That is what I was thinking. If OK for you, I'll try make a ForwardMolSupplier class that does not store does these values, as for the application I have in mind I don't need it.
Hans On 21 Jul 2011, at 05:42, Greg Landrum wrote: > Dear Hans, > > On Wed, Jul 20, 2011 at 10:50 PM, Hans De Winter <[email protected]> wrote: >> >> Hi Eddie, >> your kindfull suggestions do not work neither. I browsed through the code, >> and - if I'm not mistaken, I think that the SmilesMolSupplier class does not >> correctly free the memory of previous read molecules. I'll look at this >> further, because it could well be that I am wrong! Maybe I should write my >> own reader class to make sure this is the case. >> > > As Eddie said: the SmilesMolSupplier itself does not cache > molecules.Using valgrind and running your example code for 10K > molecules or so (add a break at the end of your loop after 10K) makes > it look like it's not leaking any memory either. The only problems > that points out have to do with the singleton PeriodicTable class. > > The SmilesMolSupplier does, however, cache two values per molecule: > the line number and the position in the file. These allow efficient > random-access useage of the supplier and more accurate error > reporting. They will result in a small increase in memory useage as > you run through a smiles file. I've got one running now that has made > it through 1.5million molecules and is currently occupying 72MB of > RAM. If this small memory increase is something that concerns you, it > would be reasonably easy to construct a ForwardSmilesMolSupplier (one > that does not support random access) that does not store these values. > > -greg
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