Re: [AMBER-Developers] Experiences with sleap

From: Justin MacCallum <>
Date: Sat, 05 Nov 2011 11:18:46 -0400

On Nov 5, 2011, at 9:58 AM, case wrote:

> For an contrarian view:

With all due respect, that's hardly a fair comparison. We're talking about re-writing a small---but, admittedly complex---utility and not a major web browser. The problem with leap isn't that it's badly architected or written. The problem is that it's written in the wrong language. IMO, C, fortran and even C++ are too low-level for this sort of task.

FWIW, a friend of mine worked at Amazon for ~5 years and they re-wrote their entire infrastructure twice. They seem to be doing just fine. A little closer to home, Rosetta has been re-written several times and Baker & co seem no worse for wear. In my opinion the only compelling reason to stick with tleap is that it is there and it (mostly) works.

Finally, although I'm not necessarily suggesting we do this, I am willing to bet that if we locked two experienced python programmers and two people comfortable with the format of the various tleap database files and parm format in a room for a week that you would have a working, modular, extensible, human readable(!) replacement for tleap that has 1/10 the amount of code.

 -- Justin

Justin MacCallum - Laufer Junior Fellow
Laufer Center for Physical and Quantitative Biology
Stony Brook University
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Received on Sat Nov 05 2011 - 08:30:04 PDT
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