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Re: [IMP-dev] [IMP-commits] r2924 - in trunk/modules/em: . include pyext src test test/input
by Ben Webb 26 May '09

26 May '09

> Modified: trunk/modules/em/SConscript > =================================================================== > --- trunk/modules/em/SConscript 2009-05-26 21:43:25 UTC (rev 2923) > +++ trunk/modules/em/SConscript 2009-05-26 22:11:25 UTC (rev 2924) > @@ -6,8 +6,9 @@ > > env.validate() > > -env.Append(LIBS=['imp_core', 'imp_atom','imp_algebra']) > +env.Append(LIBS=['imp_core', 'imp_atom','imp_algebra','imp_display','imp_helper']) > > + Please don't make EM depend on all those other things (particularly helper)! It'll never compile, because we're going to end up with circular dependencies. 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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Rigid body - set transformation
by Keren Lasker 25 May '09

25 May '09

Is the transformation given in set_transformation relative to a global internal coordinate system or to the rigid body internal coordinate system ? If the answer is that it is relative to the rigid body internal coordinate system -how can you move the rigid body to a specific position in space ? Thank you ! Keren.

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IMP's first application
by Daniel Russel 25 May '09

25 May '09

Since Keren is too shy to ask, where it should go, I will. I propose an "applications" directory which than would have a dir per app. Then data and example scripts can go with it. Alternatives?

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fleshing out atom.Hierarchy
by Daniel Russel 25 May '09

25 May '09

I suggest that we impose that in an atom.Hierarchy - if any of the hierarchy has coordinates, all the leaves do (they can be at any level of the hierarchy though) - all residues in each molecule must be either a) explicitly represented as a Residue, b) part of a Domain which is a leaf (which would be expanded to allow non-contiguous sets of residues--or we could split off a new type of decorator for this) - any member of the hierarchy other than an Atom which has coordinates also has a radius. The interpretation is that this radius bounds where members of the (possibly elided) subtree can be. These would ensure several useful properties: 1) it be clear what the highest resolution representation of any hierarchy is 2) one be able to find out where in the hierarchy any residue is located 3) code does not need to look at the most detailed representation to get a rough picture of the structure, it only has to search down the tree (I'm from CS) to find a representation with small enough balls. Comments?

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This week in IMP
by Daniel Russel 21 May '09

21 May '09

- The IMP::helper<file:///flute1/home/drussel/src/IMP/npc/doc/html/namespaceIMP_1_1helper.html>module was added and various functionality moved there. See its documentation page for a list of what is there. - IMP::algebra::SphericalCoords was renamed to IMP::algebra::SphericalVector3D<file:///flute1/home/drussel/src/IMP/npc/doc/html/classIMP_1_1algebra_1_1SphericalVector3D.html>to be consistent with other algebra classes. - IMP::algebra::Rotation2D<file:///flute1/home/drussel/src/IMP/npc/doc/html/classIMP_1_1algebra_1_1Rotation2D.html>is now IMP::InvalidDefault to be consistent with the other similar classes. - We are trying to be a bit more specific about what is expected from a IMP::atom::Hierachy. Towards that end, there are two tentive methods for extracting a representation from a hierarchy, IMP::atom::get_detailed_representation()<file:///flute1/home/drussel/src/IMP/npc/doc/html/namespaceIMP_1_1helper.html#6ebb80f0a1ed2dde6358aa3c883a9560>, and IMP::atom::get_simplified_representation(). <file:///flute1/home/drussel/src/IMP/npc/doc/html/namespaceIMP_1_1helper.html#4dd4545819a876aae5e790d70c22a6bd> - A method has been added to produce a simplified copy of an IMP::atom::Hierarchy<file:///flute1/home/drussel/src/IMP/npc/doc/html/classIMP_1_1atom_1_1Hierarchy.html>. The method is still a bit crude and could benefit from other people inspecting the output and saying how it should be improved. - There is now an IMP::algebra::BoundingBoxD<file:///flute1/home/drussel/src/IMP/npc/doc/html/classIMP_1_1algebra_1_1BoundingBoxD.html>to track bounding box. There will be methods like IMP::algebra::bound_box(Sphere3D) which get the bounding box. - Each IMP::Object<file:///flute1/home/drussel/src/IMP/npc/doc/html/classIMP_1_1Object.html>has its own log level. If IMP::Object::set_log_level()<file:///flute1/home/drussel/src/IMP/npc/doc/html/classIMP_1_1Object.html#0d3a43f589e45a6b4a61115b127ec054>is called with a value other than IMP::DEFAULT, the value is used for code within and called by the object. To support this in your objects you need to add IMP_OBJECT_LOG to the start of each major method. It has been added to some of the core objects.

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Different layers of functionality in IMP
by Daniel Russel 20 May '09

20 May '09

We now have several different layers of functionality in IMP, which are kind of jumbled together in core. For example, with rigid bodies, you can create one by - decorating a particles - creating a couple of score states from relatively general purpose singleton modifiers and container based score states - adding them to the model or - use a create_rigid_body function to do it all for you Having all of these together clutters the documentation and makes it harder to find out what you should be doing. That said, we need at least some of the detail bit available to users, so we can't really hide them away as internal. One option would be to pull these into their own module (I can't think of the right name offhand, perhaps helpers), and reserve core for very general purpose things like PairsRestraint. Not sure what other options are.

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This week in IMP
by Daniel Russel 15 May '09

15 May '09

First, can everyone please clean up the warnings in your code and docs (do "scons doc > "dev/null"). There are currently quite a few and it is annoying to have to wade through all of them every time I compile to figure out if each is important or not (at least one of the current warnings is pointing out that the wrong function will be called in certain circumstances). Remember, the only reason that warnings are not counting as errors (that break compilation) is that there were a couple of warnings in boost headers and gcc doesn't offer fine grained control. Lots of (mosty cosmetic) changes and added functionality. - IMP::atom::MolecularHierarchy has been renamed to IMP::atom::Hierarchy<file:///flute1/home/drussel/src/IMP/realsvn/doc/html/classIMP_1_1atom_1_1Hierarchy.html>. Use sed -i.old "s#MolecularHierarchy#Hierarchy#g" my_files - the long-deprecated Name(Decorator) was removed - The decorator suffix has been removed from decorator names. To update your code do sed -i.old "s#\([a-zA-Z]\)Decorator#\1#g" **/*.h **/*.cpp **/*.py **/*.i or sed -i.old "s#\([a-zA-Z]\)Decorator#\1#g" `find * -name \*.h -or -name \*.cpp` (and the various suffixes). - Unit conventions have been established and documented for distance, energy, force and angle. - there is a function IMP::atom::create_protein()<file:///flute1/home/drussel/src/IMP/realsvn/doc/html/group__unstable.html#gb0c6db2fc2ced9b37dca1587fe310412>to create a coarse grained protein. The function is crude so far, but the idea is that we should have standard ways of generating such things so that everyone can benifit from best practices. - a class IMP::atom::BondGraph<file:///flute1/home/drussel/src/IMP/realsvn/doc/html/classIMP_1_1atom_1_1BondGraph.html>has been added so Boost.Graph algorithms can be used with bond graphs - the IMP-specific doxygen commands have been documented. There is a link from the developers guide page. - the doxygen commands \unstable{name}, \untested{name}, \unimplemented{name} have been added to doxygen to be used for marking methods and functions as likely to change or not well tested or not yet implemented. Pass the name of the class or method as name. - bonds can now be added to molecular hierarchies automatically see IMP::atom::add_bonds()<file:///flute1/home/drussel/src/IMP/realsvn/doc/html/namespaceIMP_1_1atom.html#69dcb8361d5bb4b68f641a6367e95743>

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Shortening names
by Daniel Russel 15 May '09

15 May '09

The names of some of the decorators (eg IMP.atom.MolecularHierarchyDecorator) are rather annoyingly long. For example mh= IMP.atom.MolecularHierarchyDecorator.create(p, IMP.atom.MolecularHierarchyDecorator.PROTEIN) One uniform way of shortening them would be to just drop the decorator bit. On the documentation side, it works since I had already established the shorthand of saying XYZ particle instead of XYZDecorator instance particle. Such a change would just require running a sed script on people's code, so the cost of the update would be small. Thoughts? The new names would include: XYZ XYZR Residue Atom MolecularHierarchy: still kind of long, since it is now in atom we could drop the Molecular part and just make it IMP.atom.Hierarchy, but this causes problems if you do using or import on IMP.atom and IMP.core (as I tend to do) RigidBody Thoughts, comments?

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measurement units in IMP
by Daniel Russel 14 May '09

14 May '09

Should we establish an explicit rule in IMP that all distances are in angstroms? The range of scales is small enough that we don't have accuracy issues for doing this. In addition, we then don't have to worry about some things being in nanometers (since we have no way of tagging things with units). Ben already established a convention of having units if kCal/MolAngstrom for derivative quantities. So angstroms fits with that.

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Compiling error on Mac only?
by Seung Joong Kim 13 May '09

13 May '09

Today I updated IMP with the latest revision 2830, and I am having a compiling error on Mac only. It seems that there is a problem with the boost binding (I have installed boost version 1.38 by using Macport) Currently I don't have any problem with my linux machine. It happens only in my Mac.. Could you anyone figure out what was wrong? Thanks! - SJ g++ -o modules/atom/src/bond_graph.os -c -Woverloaded-virtual -Wall -O3 -fvisibility=hidden -fPIC -DNDEBUG -DIMP_LITTLE_ENDIAN -DIMPATOM_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/opt/local/include modules/atom/src/bond_graph.cpp build/include/IMP/internal/NestedIterator.h: In member function 'const IMP::internal::NestedIterator<T>& IMP::internal::NestedIterator<T>::operator++() [with T = IMP::atom::BondGraph::NestedTraits]': /opt/local/include/boost/concept_check.hpp:473: instantiated from 'boost::InputIterator<TT>::~InputIterator() [with TT = IMP::internal::NestedIterator<IMP::atom::BondGraph::NestedTraits>]' /opt/local/include/boost/concept/detail/general.hpp:29: instantiated from 'static void boost::concept::requirement<Model>::failed() [with Model = boost::InputIterator<IMP::internal::NestedIterator<IMP::atom::BondGraph::NestedTraits> >]' /opt/local/include/boost/graph/graph_concepts.hpp:47: instantiated from 'boost::concepts::MultiPassInputIterator<T>::~MultiPassInputIterator() [with T = IMP::internal::NestedIterator<IMP::atom::BondGraph::NestedTraits>]' /opt/local/include/boost/concept/detail/general.hpp:29: instantiated from 'static void boost::concept::requirement<Model>::failed() [with Model = boost::concepts::MultiPassInputIterator<IMP::internal::NestedIterator<IMP::atom::BondGraph::NestedTraits> >]' /opt/local/include/boost/graph/graph_concepts.hpp:219: instantiated from 'boost::concepts::EdgeListGraph<G>::~EdgeListGraph() [with G = IMP::atom::BondGraph]' /opt/local/include/boost/graph/graph_concepts.hpp:209: instantiated from 'static void boost::concept::requirement<Model>::failed() [with Model = boost::concepts::EdgeListGraphConcept<IMP::atom::BondGraph>]' /opt/local/include/boost/concept_check.hpp:43: instantiated from 'void boost::function_requires(Model*) [with Model = boost::concepts::EdgeListGraphConcept<IMP::atom::BondGraph>]' modules/atom/src/bond_graph.cpp:60: instantiated from here build/include/IMP/internal/NestedIterator.h:41: error: 'CGAL_assertion' was not declared in this scope /opt/local/include/boost/concept_check.hpp: In destructor 'boost::SignedInteger<T>::~SignedInteger() [with T = unsigned int]': /opt/local/include/boost/concept/detail/general.hpp:29: instantiated from 'static void boost::concept::requirement<Model>::failed() [with Model = boost::SignedInteger<unsigned int>]' /opt/local/include/boost/concept_check.hpp:468: instantiated from 'boost::InputIterator<TT>::~InputIterator() [with TT = IMP::internal::IndexingIterator<IMP::atom::BondedDecorator::GetBonded>]' /opt/local/include/boost/concept/detail/general.hpp:29: instantiated from 'static void boost::concept::requirement<Model>::failed() [with Model = boost::InputIterator<IMP::internal::IndexingIterator<IMP::atom::BondedDecorator::GetBonded> >]' /opt/local/include/boost/graph/graph_concepts.hpp:47: instantiated from 'boost::concepts::MultiPassInputIterator<T>::~MultiPassInputIterator() [with T = IMP::internal::IndexingIterator<IMP::atom::BondedDecorator::GetBonded>]' /opt/local/include/boost/concept/detail/general.hpp:29: instantiated from 'static void boost::concept::requirement<Model>::failed() [with Model = boost::concepts::MultiPassInputIterator<IMP::internal::IndexingIterator<IMP::atom::BondedDecorator::GetBonded> >]' /opt/local/include/boost/graph/graph_concepts.hpp:148: instantiated from 'boost::concepts::AdjacencyGraph<G>::~AdjacencyGraph() [with G = IMP::atom::BondGraph]' /opt/local/include/boost/graph/graph_concepts.hpp:139: instantiated from 'static void boost::concept::requirement<Model>::failed() [with Model = boost::concepts::AdjacencyGraphConcept<IMP::atom::BondGraph>]' /opt/local/include/boost/concept_check.hpp:43: instantiated from 'void boost::function_requires(Model*) [with Model = boost::concepts::AdjacencyGraphConcept<IMP::atom::BondGraph>]' modules/atom/src/bond_graph.cpp:59: instantiated from here /opt/local/include/boost/concept_check.hpp:91: error: request for member 'error_type_must_be_a_signed_integer_type' in '((boost::SignedInteger<unsigned int>*)this)->boost::SignedInteger<unsigned int>::x', which is of non-class type 'unsigned int' /opt/local/include/boost/concept_check.hpp: In destructor 'boost::SignedInteger<T>::~SignedInteger() [with T = long unsigned int]': /opt/local/include/boost/concept/detail/general.hpp:29: instantiated from 'static void boost::concept::requirement<Model>::failed() [with Model = boost::SignedInteger<long unsigned int>]' /opt/local/include/boost/concept_check.hpp:468: instantiated from 'boost::InputIterator<TT>::~InputIterator() [with TT = IMP::internal::NestedIterator<IMP::atom::BondGraph::NestedTraits>]' /opt/local/include/boost/concept/detail/general.hpp:29: instantiated from 'static void boost::concept::requirement<Model>::failed() [with Model = boost::InputIterator<IMP::internal::NestedIterator<IMP::atom::BondGraph::NestedTraits> >]' /opt/local/include/boost/graph/graph_concepts.hpp:47: instantiated from 'boost::concepts::MultiPassInputIterator<T>::~MultiPassInputIterator() [with T = IMP::internal::NestedIterator<IMP::atom::BondGraph::NestedTraits>]' /opt/local/include/boost/concept/detail/general.hpp:29: instantiated from 'static void boost::concept::requirement<Model>::failed() [with Model = boost::concepts::MultiPassInputIterator<IMP::internal::NestedIterator<IMP::atom::BondGraph::NestedTraits> >]' /opt/local/include/boost/graph/graph_concepts.hpp:219: instantiated from 'boost::concepts::EdgeListGraph<G>::~EdgeListGraph() [with G = IMP::atom::BondGraph]' /opt/local/include/boost/graph/graph_concepts.hpp:209: instantiated from 'static void boost::concept::requirement<Model>::failed() [with Model = boost::concepts::EdgeListGraphConcept<IMP::atom::BondGraph>]' /opt/local/include/boost/concept_check.hpp:43: instantiated from 'void boost::function_requires(Model*) [with Model = boost::concepts::EdgeListGraphConcept<IMP::atom::BondGraph>]' modules/atom/src/bond_graph.cpp:60: instantiated from here /opt/local/include/boost/concept_check.hpp:91: error: request for member 'error_type_must_be_a_signed_integer_type' in '((boost::SignedInteger<long unsigned int>*)this)->boost::SignedInteger<long unsigned int>::x', which is of non-class type 'long unsigned int' scons: *** [modules/atom/src/bond_graph.os] Error 1 scons: building terminated because of errors. -- Seung Joong Kim, Ph.D. Postdoctoral Scholar, Andrej Sali group Department of Biopharmaceutical Sciences, School of Pharmacy University of California at San Francisco (UCSF)

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