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.
- various bits of IMP should be faster (at least with fast builds), including non-bonded lists. I added a section on speeding things up in the introduction, http://salilab.org/imp/nightly/doc/html/introduction.html.
- 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").
As a note, if you are not doing out of source builds, you probably should be as it makes switching between fast and debug builds painless. See instructions at http://salilab.org/imp/nightly/doc/html/installation.html.
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.
Hi Daniel,
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. > > - various bits of IMP should be faster (at least with fast builds), > including non-bonded lists. I added a section on speeding things up > in the introduction, http://salilab.org/imp/nightly/doc/html/introduction.html > . > > - 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"). > > > As a note, if you are not doing out of source builds, you probably > should be as it makes switching between fast and debug builds > painless. See instructions at <http://salilab.org/imp/nightly/doc/html/installation.html > >. > > 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. > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Sebnem Essiz Gokhan
:-)
On Oct 11, 2010, at 2:12 PM, Sebnem Essiz wrote:
> > > > > > > > > > > > > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
-
Daniel Russel -
Sebnem Essiz