- IMP-dev - salilab.org

imppy.sh
by Javier Ángel Velázquez Muriel 25 Jan '10

25 Jan '10

I am not really sure why this script overrides the variable PYTHONPATH. I would suggest be nicer and add the line PYTHONPATH=$PYTHONPATH'/imp/blah/blah/' Is not a big deal, but a bit annoying when using other libraries.

3 2

RigidBody::.get_members
by Keren Lasker 25 Jan '10

25 Jan '10

To get the particles within a rigid body, it is better using IMP::core::get_leaves or get_members, i.e.: does get_members return the leaves or the children of the RigidBody ?

2 7

weight decorator
by Keren Lasker 25 Jan '10

25 Jan '10

hi, Currently we have a generic XYZR decorator. For mass we have atom::Mass, but when dealing with beads, it does not really make sense to use it. Do you think it makes sense to create a generic XYZRW decorator in core ? the default W key can be atom::Mass::get_mass_key() ?? Keren.

3 5

USAGE_AND_INTERNAL
by Keren Lasker 23 Jan '10

23 Jan '10

sometime the check requires more than a single command. do we have something like : IF_USAGE_AND_INTERNAL ?? thanks, Keren.

2 2

do we have a backbone selector ?
by Keren Lasker 22 Jan '10

22 Jan '10

i think we do not, but remember Ben saying something about it. so - should i write it or not ?

2 2

problem committing code ?
by Keren Lasker 21 Jan '10

21 Jan '10

hi - trying to commit a file and getting an error message: svn ci modules/domino/pyext/junction_tree_from_pair_list.py -m"allow of pairs to be strings and not numbers" Authentication realm: <https://svn.salilab.org:443> Private Sali Group pages Password for 'kerenl': Sending modules/domino/pyext/junction_tree_from_pair_list.py Transmitting file data .svn: Commit failed (details follow): svn: 'pre-commit' hook failed with error output: Traceback (most recent call last): File "/cowbell1/svn/imp/hooks/pre-commit", line 7, in ? import cpp_format File "/cowbell1/svn/imp/hooks/cpp_format.py", line 3, in ? from pygments import token ImportError: No module named pygments does it make sense ?? thanks, Keren.

2 1

opaqueness of RestraintSets
by Daniel Russel 19 Jan '10

19 Jan '10

Currently RestraintSets are opaque to the kernel, meaning that the kernel doesn't know anything about the restraints contained in them. This was fine for a while, but recently has been causing problems - Model::evaluate(restraints) called with restraints from a restraint set fails because the Model doesn't know about the dependencies of the restraint. - Restraint::evaluate() fails on restraints in restraint sets because it uses the above function - RestraintSets containing a mix of incremental and non-incremental restraints don't support incremental evaluation, making using restraint sets much slower than not using them in certain circumstances There are two solutions that I see: - move RestraintSet to the kernel and have the model traverse them internally so it is aware of the whole tree. This would slightly complicated the Model and would break some existing code (we could leave a deprecated core::RestraintSet with the above limitations) - directly address the above problems by having the Model compute the dependencies of unknown restraints on the fly and adding a mixed evaluation mode to restraints which do some of both incremental and non-incremental. This might complicate all restraints a bit and I worry that we would run into other problems later. Not too sure of all of the implications of this route. Thoughts?

4 4

no imp-dev meeting tomorrow
by Daniel Russel 18 Jan '10

18 Jan '10

1 0

The last while in IMP
by Daniel Russel 15 Jan '10

15 Jan '10

It has been a while, so the list is long: - IMP::core::RestraintSet moved to IMP::RestraintSet. The restraint sets now simply define a tree with weights which the model traverses as opposed to being an opaque IMP::Restraint themselves. This means that incremental evaluation of restraints in restraint sets now works and that restraints in restraint sets can be individually evaluated. Existing working usage should not have changed (so \c sed should manage updates just fine), but the internal implementation is completely new, so pay attention. - The IMP.examples module now documents how to use the needed aspects of scons and SWIG. - \imp now has a text i/o layer consisting of IMP::TextInput and IMP::TextOutput. These classes are convertible to C++ streams and implicitly constructable from both streams and file paths. As a result, functions that take them will work when called with a string for a file path, a Python file or a C++ stream. - a new base class IMP::Constraint has been added for constraints. Various other classes have been renamed to be consistent. - The IMP::Model now uses dependency information from IMP::ScoreStates to automatically reorder the IMP::ScoreStates so that they are evaluated in the right order. Also, IMP::Model::evaluate() on a subset of the restraints now only updates the needed score states, not all of them. - Functions on rigid bodies no longer provide the IMP::core::RigidMemberRefiner as a default as it is, pretty much always, the wrong thing to use. That class may go away without notice in the future and is no longer documented. - IMP::UsageException and IMP::InternalException are now reserved for their respective checks (and cannot be thrown by IMP_THROW()). This makes the distinction between API exceptions (which are thrown in any build mode and should be documented and tested) and helper exceptions which are only thrown when debug checks are turned on (and hence should not be documented or tested) clearer. - The IMP.examples module is used as the basis for new modules created by the make-module script, so those include more documentation and are tested. - Module overview pages are now generated from the information passed in the SConscript file, rather than from the (now removed) modulename.dox file. See the examples file for an example of the things you can do there. - boost program options is now a checked for dependency. - the IMP::helper::create_simple_connectivity_on_rigid_bodies() and IMP::helper::create_simple_excluded_volume_on_rigid_bodies() now both take an IMP::Refiner as an (optional) final argument. This makes it so they can be used with the rigid bodies created from molecular hierarchies. This code still needs to be updated and the docs don't reflect what the code was or is doing, so use with caution (see notes in the header file).

1 0

IMP_LOG in fast mode ?
by Keren Lasker 09 Jan '10

09 Jan '10

is there a way to print messages using IMP_LOG using build=fast ? or should i just use std::cout ? thanks , keren.

2 4