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869 discussions

density map volumetrics insertion
by Benjamin SCHWARZ 07 Mar '11

07 Mar '11

Added densityMapVolumetrics{.cpp/.h} files to the IMP::em module They provide - functions to compute mass/volume of a densityMap at a given threshold - functions to compute the threshold one needs to apply in an EM map to attain a given mass/volume In addition, one can use different protein density values in these computations. The default density being used remains 1/1.21 Da/A^3, the value that was used since then. A small duplication issue remains to leverage : DensityMap::approximate_molecular_mass() should probably disappear or be remapped on compute_molecular_mass_at_threshold( DensityMap* m, Float threshold); Shall I do it ? --Ben(S)

2 1

strange behavior with Vector3D operator== under python
by Benjamin SCHWARZ 23 Feb '11

23 Feb '11

Don't know if it has already been reported or if this is an expected behavior… Tested with latest IMP svn release. import IMP import IMP.algebra a=IMP.algebra.Vector3D(1,1,2) b=IMP.algebra.Vector3D(1,1,2) a==b --> False --Ben (schwarz)

3 3

IMP meeting today on file formats and IO
by Daniel Russel 22 Feb '11

22 Feb '11

Let's discuss what we currently have in IMP, what is being discussed which the Chimera folks and what we would like to see. 1pm.

2 1

towards an IMP/Chimera/global coarse grained molecule file format
by Daniel Russel 16 Feb '11

16 Feb '11

We have been having meetings with various of the Chimera developers discussing a file format to act as a rich format for saving and loading hierarchical (and coarse grained) structures within IMP and Chimera (with the intent to push a library supporting it as a general standard for interchanging biological data). The current idea is to support one or more conformations of an IMP::atom::Hierarchy along with markup including geometry associated with one or more particles from the hierarchy, and more abstract features (think restraints) which contain information about sets of particles, scores and other text. The proposed IMP interface would look something like /** A file storing one or more configurations of an atom::Hierarchy \note Changes in the structure of the hierarchy after constructor are not permitted, only coordinates are allowed to change. \note XYZ, XYZR, Bond, Bonded, Hierarchy, Atom, Residue, Molecule, Chain, Domain, Fragment, information is stored when available. */ class IMPHDF5EXPORT File { boost::scoped_ptr<H5::H5File> file_; atom::Hierarchy hierarchy_; void initialize_file(); void check_hierarchy() const; void create_hierarchy(); void create_mapping(); public: //! Load the data from a file into the model File(Model *m, std::string fname); //! Tie a (possibly empty) file to the given hierarchy File(atom::Hierarchy h, std::string fname); atom::Hierarchy get_hierarchy() const; /** \name ConfigurationSet-like methods @{ */ void save_conguration(); void save_configuration_as(unsigned int i); void load_configuration(unsigned int i) const ; void remove_configuration(unsigned int i); void clear_configurations(); unsigned int get_number_of_configurations() const ; /** @} */ //! Associate some geometry with a node in the hierarchy /** If the geometry is particle-derived it will have different coordinates for each frame, if not it just has one set of coordinates. */ void add_geometry(atom::Hierarchy h, display::Geometry*g); //! Associate a more general feature with a node in the hierarchy void add_feature(atom::Hierarchy h, Feature h); }; If anyone has usage scenarios that might not be covered or other comments please let me know. The initial version of the format will be based on HDF5. This should allow "fast" random access to individual conformations (without loading all of them).

1 0

Recently in IMP
by Daniel Russel 04 Feb '11

04 Feb '11

- IMP::domino::TrivialParticleStates renamed to IMP::domino::IndexParticleStates to be less judgmental. IMP::domino::CompoundParticleStates and IMP::domino::RecursiveParticleStates added. - IMP::domino::DominoSampler now supports maximum scores on IMP::RestraintSets. - the name of the clustering methods have been changed to create_ from get_ since they create objects. - the names of the recently added metric based clustering support has been changed to Metric rather than Distance. - IMP now has the ability to have certain tests designated as expensive and to skip those tests when test-fast is run. The motivation for this is that the tests take a really long time making it impractical to run before every commit. And it is hard to tell which tests have not been run when running with the necessary multiple build processes. My thought is that tests that take about a second or less on a debug build should be left along (this is probably >95% of the tests), but the few that take longer should be marked as expensive. To do that, rename the test to expensive_text_XXX.py (from test_XXX.py) and add expensive_python_tests= env.IMPModuleGetExpensivePythonTests() to the IMPModuleTest call in the test SConscript. - the fuction IMP::display::create_restraint_geometry() was added to do what its name says. - runtime dimensional geometric objects have been added. These include IMP::algebra::VectorKD, IMP::algebra::BoundingBoxKD and IMP::algebra::SphereKD. The IMP::statistics::Embedding classes now use IMP::algebra::VectorKD instead of Floats. The sparse grids also support variable dimensions as to the nearest neighbor searches. - IMP::atom::DopePairScore has been added to \imp. - IMP::atom::CHARMMStereochemistryRestraint provides a high-level simplified interface to the bonded part of the CHARMM forcefield. - \imp modules are now built by first combining all the .cpp files into one, and then building that file. This greatly accelerates building of a module from scratch as build time is dominated by parsing headers. This does change the semantics of .cpp files as they see headers included by and functions declared by an arbitrary subset of other .cpp files. For now they are still required to be able to be compiled separately. To get the only behavior back either globally or on a per-module basis, see the percppcompilation parameter to scons. - Instructions and scripts have been added for building modules and things externally to the \imp build. See the installation guide.

1 0

inactivate restraints
by Pia Unverdorben 04 Feb '11

04 Feb '11

dear all, is there any way to deactivate individual restraints? thanks pia & frido

4 3

checklist of IMP 1.1
by Daniel Russel 25 Jan '11

25 Jan '11

I added a wikipage to serve as a todo list for the IMP 1.1 release and put a few things on it. Please take a look, think about anything else that should be there or whether things that are there should be dropped. <http://salilab.org/imp/wiki/imp_1_1>

1 0

distributed imp part II
by Daniel Russel 24 Jan '11

24 Jan '11

Let's have a continuation of the conversation of a distributed framework for IMP. I put a few new ideas up on the wiki page (particularly see the the task based model). The questions are then: - does that task based model do what we need? - what is the best way to provide an implementation? OK?

1 0

how to install executable python scripts in a bin subdir ?
by Benjamin SCHWARZ 24 Jan '11

24 Jan '11

Hi list, Just wondering where I am supposed to place my personal-module-specific python scripts so that they will ultimately be placed in the imp-install/bin subdir. More specifically, I wrote a module emben hosting some cpp code to assess the intensity threshold I should use in an EM map to obtain a given mass or volume. Everything compiles and runs ok, and I am able to access my functions in the python interpreter. Now, I wrote a python script computeMapThreshold.py to specifically achieve the task on a command line basis, but I don't know where to place the script so that "scons install" will place it in the install bin subdir… emben/bin does not do the trick… it seems only cpp code is considered here emben/pyext/src does not work any better : the file is simply copied to the IMP.emben python library. Any hint ? --Ben

3 2

Compiling IMP and slow machines
by Daniel Russel 21 Jan '11

21 Jan '11

If you computer has been getting unusually slow while building IMP, that is a side effect of the change I made a few days back (merging C++ .cpp files in a module before compilation). The "problem" is that it makes compilation significantly faster (1000s vs 2000s for a clean build of IMP on my desktop), making the total build mostly limited by disk I/O. The result is that one often ends up with all the compilation processes writing as fast as possible to your hard drive, which can make the gui sluggish. One can trade off slower compilation for more ability to do other things while it is compiling by either turning off the merge of .cpp files (percppcompilation="yes") or compiling with fewer processes (eg -j 2 instead of -j 4).

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