Hi Noel, Thanks for the hint!
So what do you think, what is the more time-consuming part of the optimization for large molecules with >10 rotatable bonds? Is that the systematic search with the first 10 bonds or the subsequent greedy search for the remaining ones? If the latter, it might help to have an option to set it even more greedy :) A few tests suggest that time is typically below 1 sec up to 10 rot.bonds, but it can go up to minutes for molecules with a few more rot.bonds. Regards, Robert >-----Original Message----- >From: Noel O'Boyle [mailto:baoille...@gmail.com] >Sent: Tuesday, January 17, 2012 7:56 PM >To: Róbert Kiss >Cc: openbabel-discuss@lists.sourceforge.net >Subject: Re: [Open Babel] gen2D parameters, documentation > >Check out my revision r4534 at >http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/src/m >cdlutil.cpp?view=log > >"mcdlutil.cpp: Speed up structure layout in the general case, by >carrying out systematic search on the inner N=10 rotbonds, and >greedily searching the remainder. (The original code carried out >systematic search on the 'first' N=20 rotbonds leaving the others >unchanged.)" > >Naturally, for a very large number of rotbonds, the code will hit a >wall. A better strategy might be to set a limit on the greedy search >after an initial full greedy search. > >Any suggestions for improvements, or better still patches, would be >appreciated. > >- Noel > >On 17 January 2012 17:41, Róbert Kiss <rk...@mcule.com> wrote: >> Dear Developers, >> >> Is there any documentation available on the --gen2D option of babel? >> It would be great to know more about how it works. We did some testing >> and it works well in general. But with some rather complicated >> molecules it really slows down. I was wondering if there are any >> parameters that can control the time vs. quality of the 2D structures >> it generates? >> >> Thanks! >> Robert >> >> -- >> >> Robert Kiss >> http://mcule.com >> >> ------------------------------------------------------------------------- >----- >> 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-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ 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-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
