Subject: Re: [IMP-dev] NBL cleanup and other small patches
From: Friedrich Foerster <>
Date: Tue, 13 May 2008 13:57:57 -0700
Reply-to: List for IMP development <>
could anyone also create a simple README/directory explaining, which
packages (including supported versions) are needed and where to get
them? the file should be be in the root IMP directory to maximize
visibility.
that would make the installation way simpler and avoid things like
frank's hassle with boost.
thanks
frido
Daniel Russel wrote:
Since by now things are a bit mixed up, here is a monster diff.
The changes that I remember are:
API Changes:
- There are now just AllNonbondedListScoreState and
BipartiteNonbondedListScoreState. The default algorithm should be the
best currently available in your build.
- The level of checks can now be set at runtime using the methods
set_check_level and get_check_level. Valid values for the levels are
NONE, CHEAP, EXPENSIVE. NDEBUG works as before in that it permentantly
turns off various checks but the speed difference compared to running
with NONE appears to be small. I suggest that python code be run with
cheap checks and interactive python run with expensive checks.
- The ChainBondedList went away as the speed advantage didn't seem to
be worth having an extra class.
- A new class BondCoverScoreState is added which adds x,y,z,r to bonds
passed to it in order cover the bonds with spheres for collision
detection purposes.
- there is now BD optimizer. The tests for it suck and occasionally
fail. I am not sure of a good way to test such stochastic things.
- the previously mentioned WLCEnergy unary function has been added
Internal API changes:
- ScoreStates should now implement do_before_evaluate and
do_after_evaluate instead of update and after_evaluate. Model calls
before_evaluate and after_evaluate which check the iteration numbers
as mentioned before and calls the internal methods if appropriate.
- I tried to roll back Ben's disabling of some tests which had been
failing, but didn't try very hard, so they might not all be back.
- The default check level should probably always be cheap and the unit
test should turn on expensive tests. I don't know how to add code to
all IMP unit tests.
- there is code in restraints and things to return how much memory
they used. I added that when I was having problems with running out of
memory (due to, as it turned out, the nonbonded lists growing too
large). Having something like that in our code is great.
Unfortunately, I'll bet that it will slowly atrophy with time. Anyway,
it is there for now as it doesn't hurt anything.
I am sure there are other changes which I forgot.
On May 12, 2008, at 3:42 PM, Ben Webb wrote:
Andrej would prefer to avoid commercial-license code in IMP, and it
would surely be a pain to remove this code in future if it became
incompatible with our license. But he prefers more to save time now, so
he's OK with linking against something like CGAL. So I can commit this
patch in essentially its current form, provided that it applies against
current SVN (it doesn't right now, e.g. because it's missing some
files).
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