The 2D depiction stuff needs to be sped up. It can be sped up to any arbitary speed by sacrificing exhaustive layout for speed. I keep meaning to get back to this. There are a lot of clever ways this might be done.
- Noel On 8 October 2013 18:27, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: > On 10/08/2013 11:35 AM, Geoffrey Hutchison wrote: > >> I'm willing to hear suggestions as far as SMILES and InChI limits, >> but I don't even know if a 1000-atom SMILES would be particularly useful. > That, plus the potential for overwhelming the computer (i.e., the > computer would "hang" while it computes the SMILES and InChI) were the > reason for these particular limits. > > Finding duplicates is a basic database normalization task, and with > molecules you have to start with graph-based searches. Canonical smiles > and inchi strings are supposed to be useful for that. I don't know if > they actually will be, in our case, but unless I try I'll never know. > > Our off the wall DB averages are 96 residues/entity and 46 atoms/residue > -- IRL the ones we can work with will have fewer atoms, but some (many?) > will have longer sequences. > > So that's 4K+ atoms average. The part where computer "hangs" is, well, > yeah, what'd you expect. I've an entire compute cluster to ship this to, > and I don't care if it takes a week to calculate: the source sequences > won't change while it's crunching. > > It may well be worth keeping the limit if the job's started from the GUI > -- or at least popping up a dialog box saying "are you sure you wanna do > this?". And even then I'd say the issue is memory usage: these days you > probably have at least 3 more cores for other stuff, so as long as OB > doesn't gobble up all the RAM it shouldn't "hang". > > my $.02 > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > > ------------------------------------------------------------------------------ > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
