i have graphviz now, and I am seeing a function
get_subset_graph_geometry. how am i supposed to use this? I would like
to display subset with particles in them.
IMP.domino2.get_subset_graph_geometry(junct_tree) seems not doing
enough/anything.
Some recent changes that might be of interest
- a wrapper for the Bullet physics simulation system was added to
allow it to be used to optimize models. I recommend everyone take a
look at it as a possible a replacement for conjugate gradients in
certain contexts. It is not general purpose (it works best when
excluded volume and harmonics dominate), but it is very stable and
can get to a decent configuration from quite bad ones. We can add
support for rigid bodies if desired, but currently only XYZR
particles are optimized. An example is provided.
- modules can be selectively ignored when running scons by using
"disabledmodules=helper:restrainer:domino" (or some other list of
modules) on the command line or the config.py. This can make scons
run much faster when you are working on modifying one module since
it won't configure the listed modules. Be aware that modules that
require the disabled modules will also be disabled (and so ignored).
Also note that you can skip the scons dependency checks by doing, eg
fftw3="yes" and fftw3libs="fftw3". or create a fully specified
config file configuration file (by doing "scons config.py").
Likewise, everyone should probably have their own module (see
"managing your own module" on <http://salilab.org/imp/nightly/doc/html/devguide.html>), checked in to your own svn repository so you have an easy way to
fiddle with things.