subshape. I briefly showed how to use this in the UGM tutorial on 3D structures, http://nbviewer.ipython.org/4316435/ The subshape algorithm is different from most SBA methods in that it works for molecules of different sizes. That was the good news, the bad news: The RDKit implementation of subshape alignment is primarily there as a proof-of-concept to demonstrate the idea and to motivate further work. It's never been properly optimized, so it's pretty slow. > If this is not RDKit-doable anyone else has come across some publicly > available tools to do this? A quick search lead me to Shape-it, from Hans > (who I met at the user group meeting) - anyone used this before? > > p.s. no one ever sent/made available the group photo we took at the 1st > RDKit meeting :( good point. That slipped through the cracks. I'll get it posted. -greg ------------------------------------------------------------------------------ Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
