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869 discussions

bug in core::Centroid class derivative propagation to fine particles?
by Barak Raveh 14 Apr '14

14 Apr '14

I was wondering whether there is a bug in derivative propagation in the core::Centroid class - is anybody else using it? As it is now, the derivatives of the centroid are copied to the finer particles as is, using the DerivativesToRefinedas class. Shouldn't the derivatives be rescaled first according to the mass contribution of each fine particle to the centroid? For instance, let p1 and p2 be particles of masses 10 and 20 respectively. Then if a derivative of 3 units is accumulated in C, then right now, a derivative of 3 units is also copied to p1 and p2 each. Shouldn't this be reweighted such that p1 get 1 derivative units and p2 gets 2 derivative units? -- Barak

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IMP 2.2.0 release
by Ben Webb 10 Apr '14

10 Apr '14

IMP 2.2.0 is now available. It contains a number of new features, notably support for SOAP scoring and a more reliable RMF file format. See https://github.com/salilab/imp/releases/tag/2.2.0 for the full change log. Check it out at http://integrativemodeling.org/ As always, we'll make a a 2.2.1 release in a few weeks if any significant bugs show up in 2.2.0. 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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Algebra::Rotation3D::get_derivative
by Barak Raveh 31 Mar '14

31 Mar '14

Does anyone know what Algebra::Rotation3D::get_derivative() computes precisely? -- Barak

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Harmonic restraint on rotation in IMP
by Barak Raveh 25 Mar '14

25 Mar '14

Does anybody know of an existing implementation of a harmonic restraint on rotational degrees of freedom? Namely, I have two reference frame of two particles p1 and p2. For simplicity, assume xyz(p1) = xyz(p2). I would like to add a harmonic restraint over the delta in their reference frame, for some definition of that delta. Thank you Barak

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Preparation for the 2.2 release
by Ben Webb 20 Mar '14

20 Mar '14

So, the next stable release of IMP is coming up soon. My release criteria are pretty simple (let me know if you disagree ;) 1. The nightly build should be close-to-clean: http://integrativemodeling.org/nightly/results/ i.e. a) it should build, b) the documentation shouldn't be full of broken links, and c) the tests and examples should work (as completely as we can manage). I've already taken care of a) and b) and am working on c). If you can take a moment to look at any modules/applications you work on and see if you can help out with any test failures, that would really help! 2. All the IMP issues attached to the "IMP 2.2 release" milestone should be addressed[*]. If you have a "favorite" IMP bug that isn't in the list at https://github.com/salilab/imp/issues?milestone=7&state=open, go add the 2.2 release milestone to your issue, otherwise it likely won't get fixed. (And if it doesn't have an open issue at all, open one...) Those currently in there shouldn't be too disruptive, although I will be removing the code we deprecated in 2.1, which will likely break a few things. 3. The biological systems at http://integrativemodeling.org/systems/ should all work with latest IMP. (I'll start a run of them once the deprecated code is gone - most likely some of them use at least one deprecated function.) [*] Not necessarily "fixed"... we may decide to push some issues back to the next release. 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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Moving on
by Daniel Russel 04 Mar '14

04 Mar '14

As many of you know, I'm moving to a startup in the next couple of weeks. I've had lots of fun with IMP and will miss it a lot and hope it continues to thrive. If people have particular things that they would like me to do before I go (e.g. areas to add to https://github.com/salilab/imp/wiki/Internals), please let me know. Not that I won't have email later on too :-) --Daniel

2 2

Recently in IMP
by Daniel Russel 16 Feb '14

16 Feb '14

There have been a couple of problematic bugs that have been fixed recently in close pairs/excluded volume code. One was a bug that caused the close pairs list to be built too often for a good part of January. The other was a longer standing bug with close pairs lists not being updated properly with rigid bodies under certain cases, which I don't entirely understand exactly. - A module IMP.module_template was added to act as a template for creating new external modules. It includes setting up git hooks for format checks and things like that. You can clone it and then check out your clone to quickly get started with your own module. - The python support for grids was cleaned up. Hopefully this makes it more robust. If you were using a grid in python that no longer exists, ping us, we can add it back. - The generic geometry functions were simplified slightly and renamed to IMP::algebra::get_vector_geometry(). - The IMP::base::Flag class was added to simplify adding flags in C++. - The `--log_level` and `--check_level` command line argument now take strings (eg VERBOSE) to specify their values, rather than cryptic (and a bit unstable) numbers. - Command line options are now divided into normal and advanced ones. You do `--help_advanced` to show the advanced ones. - Support for computing Connolly surfaces was added with IMP::algebra::get_connolly_surface(). In addition, there is now IMP::algebra::get_uniform_surface_cover(const IMP::algebra::Sphere3Ds&,double) to sample the surface of a collection of balls. - IMP::atom:: create_simplified_from_volume() was added to create a simplified representation of a hierarchy that preserves the surface are and occupied volume. It uses IMP::algebra::get_simplified_from_volume(). If you want to play with such representations, you can use the rmf_simply application. - IMP::atom::get_rmsd(IMP::atom::Selection, IMP::atom::Selection, const IMP::algebra::Transformation3D&) was deprecated. Use IMP::atom::get_rmsd_transforming_first() instead. - IMP::algebra::get_rmsd() and IMP::algebra::get_rmsd_transforming_first() were added. - The family of macros IMP_BASE_[SMALL,LARGE]_[UNORDERED,ORDERED]_[MAP,SET] have been added (eg IMP_BASE_SMALL_ORDERED_SET ()). They provide platform and boost-version independent ways to take advantage of the best set/map for an application. In particular, they use boost::container::flat_set and kin when available. - IMP::atom::State and IMP::atom::Representation decorators have been added to provide support for multiple states and multiple representation schemes. They are integrated with RMFs and IMP::atom::Selection. See atom/multiresolution.py and atom/multistate.py for examples. - The container imlementations has been cleaned up and simplified a bit. This should not change most usage. - [RMF](http://salilab.github.io/rmf) has been updated. There are a few minor API changes, in addition to a new, faster format (`.rmf3`). - [Eigen](#Eigen) is now included with IMP. - The deprecated function IMP::kernel::Optimizer::set_restraints() was removed. Use IMP::kernel::Optimizer::set_scoring_function() instead. - The deprecated constructor for IMP::kernel::ModelObject that does not take an IMP::kernel::Model was removed. This propagates to constructors IMP::kernel::Restraint, IMP::kernel::ScoreState and kin. Make sure you pass an IMP::kernel::Model as the first constructor argument. Related to this, deprecated functions like get_is_part_of_model(), set_model() were removed as they don't serve any purpose. - The deprecated methods in IMP::kernel::Optimizer that pertain to attribute optimization were removed. Inherit from IMP::kernel::AttributeOptimizer instead if you want to use them in your optimizer. - Some deprecated functionality was removed. If you encounter problems, replace IMP::base::OwnerPointer with IMP::base::PointerMember, find logging stuff in IMP/base/log.h, object in IMP/base/Object.h and random in IMP/base/random.h. - IMP::atom::Chain now uses strings for the chain ids, to be consistent with changes in the PDB. PDB files are written using the first character of the chain string. - Added orientation-dependent SOAP scoring (IMP::score_functor::OrientedSoap and IMP::atom::OrientedSoapPairScore). Orientation-dependent SOAP scores include those that score loops (SOAP-Loop), protein-peptide interfaces (SOAP-Peptide) and proteins (SOAP-Protein). The library files themselves are rather large (~1.5GB) and so are not included with IMP. They can be downloaded separately from http://salilab.org/SOAP/.

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Recently in IMP
by Daniel Russel 21 Jan '14

21 Jan '14

Since we haven't had such emails in a while: - The IMP::base::Flag class was added to simplify adding flags in C++. - The `--log_level` and `--check_level` command line argument now take strings (eg VERBOSE) to specify their values, rather than cryptic (and a bit unstable) numbers. - Command line options are now divided into normal and advanced ones. You do `--help_advanced` to show the advanced ones. - Support for computing Connolly surfaces was added with IMP::algebra::get_connolly_surface(). In addition, there is now IMP::algebra::get_uniform_surface_cover(const IMP::algebra::Sphere3Ds&,double) to sample the surface of a collection of balls. - IMP::atom:: create_simplified_from_volume() was added to create a simplified representation of a hierarchy that preserves the surface are and occupied volume. It uses IMP::algebra::get_simplified_from_volume(). If you want to play with such representations, you can use the rmf_simply application. - IMP::atom::get_rmsd(IMP::atom::Selection, IMP::atom::Selection, const IMP::algebra::Transformation3D&) was deprecated. Use IMP::atom::get_rmsd_transforming_first() instead. - IMP::algebra::get_rmsd() and IMP::algebra::get_rmsd_transforming_first() were added. - The family of macros IMP_BASE_[SMALL,LARGE]_[UNORDERED,ORDERED]_[MAP,SET] have been added (eg IMP_BASE_SMALL_ORDERED_SET ()). They provide platform and boost-version independent ways to take advantage of the best set/map for an application. In particular, they use boost::container::flat_set and kin when available. - IMP::atom::State and IMP::atom::Representation decorators have been added to provide support for multiple states and multiple representation schemes. They are integrated with RMFs and IMP::atom::Selection. See atom/multiresolution.py and atom/multistate.py for examples. - The container imlementations has been cleaned up and simplified a bit. This should not change most usage. - [RMF](http://salilab.github.io/rmf) has been updated. There are a few minor API changes, in addition to a new, faster format (`.rmf3`). - [Eigen](#Eigen) is now included with IMP. - The deprecated function IMP::kernel::Optimizer::set_restraints() was removed. Use IMP::kernel::Optimizer::set_scoring_function() instead. - The deprecated constructor for IMP::kernel::ModelObject that does not take an IMP::kernel::Model was removed. This propagates to constructors IMP::kernel::Restraint, IMP::kernel::ScoreState and kin. Make sure you pass an IMP::kernel::Model as the first constructor argument. Related to this, deprecated functions like get_is_part_of_model(), set_model() were removed as they don't serve any purpose. - The deprecated methods in IMP::kernel::Optimizer that pertain to attribute optimization were removed. Inherit from IMP::kernel::AttributeOptimizer instead if you want to use them in your optimizer. - Some deprecated functionality was removed. If you encounter problems, replace IMP::base::OwnerPointer with IMP::base::PointerMember, find logging stuff in IMP/base/log.h, object in IMP/base/Object.h and random in IMP/base/random.h. - IMP::atom::Chain now uses strings for the chain ids, to be consistent with changes in the PDB. PDB files are written using the first character of the chain string. - Added orientation-dependent SOAP scoring (IMP::score_functor::OrientedSoap and IMP::atom::OrientedSoapPairScore). Orientation-dependent SOAP scores include those that score loops (SOAP-Loop), protein-peptide interfaces (SOAP-Peptide) and proteins (SOAP-Protein). The library files themselves are rather large (~1.5GB) and so are not included with IMP. They can be downloaded separately from http://salilab.org/SOAP/.

1 0

AngleRestraint
by Davide Baù 13 Jan '14

13 Jan '14

Hi, I'm having some (random) errors with the AngleRestraint function. I get a Segmentation fault (core dumped) error when applying an AngleRestraint restraint like: i = 0 while (i <= particles-3): p1 = ps.get_particle(i) p2 = ps.get_particle(i+2) p3 = ps.get_particle(i+3) ar = IMP.core.AngleRestraint(IMP.core.Harmonic(0, 1), p1, p2, p3) m.add_restraint(ar) i += 3 The error is not persistent, meaning that if I run the code severe times, the error disappear and the code ends normally. Is there any specify reason for such an error? Thanks! Davide

3 5

GPUs
by Barak Raveh 07 Jan '14

07 Jan '14

A bit of the work that was being done to tune AMBER for GPUs in collaboration with NVIDIA http://www.wmd-lab.org/, I head the performance is phenomenal even on a regular desktop machine. Perhaps we can draw some ideas and apply in IMP? There are now also designated GPU servers available from NVIDIA.

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