Oh yes, I forgot. I've already done this some time ago...I was just waiting for 2.3.1 to be released...
https://gist.github.com/974477 - Noel On 17 January 2012 09:48, Visvaldas K. <[email protected]> wrote: > 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
