January 2011 - IMP-dev

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>

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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?

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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

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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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recently in IMP
by Daniel Russel 21 Jan '11

21 Jan '11

BTW, if you updated IMP this morning, you probably should do so again as there was a subtle bug that only appeared in fast builds. - 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. - IMP::atom::CHARMMParameters can now automatically map CHARMM-style atom and residue naming to PDB-style, so CHARMM topology files can be used unmodified. - IMP::atom::CHARMMTopology::add_sequence() provides a simple way to generate a topology from a string of amino acid one-letter codes. - IMP::atom::CHARMMTopology::add_coordinates() will generate atomic Cartesian coordinates from CHARMM internal coordinate information. - IMP::atom::CHARMMTopology::add_missing_atoms() and IMP::atom::remove_charmm_untyped_atoms() can now be used to ensure that atoms read from a PDB file match the CHARMM topology. - building of deprecated functionality is now false by default - the IMP_COMPARISONS(), IMP_COMPARISONS_1(), IMP_COMPARISONS_2() macros now take the name of the class as an additional (first) argument. This avoids the formerly needed, \c This typedef and makes them more consistent with the other macros in \imp. - modules can now be built externally to the \imp svn in addition to applications and biological systems. To do so, create a directory with your module in a subdir containing links to the \imp SConscript file and scons_tools and a config.py that has information needed to run \imp (eg an appropriate \c pythonpath, \c ldpath). - removed IMP::algebra::GridD::get_index(VectorD) as it wasn't very safe (in that vectors coordinates can get rounded between the IMP::algebra::GridD::get_has_index() and IMP::algebra::GridD::get_index() calls. Use IMP::algebra::GridD::get_nearest_index() or IMP::algebra::GridD::get_extended_index() or IMP::algebra::GridD::operator[]() instead.

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doc for nightly builds
by Daniel Russel 20 Jan '11

20 Jan '11

Since the docs for the nightly builds have been broken for a while (not showing inheritance diagrams and any other graphs due to a bug in the doxygen setup on synth), I'm putting a nightly build of the docs up at <http://www.salilab.org/~drussel/unstructured/imp_doc/> until that gets worked out.

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Fragment.set_residue_indexes
by Pia Unverdorben 19 Jan '11

19 Jan '11

dear all, we tried to set the indexes of a fragment explicitly. however, the procedure seems to be incredibly slow in the following example where we tried to add residue numbers to a particle 'frag' (set up as a fragment). somehow, the last line takes ages (dies?). any hints would be appreciated. thanks pia & frido rs= IMP.Ints() for ii in (ifirst, ilast+1): rs.append(ii) tfrag = IMP.atom.Fragment(frag) tfrag.set_residue_indexes(rs)

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wiki page for imp-dev meeting Tuesday on distributed imp
by Daniel Russel 19 Jan '11

19 Jan '11

I added a wiki page with some ideas for providing the needed functionality for weakly communicating distributed computations in IMP. Please add you comments/ideas/refinements. <http://salilab.org/imp/wiki/distributed_computations>

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imp dev meeting will be a bit late
by Daniel Russel 18 Jan '11

18 Jan '11

The talk is running long.

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recently in IMP
by Daniel Russel 14 Jan '11

14 Jan '11

- Instructions and scripts have been added for building modules and things externally to the \imp build. See the installation guide. Doing this can make the build cycle much faster as you don't have to wait for the scripts to parse all of IMP every time and while scons randomly rebuilds the swig wrappers. - IMP::atom::CHARMMParameters can now automatically map CHARMM-style atom and residue naming to PDB-style, so CHARMM topology files can be used unmodified. - IMP::atom::CHARMMTopology::add_sequence() provides a simple way to generate a topology from a string of amino acid one-letter codes. - IMP::atom::CHARMMTopology::add_coordinates() will generate atomic Cartesian coordinates from CHARMM internal coordinate information. - IMP::atom::CHARMMTopology::add_missing_atoms() and IMP::atom::remove_charmm_untyped_atoms() can now be used to ensure that atoms read from a PDB file match the CHARMM topology. - building of deprecated functionality is now false by default - the IMP_COMPARISONS(), IMP_COMPARISONS_1(), IMP_COMPARISONS_2() macros now take the name of the class as an additional (first) argument. This avoids the formerly needed, \c This typedef and makes them more consistent with the other macros in \imp. - modules can now be built externally to the \imp svn in addition to applications and biological systems. To do so, create a directory with your module in a subdir containing links to the \imp SConscript file and scons_tools and a config.py that has information needed to run \imp (eg an appropriate \c pythonpath, \c ldpath). - removed IMP::algebra::GridD::get_index(VectorD) as it wasn't very safe (in that vectors coordinates can get rounded between the IMP::algebra::GridD::get_has_index() and IMP::algebra::GridD::get_index() calls. Use IMP::algebra::GridD::get_nearest_index() or IMP::algebra::GridD::get_extended_index() or IMP::algebra::GridD::operator[]() instead. - renamed IMP::domino::ParticleStatesTable::get_particles() to IMP::domino::ParticleStatesTable::get_subset() as it is more useful to be able to get the subset containing all the particles. - rename IMP::restrainer::Restraint::print_all_restraints() to IMP::restrainer::Restraint::show_all_restraints() to be consistent with the rest of \imp. - renamed IMP::atom::get_conect_record_string() to IMP::atom::get_pdb_conect_record_string() to make clearer what it is. - class and method names are now spell checked. Add missing words to spelling_exceptions in the module test call in modulename/test/SConscript

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