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868 discussions

Helper functions
by Daniel Russel 02 Nov '07

02 Nov '07

I have various helper functions that are probably generally useful. I am ambivalent about what to do with them. One set is utilities for getting and setting attributes which look like /** Set the value of the string attribute name to val, whether or not it was already there. */ bool set_string(ModelData *m, Particle *p, const String& name, std::string val) and /** Get the string attribute name or return default_value if the particle does not have any such attribute. */ const String& get_string(ModelData *m, Particle *p, const String& name, const String& default_value=String()) Obviously there are int and float versions. Should such things go in to imp proper? On one hand they are extremely useful. On the other it is increasing the size of the interface and while it makes it more convenient, it doesn't add any power. Next I have some helpers for manipulating hierarchy and bond particles (getting the number of children, getting specific children etc). These should go somewhere to establish norms for hierarchies.

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imp
by Andrej Sali 02 Nov '07

02 Nov '07

just occurred to me that I am not capable of following your email threads very carefully, yet I am likely to have opinions about things. we should be meeting every 2-3 weeks. next week? Andrej

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shared state - a new thread ... :)
by Keren Lasker 02 Nov '07

02 Nov '07

ok - my thought on the relationship between particles/restraints and optimizers. It might be that I am missing something since I used only I looked at about half of the IMP classes - not all. To my understating ( please correct me if I am wrong here) in the current design: 1- attributes are used for two purposes to store the particles information (x,y,z, radii, weight, .... ) and to manage the optimization (is-opt) and Model data has two responsibilities - hold the particles and participate in the optimization process. 2 - The restraints holds a state (ie they know in construction time what is the particle list that they are going to work on) I think that we should divide the two. Have ModelData which does not care at all about optimization, its only responsibility is to maintain a valid set of particles. We should have an additional class OpimizationData which holds all optimization header data (is optimizable, should be included in the scoring ). It can implement optimization logic nonbonded list , it might be that we'll come up with other optimization logics as well ... . So the Statistics class for example should be within the OptimizationData class. The restraints should be stateless - at each evaluation time they will get the relevant attribute list and derivative list ( which might be different from the attribute list) from the optimizationData For example, for the nonbonded list case: 1 - ModelData holds all the particles. 2 - The user sets its attributes for optimization ( which sets the OpimizationData class) 3 - At each optimization stage a - the restraints are given a pointer to the OptimizationData class - where all the header-optimization information about the attributes and a reference to them is stored. b - at the end of the optimization step the OptimizationData class updates the header information in case some optimization properties should be changed 4 - when adding or removing particles, the OptimizationData object ( there might be more than one - when dealing with hierarchy for example - the OptimizationData objects are updated accordingly). anyway , as I discussed earlier with Ben, I think that we can not really have a serious discussion without having a few detailed use- cases ( there are other than the non-bonded list one). I will write a python unitest for fitting and docking of multiple components, we should probably have another single protein refinement one and maybe also ligand docking and then we can assess solutions more realistically.

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Re: directory structure
by Ben Webb 23 Oct '07

23 Oct '07

Daniel Russel wrote: > Can we have an include directory (new_imp/include) where and a > (new_imp/include/IMP) directory for the headers? Now I have to do > -Inew_imp/src which looks funny and would presumably change for any > distribution of IMP (since almost all of the headers in src need to be > installed in an include directory for anyone to write their own > restraints or use IMP through C++ and their names are too generic to > just into /usr/include). Thanks. How does this differ from what we talked about last week? If it's the same, then the same deal applies: I'm waiting on the scons guys to resolve some build issues before making any big changes. But the good news there is that we resolved those today, so I can do this tomorrow. Does anybody object to Daniel's suggestion? If it's not the same, then perhaps you can point out the difference, because it looks the same to me. ;) P.S. What is this mystery project which needs to include the IMP headers? In my opinion, it'd be great to have at least some version of this in the IMP SVN repository with Keren's impEM stuff, because it's really the applications which define what we do (and need to do) with IMP. Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Re: IMP/BALL and directory structure
by Ben Webb 16 Oct '07

16 Oct '07

Daniel Russel wrote: > I have written some code to use BALL to > read PDB files and turn them in to particles and a hierarchy (and to > evaluate MD energy for such a hierarchy). Keren wanted to use this too. > Do you have a preferred SVN structure/location for this sort of thing? > Something like trunk/IMP_BALL with include and src directories? And > pyext too I guess. Sure, my policy is, roughly speaking: if it doesn't break the core unit tests, put it in. Better to have it in SVN where we can poke holes in it than it to live on your laptop for ever. But this may be an opportune point to discuss the layout of the IMP repository. Right now it looks basically like: imp libsaxs src doc mdt bin src doc pyext test new_imp bin IMP tests impEM rsr doc pyext od_dope src doc pyext test tnt python test tools The top-level directories are independent modules which are built separately but use a shared set of build scripts (in the tools directory). libsaxs is Frido's SAXS module, which plugs in to Modeller; mdt uses the Modeller C and Python interfaces; od_dope uses the Modeller C interface; tnt and new_imp use the Modeller Python interface. new_imp is essentially what Bret turned in before he left, and which Daniel, Keren and I are currently working on. The projects have similar sub-directories: bin for generated binaries; src for C/C++ source code; doc for documentation; pyext for Python extensions; python for pure Python code; test for testcases. However, new_imp uses 'IMP' as its source code directory, and the tests live under that. new_imp also contains some sub-projects, such as Keren's impEM interface and Bret's RSR (Restrainer web interface). As Daniel pointed out, new_imp's naming is a little inconsistent (e.g. imp/new_imp/IMP to get to the sourcecode) so what about renaming the IMP subdirectory to src, and the new_imp top-level directory to kernel (or perhaps base) ? Dependent projects such as impEM and rsr would then become top-level directories: imp libsaxs mdt kernel bin src test doc pyext rsr impEM od_dope tnt tools This scheme would, however, require you to manually handle dependencies between the projects (e.g. impEM and rsr would be independent projects) but that's not a huge hurdle - just run 'scons' in the kernel directory before running 'scons' in the impEM directory. A slightly more radical rearrangement could look like imp libsaxs mdt bin kernel src test doc pyext rsr impEM od_dope tnt tools and use a top-level build system which would track dependencies between projects, staging binaries and libraries for all IMP projects to the bin directory (but the downside is the targets are a bit more wordy - e.g. 'scons kernel', 'scons kernel-test', 'scons 'impEM', scons 'impEM-test' rather than just 'scons' and 'scons test' in the kernel and impEM directories). Thoughts? There is, of course, also the issue over whether libsaxs, mdt, od_dope and tnt belong here or in their own repository. My understanding is that the Grand Plan is that they'll become part of IMP eventually, which is why they're there. But if we want to distribute them under a non-free license for any reason, it might make sense to put them in a separate repository in the future. Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Re: Shared state
by Ben Webb 16 Oct '07

16 Oct '07

Daniel Russel wrote: > We had discussed but never implemented some mechanism for having shared > state (such as non-bonded lists). It seems to me the right way to do it > is to have a class State (or some better name) which has a single > virtual method "void update()" which is called in Model::evaluate before > the restraints are evaluated. As with Particle, Restraint it stores a > ModelData pointer and Model would have add_state and get_state methods. Well, I think we need to discuss this further, so let's drag in others here: I agree that a shared state class is needed, and could be used by nonbonded lists. But what do you need it for right now, i.e. what else would people use it for? Calling State::update() in Model::evaluate() would not be sufficient, at least for nonbonded lists, because you can also call Restraint::evaluate() on individual restraints from the Python interface. How would a nonbonded list know that it needs to do an update? I don't like the Statistics class proposed in ModelData.h. (The idea of that class is to automatically keep min/max/change statistics on all float variables.) Why: because 1. if you don't want nonbonded lists, maintaining these statistics is inefficient, and 2. because it's part of the ModelData class, it can't easily be extended by other classes. Two suggestions: 1. Classes can register callbacks/actions with ModelData::set_float, or this could trigger a State::set_float method, to be notified whenever the model is changed. The advantage of the former is that the callback can go away after a nonbond update is triggered, saving the overhead of a function call for subsequent set_float()s. 2. Classes to allow the get/set of the 'optimizable state' (right now, this is just all optimizable floats) could have similar methods, useful for optimizers such as CG and steepest descent which change all attributes simultaneously. Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Re: a few more things, right?
by Andrej Sali 15 Oct '07

15 Oct '07

3 but it seems that a subset of the categories on the modeller web page would apply. andrej On Oct 15, 2007, at 12:44 AM, Ben Webb wrote: > Andrej Sali wrote: >> where are they? a > > https://salilab.org/internal/imp/index.html > https://salilab.org/internal/imp/imp2.html > https://salilab.org/internal/imp/imp3.html > > Ben > -- > ben(a)salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle -- Andrej Sali, Ph.D. Professor and Vice Chair, Department of Biopharmaceutical Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant, Ms. Karin Asensio, Tel +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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IMP class and module naming scheme
by Ben Webb 11 Oct '07

11 Oct '07

I'd like to get a consensus on naming for IMP modules and classes (well, OK, I'm going to say what I think it should be, and people can agree or disagree). Currently, on the C++ side, all classes use a Capitalized_Words_With_Underscores naming scheme (e.g. Restraint_Set) and live in the 'imp' namespace. This is translated to the 'imp2' module on the Python side, with the same class names. This has a few problems: 1. The Python 'imp2' name is ugly - Bret presumably had to call it that because Python has a built-in module called 'imp' already. The Python guys (http://www.python.org/dev/peps/pep-0008/) prefer "short, lower-case" names for modules, but I don't think this really makes sense for initialisms anyway - for example, there are already EMAN and CORBA Python libraries out there (the BALL guys also use "BALL"). So I propose "IMP". 2. Python pretty much mandates CamelCase for class names (e.g. RestraintSet). Since the Python class names match the C++ names, we either have to do lots of ugly renaming in the Python interface, or just rename the C++ classes to match. Lots of C++ people use CamelCase anyway (e.g. BALL at http://www.bioinf.uni-sb.de/OK/BALL/Documentation/1.1.1/V1.1.1/hierarchy_ht…). So I propose CamelCase names for IMP C++ classes. 3. There are a bunch of utility Python modules in tests/python_libs: IMP_Modeller_Intf.py IMP_Test.py IMP_Utils.py load_imp_xml_model.py I propose renaming these to IMP.modeller, IMP.test, IMP.utils, IMP.xml. 4. I propose renaming derived classes such as imp::RSR_Exclusion_Volume (exclusion volume restraint, although what the second R in RSR stands for, I don't know ;) as either imp::ExclusionVolumeRestraint or imp::restraint::ExclusionVolume. I prefer the latter because it would more easily translate into the Python IMP.restraint.ExclusionVolume class, and by changing from a class name prefix (RSR) to a namespace we both allow for more readable Python scripts (e.g. "import IMP.restraint as r; r.ExclusionVolume()" or even "from IMP.restraint import *"), and finally because this would greatly simplify moving restraints to their own C++ module. What do others think? Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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