IMP-dev

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869 discussions

Exception cleanup and mover cleanup
by Daniel Russel 16 Feb '08

16 Feb '08

The first patch - moves the exception definitions to a new header (IMP/exception). log.h includes this so no other headers have to change directly. As a side effect, exceptions are no longer exported to python. We can revert this easily enough - adds a IMP::Exception base class for all exceptions which stores a string and implements what() so the the string is passed to python - all exceptions (except ErrorException) now require a string (or const char*) in their constructor so that python gets the message - adds a ValueException to thrown when you have out of range values. I was throwing other more awkward ones before the second patch cleans up comments in the movers and adds methods to set the radius/standard deviation. As a side note, don't we want IMPDLLEXPORT on Linear? As it is, you end up with two separate copies of the class, on in libimp and one in _IMP. Not catastrophic, but probably not what we want. Such a problem appears to be catastrophic with exceptions :-)

2 1

Montecarlo doc tweaks
by Daniel Russel 15 Feb '08

15 Feb '08

Added montecarlo to the optimizers group and created a subgroup for the movers. Also removed duplicate restraint documentation which snuck in there somehow.

1 0

slight tweak of first patch
by Daniel Russel 15 Feb '08

15 Feb '08

1 0

Two minor cleanups
by Daniel Russel 15 Feb '08

15 Feb '08

First I added protection to the container macros to hide away certain implementation details. Second, I hadn't used the update_state function in Montecarlo since I had looked for states. I changed the name to update_states and fixed the optimizers.

1 0

no more trajectory
by Daniel Russel 14 Feb '08

14 Feb '08

I thought it went away before, but apparently not. This patch kills it.

1 0

Real optimized indexes iterator in ModelData
by Daniel Russel 14 Feb '08

14 Feb '08

I replaced the weird pseudo-iterator with a real one in ModelData (and fixed the optimizers). BTW, impem still doesn't find boost on my mac.

2 1

No unused stats
by Daniel Russel 14 Feb '08

14 Feb '08

I removed the unused stats code in ModelData.h. We can do the same things through ScoreStates (see MaxChangeScoreState) It also removes the flag which is set when particles are activated or deactived since that is not used any more. If we have one, it should be in Model anyway. And moves the vector include to after the IMP includes so it doesn't mask any missing vector includes in them.

1 0

Embed and IMP
by Daniel Russel 14 Feb '08

14 Feb '08

Can we have it so that IMP looks for EMBED with a normal looking directory structure? By this I mean it expects embedroot/include, embedroot/lib embedroot/lib/python-ver/site-packages). Currently I have to point scons to the copy of EMBed in its source dir, but it actually uses the installed copy for most things (since imppy.sh picks up environment variables when the tests are run). I need an installed copy so I can use it without pain in the NPC stuff. Thanks. I'll even overlook that IMP will get the python version wrong on my mac :-)

1 0

Specifying the location of EMBED and MODELLER
by Ben Webb 14 Feb '08

14 Feb '08

As of r376, I removed the compatibility-with-old-lab-people feature of checking for Modeller in $MODINSTALLSVN. If you want to build IMP with support for Modeller, either specify this on the command line, i.e. scons modeller=/my/modeller/location or (recommended) make a file called config.py in the top-level IMP directory and set it like any other Python variable in there: modeller="/my/modeller/location" The same is true for EM/emlib/EMBED; set its location with the embed variable: embed="/my/embed/location" Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

1 0

boost check
by Daniel Russel 14 Feb '08

14 Feb '08

it fails on my mac even though I have boost installed (from macports). And I can't even run scons --help to see if there is a way to point it at the right place. More reason to respect environment variables.

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