Bugs item #2889708, was opened at 2009-10-30 17:30 Message generated for change (Tracker Item Submitted) made by fab5 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=2889708&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Command-line Tools Group: 2.3.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: Fabian (fab5) Assigned to: Nobody/Anonymous (nobody) Summary: SelectRootAtoms(...) efficiency Initial Comment: Hi, Not really a bug, but here it goes anyway: I'm using babel (parts of the source code) to process protein structures from the PDB and realized that for a couple of (admittedly very) large protein structures such as the ribosome, babel takes quite some time ( up to one hour) to prepare a file with the "-p7" option. Profiling revealed that a considerable amount of time is spent in OBAromaticTyper::SelectRootAtoms(...) (typer.cpp), due to the fact that the root atoms are always checked against all rings (which are numerous in large proteins) - even though not actually being part of it. Attached is a proposal for a slightly modified new version of the function with some loop re-organization and including a look-up list for which atom is part of which ring. This ensures that rootAtoms are only analyzed in the relevant rings. This reduced the amount to time spent in the SelectRootAtoms()-function to a fraction of the original time used. cheers F ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=2889708&group_id=40728 ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
