On Thu, Oct 14, 2010 at 5:31 PM, Noel O'Boyle <baoille...@gmail.com> wrote: > On 22 September 2010 14:33, Tim Vandermeersch > <tim.vandermeer...@gmail.com> wrote: >> >> The automorphism based version was not usable for general use since >> there were memory issues. The automorphism search is actually memory >> efficient but simply storing all automorphisms for many cases can >> require GBs of memory. As a result, the automorphisms are not used for >> anything right now. > > I don't know if it's too late for this, but you know what would be > nice, is either to get back the automorphisms one-by-one (e.g. using > Next()) or be able to specify a maximum number of them (e.g. > FindAutomorphisms(cutoff=1000)). I'm using this code for RMSD > calculation and my computer explodes when it comes to certain > molecules.
The number of automorphisms for certain graphs can be very large taking up GBs of memory. I'm going to add a function that takes a functor to handle found isomorphisms. I'll leave the current MapFirst, MapAll and MapUnique in place since these are reasonable defaults for a substructure search. In your function, you can decide to store the automorphisms, discard them, ... and indicate to stop by returning a boolean. This will be using virtual functions but we already use virtual functions for query objects. Tim > - Noel > ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
