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set_log_level
by Keren Lasker 20 Apr '10

20 Apr '10

hi - is there a way to set different log levels to different modules ? thanks, keren.

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examples not working in IMP version 1.0
by Friedrich Foerster 16 Apr '10

16 Apr '10

dear all, i have been trying to run the example for the non-bonded list in IMP (the official release 1.0) and sadly, it did not work: sendling 1026% /fs/pool/pool-foerster/apps/src/imp/branches/1.0/tools/imppy.sh python test_imp.py Traceback (most recent call last): File "test_imp.py", line 10, in <module> ps = IMP.core.ListSingletonContainer(IMP.core.create_xyzr_particles(m, 20, 1.0)) AttributeError: 'module' object has no attribute 'ListSingletonContainer' test_imp.py is the IMP example: import IMP import IMP.core import IMP.atom # This example addes a restraint on nonbonded interactions # after excluding a set of bonded interactions. m= IMP.Model() # The set of particles ps = IMP.core.ListSingletonContainer(IMP.core.create_xyzr_particles(m, 20, 1.0)) # create a bond between two particles bd0= IMP.atom.Bonded.setup_particle(ps.get_particle(0)) bd1= IMP.atom.Bonded.setup_particle(ps.get_particle(1)) IMP.atom.custom_bond(bd0, bd1, 2.0) # Set up the nonbonded list for all pairs at are touching # and let things move 3 before updating the list nbl= IMP.core.ClosePairContainer(ps, 0.0, 3.0) nbl.add_pair_filter(IMP.atom.BondedPairFilter()) # Set up excluded volume sdps= IMP.core.SphereDistancePairScore(IMP.core.HarmonicLowerBound(0,1)) evr= IMP.core.PairsRestraint(sdps, nbl) m.add_restraint(evr) # Set up optimizer o= IMP.core.ConjugateGradients() o.set_model(m) o.optimize(1000) any suggestions? thanks p.s.: IMP is compiled with build='fast'. all 'required' packages (specified in the installation doc) are installed: * scons (0.98 or later) * Boost (1.33 or later) * A Subversion (svn) client to access the repository If you wish to build the Python interfaces, you will also need: * Python (2.3 or later) * SWIG (1.3.40 or later) -- Dr. Friedrich Foerster Max-Planck Institut fuer Biochemie Am Klopferspitz 18 D-82152 Martinsried Tel: +49 89 8578 2632 Fax: +49 89 8578 2641 www.biochem.mpg.de/foerster

2 2

OpenMM
by Dina Schneidman 25 Mar '10

25 Mar '10

Hi, It can be interesting for us to look at OpenMM https://simtk.org/home/openmm OpenMM is an open source software library for Molecular Dynamics simulations with GPU support. Quote from their website: "As a library it can be hooked into any code, allowing that code to do molecular modeling with minimal extra coding". Dina

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proposed api changes
by Daniel Russel 21 Mar '10

21 Mar '10

First, an effort to make compilation of the python wrapper feasible again. To do this, I propose we use python lists instead of compiling many different versions of classes which look more or less like python lists. eg, IMP.Particles() is equivalent to [], as is IMP.Vector3Ds(). I have experimented with this and found a few effects: - this makes compilation of the python wrappers of imp much, much faster (it is now quite pleasant to build IMP on my laptop, where as before it took hours) - overloaded functions where the only way to tell the functions apart is the type of the collection are not supported. There aren't too many such cases in IMP. This is, in most cases, simply a limitation of SWIG and so we can work around it in important cases if desired. SWIG produces a warning so we will know where it is happening. - passing value types (eg IMP.Particles()) by pointer or storing pointers to passed value types would not work on calls from python. I consider this a feature as such things are bad programming practices. Second, there is a bit of a mess with the containers in terms of informing them about the model (since in increasing number of them need to register score states with the model). I propose that all containers need to get the model as part of their constructor. The main effect would be that the default constructors of List*Containers take a model (instead of being the default constructor). This would simplify a lot of things and make caching much easier in the containers which do not currently do it. Comments? Objections?

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Re: [IMP-dev] [IMP-commits] r5550 - in trunk/modules/em: include src
by Keren 20 Mar '10

20 Mar '10

Notification of IMP commits <imp-commits(a)salilab.org> wrote: >Author: kerenl(a)SALILAB.ORG >Date: 2010-03-20 20:27:30 -0700 (Sat, 20 Mar 2010) >New Revision: 5550 > >Modified: > trunk/modules/em/include/KernelParameters.h > trunk/modules/em/src/KernelParameters.cpp >Log: >move show to cpp and generate parameters to radius if none were found in get_params > >Modified: trunk/modules/em/include/KernelParameters.h >=================================================================== >--- trunk/modules/em/include/KernelParameters.h 2010-03-19 21:32:28 UTC (rev 5549) >+++ trunk/modules/em/include/KernelParameters.h 2010-03-21 03:27:30 UTC (rev 5550) >@@ -26,12 +26,8 @@ > RadiusDependentKernelParameters( > float radii,float rsigsq,float timessig, > float sq2pi3,float inv_rsigsq, float rnormfac, float rkdist); >- void show(std::ostream& s=std::cout) { >- s << "vsig : " << vsig_ << " vsigsq: " << vsigsq_ >- << " inv_sigsq: " << inv_sigsq_ << " sig: " << sig_ >- << " kdist: " << kdist_ << " normfac: " << normfac_ >- << std::endl; >- } >+ //! Show >+ void show(std::ostream& s=std::cout) const; > //! Gets the value of vsig parameter > inline float get_vsig() const { return vsig_;} > //! Gets the value of vsig square parameter >@@ -77,8 +73,9 @@ > /** The other variables of the parameters > (rsigsq,timessig,sq2pi3,inv_rsigsq,rnormfac,rkdist) must have been set. > \param[in] radius the radius >+ \param[out] the radius based parameters > */ >- void set_params(float radius); >+ const RadiusDependentKernelParameters* set_params(float radius); > > //! Finds the precomputed parameters given a particle radius. > /** > >Modified: trunk/modules/em/src/KernelParameters.cpp >=================================================================== >--- trunk/modules/em/src/KernelParameters.cpp 2010-03-19 21:32:28 UTC (rev 5549) >+++ trunk/modules/em/src/KernelParameters.cpp 2010-03-21 03:27:30 UTC (rev 5550) >@@ -11,7 +11,12 @@ > #include <IMP/constants.h> > > IMPEM_BEGIN_NAMESPACE >- >+void RadiusDependentKernelParameters::show(std::ostream& s) const { >+ s << "vsig : " << vsig_ << " vsigsq: " << vsigsq_ >+ << " inv_sigsq: " << inv_sigsq_ << " sig: " << sig_ >+ << " kdist: " << kdist_ << " normfac: " << normfac_ >+ << std::endl; >+} > RadiusDependentKernelParameters::RadiusDependentKernelParameters( > float radii, float rsigsq, > float timessig, float sq2pi3, >@@ -52,7 +57,8 @@ > lim_ = exp(-0.5 * (timessig_ - EPS) * (timessig_ - EPS)); > } > >-void KernelParameters::set_params(float radius) { >+const RadiusDependentKernelParameters* >+ KernelParameters::set_params(float radius) { > IMP_USAGE_CHECK(initialized_, > "The Kernel Parameters are not initialized"); > std::map<float ,const RadiusDependentKernelParameters *>::iterator iter = >@@ -63,6 +69,7 @@ > radii2params_[radius]=new RadiusDependentKernelParameters( > radius,rsigsq_,timessig_,sq2pi3_, > inv_rsigsq_,rnormfac_,rkdist_); >+ return radii2params_[radius]; > } > > const RadiusDependentKernelParameters* KernelParameters::get_params( >@@ -96,6 +103,8 @@ > } > if (closest == NULL) { > IMP_WARN("could not find parameters for radius:"<<radius<<std::endl); >+ IMP_WARN("Setting params for radius :"<<radius<<std::endl); >+ closest = set_params(radius); > } > return closest; > } > >_______________________________________________ >IMP-commits mailing list >IMP-commits(a)salilab.org >https://salilab.org/mailman/listinfo/imp-commits

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fast & build environment
by Keren Lasker 16 Mar '10

16 Mar '10

hi, Daniel - you once told me how to do that - but forgot .... and anyway it would be good on be on record for all, so : How can I maintain two environments (for example fast and build) on the SAME source code ? i.e how can i generate build_fast and build_build directories simultaneously ? thanks, Keren.

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compiling IMP on the cluster
by Keren Lasker 14 Mar '10

14 Mar '10

hi, trying to compile IMP on int64a I keep getting an error message: OSError: [Errno 12] Cannot allocate memory scons: building terminated because of errors. any ideas how to compile IMP on the cluster ? :) Keren.

3 4

IMP release
by Ben Webb 05 Mar '10

05 Mar '10

I intend to branch the Subversion repository for the 1.0 IMP release at 5pm today - I need a semi-stable frozen version in order to build binaries etc. for the release next week. If you have documentation, bug fixes, examples etc., please commit them before 5pm today. If you have shiny new features, interface changes, etc. please keep them to yourself for now. ;) Once I make the branches/1.0 branch, trunk will be available once again for new features, but let's try to keep it frozen for now. The IMP web pages should now be public. However, this means that the wiki and the bug tracker no longer use the Sali lab authentication system - you'll have to go in and manually create accounts. (If you already have a Bugzilla account, and it won't let you change your password, I can reset it for you.) Those of you that signed the legal stuff that came round earlier, this is your lucky day! There's one last document to fill out prior to release. I will be bugging people for signatures later. Thanks to everyone for all their hard work! 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-dev] [IMP-commits] r5347 - in trunk/modules/algebra: include pyext test
by Ben Webb 05 Mar '10

05 Mar '10

On 3/5/10 10:37 AM, Notification of IMP commits wrote: > Author: drussel(a)SALILAB.ORG > Date: 2010-03-05 10:37:46 -0800 (Fri, 05 Mar 2010) > New Revision: 5347 > > Added: > trunk/modules/algebra/test/test_plural.py > Modified: > trunk/modules/algebra/include/Cone3D.h > trunk/modules/algebra/include/Rotation3D.h > trunk/modules/algebra/include/SpherePatch3D.h > trunk/modules/algebra/include/SphericalVector3D.h > trunk/modules/algebra/pyext/swig.i-in > trunk/modules/algebra/test/test_rotation.py > Log: > add some collections of objects and shows I think you forgot the assertPlural and assertShow methods... ERROR: Test all algebra objects have show ---------------------------------------------------------------------- Traceback (most recent call last): File "/clarinet1/home/ben/imp/modules/algebra/test/test_plural.py", line 13, in test_2 return self.assertShow(IMP.algebra, ['AxisAnglePair', 'Matrix3D', 'MultiArray3D', 'NearestNeighbor2D', 'NearestNeighbor3D', 'NearestNeighbor4D']) AttributeError: 'DirectoriesTests' object has no attribute 'assertShow' ====================================================================== ERROR: Test all algebra objects have plural version ---------------------------------------------------------------------- Traceback (most recent call last): File "/clarinet1/home/ben/imp/modules/algebra/test/test_plural.py", line 9, in test_data_directory return self.assertPlural(IMP.algebra, ['FixedXYZ', 'FixedZYZ', 'LinearFit', 'Matrix2D', 'Matrix3D', 'MultiArray3D', 'NearestNeighbor2D', 'NearestNeighbor3D', 'NearestNeighbor4D', 'ParabolicFit', 'BoundingBox2D', 'BoundingBox3D', 'BoundingBox4D']) AttributeError: 'DirectoriesTests' object has no attribute 'assertPlural' 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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this week in imp
by Daniel Russel 26 Feb '10

26 Feb '10

Week of Feb 21, 2010 IMP::Object::set_was_owned() was changed to IMP::Object::set_was_used() as that better reflects what the flag means. various more interpolation and endian methods had their names fixed (by adding get_) the function get_mean() on vectors was removed as it duplicated IMP::algebra::get_centroid() build_Transformation3D_from_transformation3D was replaced by IMP.algebra.get_transformation_3d() IMP::algebra::almost_equal() is now IMP::algebra::get_are_almost_equal() to fit the naming conventions. the random vector generators have been cleaned up to remove redundant ones and make the names more consistent. They now have the form of either IMP::algebra::get_random_vector_in() or IMP::algebra::get_random_vector_on() where there is one argument describing the volume or shape (such as an IMP::algebra::SphereD<4>). or IMP::algebra::get_uniform_surface_cover() where the first argument is the primitive whose surface we are covering and the second is the number of points. Some good sed strings are Spheres in IMP::algebra are now supported in general dimensions. See IMP::algebra::SphereD. Many methods in IMP::algebra were renamed to be more consistent with other methods or general conventions. Most of these simply involved addingget_ as a prefix and/or add a _3d suffix when they did not take any arguments. build_Rotation2D_from_Vector2D became IMP::algebra::get_rotation_to_x_axis() most of the Rotation3D and Transformation3D functions (in addition, IMP::algebra::get_identity_rotation_3d() andIMP::algebra::get_identity_transformation_3d() added the _3d so we can add 2D versions at some point) IMP::algebra::Transformation3D::get_transformed() and IMP::algebra::Rotation3D::get_rotated(). IMP::algebra::get_distance(), this also carries over to the IMP::core::get_distance() The following global replacements are probably safe (in sed expressions) IMP::algebra::Vector3D and IMP::algebra::Vector3Ds were replaced by the expanded (non-typedef) version in functions parsed by SWIG as the current situation was extremely brittle. For the moment, you should not use the typedefs in definitions that swig sees. Sorry. IMP::algebra::Sphere3DPatch was renamed to IMP::algebra::SpherePatch3D to be consistent with the other geometry and allow us to support higher dimensions in the future. rigid_align_first_to_second was renamed to IMP::algebra::get_transformation_aligning_first_to_second() and build_Transformation2D_from_point_sets was renamed to IMP::algebra::get_transformation_aligning_pair() Sed substituions are included in the change log.

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