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xml support in imp
by Keren Lasker 06 Mar '09

06 Mar '09

hi all, I would like to add XML support in IMP. It seems that Arabica could be a good alternative - thoughts ? Keren.

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Simplifying IMP usage
by Daniel Russel 06 Mar '09

06 Mar '09

So far development in IMP proper has mostly focused on expanding the capabilities and flexibility of IMP. The result is a set of functionalities which can be (and has to be) combined to get what you want done. At this point we should be starting to have a good idea what common usage patterns are and think about adding higher level functions which make implementing the usage patterns easier. These higher level functions should help narrow the gap between experimental data and IMP. Currently implemented examples of such things include: - copying a molecular hierarchy - setting up a rigid body defined by a set of particles - setting up a particle as a centroid or cover of a set of particles Future examples might include: - creating a molecular hierarchy for a representation of a protein with a given number of particles based on the number of amino acids in the protein - creating a rigid representation of a protein with a given number of spheres from a molecular hierarchy loaded from the pdb - building a hierarchical representation of a protein from a molecular hierarchy loaded from the pdb - setting up efficient volume exclusion restraints for an arbitrary collection of particles, rigid bodies and hierarchies. Anyway, I set up a wiki page for people and refine ideas and requests: <https://salilab.org/imp/wiki/high_level_operations>

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This week in IMP
by Daniel Russel 06 Mar '09

06 Mar '09

- Helper functions for creating centroid and cover particles have been added since it is kind of painful and obscure to do on your own. The examples now use these helper functions. - a FixedParticleRefiner has been added for setting up ad-hoc refinement. It just returns a fixed list of particles and so means you can skip creating a hierarchy if you just have one particle you want to refine. - the atom module as been created and all atom and molecule related functionality has been moved there and the versions in core marked as deprecated. Please adjust your code accordingly. - there is a pdb reader and writer in the atom module - you can clone a hierarchy with bonds and atom information and all (but this is not tested yet, so check that the results make sense) - there is lots of new geometry: Planes, Spheres, Cylinders, spherical caps and such. When designing the interface of new code to be added to IMP, please: - look around for code that does something similar and to make the interfaces as similar as possible, this is the easiest way to make your code OK. At this point, the template coverage is pretty good. - make sure you follow the coding standards outlined on the web page. Read through those standards before you design your interface if you are not extremely familiar with them. - think about what should be part of the interface and what is an implementation detail. Hide implementation details in internal or anonymous namespaces (and if you don't know what these are and how they work, ask someone). Things should only be in the public interface if you know they will be used outside of the IMP library. - make sure all the tests pass with a non-fast build and with "deprecated=False" passed to scons to turn off deprecated classes and functions. - build the doc (scons doc > /dev/null) and make sure that there are no doc warnings from your code and that it all shows up in the resulting docs Anyway, things are filling out nicely in IMP :-)

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breaking change with move to IMP.atom
by Daniel Russel 05 Mar '09

05 Mar '09

Molecule-related classes such as ResidueDecorator and AtomDecorator are now in IMP.atom. The IMP.core versions of most things have been left for the time being (but marked as deprecated). Unfortunately, technical difficulties with SWIG prevent that being done easily for ResidueDecorator and AtomDecorator and anything which uses them. The fix is just to replace core.AtomDecorator with atom.AtomDecorator (etc.) (a good excuse to learn sed if you don't already know it :-)

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how do you call VectorD<X> from python ?
by Keren Lasker 04 Mar '09

04 Mar '09

thanks, keren.

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is there a fast way to copy attributes from one particle to another ?
by Keren Lasker 04 Mar '09

04 Mar '09

thanks, keren.

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Other optimizers and salilab only modules
by Daniel Russel 03 Mar '09

03 Mar '09

When trying to figure out why some of my optimizations were failing, I wrapped a number of optimizers available in GSL so they can be used in IMP. These include another implementation of CG, a quasi-newton optimizer and simplex (I mostly wanted CG, but the other came for free). We can't ship the wrappers (unless we want to ship a GPL-ed special edition of IMP along with the LGPL one), but they might be useful to people to experiment with. If others are interested, I'll add a salilab_modules directory in IMP for such in-house code which would not be released (we can figure out how to make it inaccessible to the outside world when such is needed).

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IMP_LOG and show
by Keren Lasker 01 Mar '09

01 Mar '09

hi, Sometimes it is useful to use X.show() in logging ( for example transformation.show()) is there a way to do that? thanks, keren.

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This week in IMP
by Daniel Russel 27 Feb '09

27 Feb '09

As per Keren's suggestion, I'll start sending out a summary email of IMP-related changes. Once Ben updates the web page, the change list can go on web page and so be frequently updated in addition to the email. - Sphere3D and Cylinder3D have been added to algebra. So we now have standard ways of specifying rotations, transformations, spheres, and cylinders. If your function takes a description of one of those, please have it take an instance of the appropriate class instead. - a new module, 'display' has been added to support exporting geometry to external programs. It currently supports spheres, cylinders, XYZRDecorator particles, BondDecorators, axis aligned boxes, and triangles, and supports output to Bild, CMM, VRML and CGO (a pymol format). - functions to generate a cover of the surface of a cylinder and sphere have been added in addition to existing functions to randomly sample in and on spheres and axis aligned boxes. - the build script has been changed so that you can add a module locally (by putting it in modules) and you don't have to change modules/SConscript (use the localmodules=True flag) - particle indexes are still scheduled to disappear (and get_particle(unsigned int) is linear time) so stop using them - rigid body support has been added both via snapping the members to preserve rigidity and via direct optimization of the rigid body orientation and translation. The code has only been tested in a limited manner. - a check has been added to IMP for incorrectly defined functions. If you get a linker error involving link_0.cpp and link_1.cpp and duplicate symbols, it probably means you defined a function in a header and forgot to make it inline. - transformations are now composable and probably a few other things I have forgotten. Before you implement something, check if it is already there by using the search in the manual and, if not, by emailing imp-dev. Emailing such questions to the list lets people know what you are using and refreshes people's picture of what is in IMP. In addition, many of us have useful code around that isn't in IMP, but easily could be. It is good practice to keep a second (or 10th) copy of IMP around that you never change directly and simply keep in sync with the current svn. When you commit changes to SVN, update your svn copy and run the tests there to check that you haven't forgotten to commit anything important (such as an SConscript or a related file in another directory).

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using algebra from em module
by Keren Lasker 27 Feb '09

27 Feb '09

hi, including algebra classes in em module does not compile - is there some change needed in the build system for that ? thanks, keren.

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