Dear Noel,
Thank you for your answers! For my 1st question, I had in mind something along the lines of openbabel python bindings. However, a "standalone" version of the rmsd calculation could be probably useful for quite a few people. Vis ________________________________ From: Noel O'Boyle <[email protected]> To: Visvaldas K. <[email protected]> Sent: Tuesday, January 17, 2012 11:40 AM Subject: Re: [OpenBabel-scripting] [Open Babel] pybel - (howto) calculation of RMSD for two molecules (but different conformers) Regarding (2), it does handle what you call "local symmetry" (automorphisms). Regarding (1), it wouldn't take long to write a C++ program (not sure about Python) that used Open Babel to calculate the RMSD in the way you describe. But I guess you are asking for an option to obabel, right? - Noel On 16 January 2012 20:25, Visvaldas K. <[email protected]> wrote: > Perhaps this should have gone a to a new thread... > > I have a couple of questions about RMSD. Maybe they could lead to "requested > features":) > > 1) from the documentation, it seems that rmsd calc _always_ does > superposition of the molecules before calculating RMSD. From some older > (2007) openbabel thread it seams there is no way to compute RMSD without > superposition. This would be very useful, say, in ligand-protein docking > calculations. > > 2) The computed RMSDs are "symmetry corrected". There is a global symmetry > and a local symmetry. Is the local symmetry also calculated for the purposes > of symmetry correction when doing RMSD? Actually, it's not a trivial > problem; one way to tackle it is to permute rotations around all rotatable > dihedrals in a reference molecule, and to try to obtain a nearly identical > molecule ("nearly" because of imperfections). Perhaps other algorithms > exist. An example would be a local symmetry of the phenyl ring in > phenylalanine: phenylalanine is non-symmetric, but phenyl inside it has two > pairs of equivalent carbons. > > Best regards, > > Vis > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Mar 27 - Feb 2 > Save $400 by Jan. 27 > Register now! > http://p.sf.net/sfu/rsa-sfdev2dev2 > _______________________________________________ > OpenBabel-scripting mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ OpenBabel-scripting mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
