IMP  2.4.0
The Integrative Modeling Platform
ChangeLog.md
1 ChangeLog {#changelog}
2 =========
3 
4 # 2.4.0 - 2015-02-27 # {#changelog_2_4_0}
5 - Python 3 is now supported.
6 - Command line tools are now placed in the `bin` directory of modules (the
7  old `bin` directory, used for utility programs that are not installed, is
8  now called `utility`). The `applications` directory is removed.
9 - Several Python modules that were only used by EMageFit have been moved from
10  IMP::em2d to IMP::EMageFit.
11 - A new tutorial that uses the IMP::pmi module is now available (modeling of
12  the RNA Polymerase II stalk).
13 
14 # 2.3.1 - 2014-12-01 # {#changelog_2_3_1}
15 - Minor bug fixes.
16 - Update to IMP::pmi to support the Nup84 and rnapolii biological systems.
17 
18 # 2.3.0 - 2014-10-24 # {#changelog_2_3_0}
19 - A new IMP::pmi module was added, containing high-level Python classes to simplify the representation, scoring, sampling and analyzing of models in IMP. This module is still under heavy development, and should be considered experimental.
20 - Binary installers for 64-bit Windows are now available.
21 - The `.py` extension has been removed from all Python applications, so that they are consistent with the C++ applications.
22 - IMP::atom::Selection objects can now be combined using basic set operations (union, intersection, difference, symmetric difference). In Python the equivalent operators (|, &, -, ^ respectively) can be used.
23 - The integrative docking (idock) application now employs SOAP to improve the scoring.
24 - IMP::atom::CHARMMParameters::create_topology() now works with a wider range of hierarchies (previously it would only accept Residues that were direct children of Chains). For example, it should do the right thing when given a Hierarchy that contains no Chain particles, or one where Residues are grouped under Fragments.
25 - Only Python 2.6 or later is now supported. We still provide IMP for RedHat Enterprise 5 (which ships with Python 2.4) but you will need to use the `python26` binary (part of EPEL) rather than the system default Python.
26 
27 # 2.2.1 - 2014-08-11 # {#changelog_2_2_1}
28 - Bugfix: PoseScore (see the ligand_score application) should now match that used by the Pose&Rank web server (http://salilab.org/poseandrank/)
29 
30 # 2.2.0 - 2014-04-09 # {#changelog_2_2_0}
31 - A module IMP.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.
32 - 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.
33 - The generic geometry functions were simplified slightly and renamed to IMP::algebra::get_vector_geometry().
34 - The IMP::base::Flag class was added to simplify adding flags in C++.
35 - 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.
36 - Command line options are now divided into normal and advanced ones. You do `--help_advanced` to show the advanced ones.
37 - 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.
38 - IMP::atom::reate_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.
39 - IMP::atom::get_rmsd(IMP::atom::Selection, IMP::atom::Selection, const IMP::algebra::Transformation3D&) was deprecated. Use IMP::atom::get_rmsd_transforming_first() instead.
40 - IMP::algebra::get_rmsd() and IMP::algebra::get_rmsd_transforming_first() were added.
41 - 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.
42 - 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.
43 - The container implementations has been cleaned up and simplified a bit. This should not change most usage.
44 - [RMF](http://salilab.github.io/rmf) has been updated. There are a few minor API changes, in addition to a new, faster format (`.rmf3`).
45 - [Eigen](#Eigen) is now included with IMP.
46 - The deprecated function IMP::kernel::Optimizer::set_restraints() was removed. Use IMP::kernel::Optimizer::set_scoring_function() instead.
47 - 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.
48 - 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.
49 - 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.
50 - 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.
51 - 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/.
52 
53 # 2.1.1 - 2013-11-04 # {#changelog_2_1_1}
54 - Added support for Mac OS 10.9
55 
56 # 2.1.0 - 2013-10-24 # {#changelog_2_1_0}
57 - There is now some limited IMP-wide gathering of timing statistics. You can add `--statistics=filename` to the command line or use the IMP::base::show_timings() function to view a summary of where IMP has spent time.
58 - Slack was being used inconsistently (and not always correctly) among the various containers and restraints. If you had heavily optimized the slack value for speed, you may want to revisit it.
59 - Class name OwnerPointer was switched to PointerMember, to denote more clearly a ref-counting pointer that is a class member.
60 - The dependency handling in IMP has been rewritten to simplify it and fix a bunch of bugs. There are now more checks of correctness, so behavior that might have silently worked (or not worked) before may now trigger errors. In particular, restraints/score states must have access to the IMP::kernel::Model to do much of anything, so either use constructors that take the model or call IMP::kernel::ModelObject::set_model(). Also, changing your set of inputs or outputs without calling IMP::kernel::ModelObject::set_has_dependencies(false) is now likely to trigger a check failure (it would just silently do the wrong thing before).
61 - Decorators have been cleaned up to make them behave consistently regarding IMP::kernel::Particle vs IMP::kernel::ParticleIndexes. This change shouldn't break existing code, but decorators should move to the new macros IMP_DECORATOR_METHODS(), IMP_DECORATOR_SETUP_0() etc.
62 - The IMP_GRAPH() and IMP_WEIGHTED_GRAPH() macros got an extra argument describing how to show the vertexes in the graph. They also now expose a method, eg IMP::kernel::show_as_graphviz() that writes the graph in graphviz format to an IMP::base::TextOutput.
63 - Support and rules for deprecating code in IMP have been updated. There are new macros and instructions on how to use them that should result in much better visibility about changes. See the C++ wiki for IMP for more information. And there is now an encoded policy of keeping deprecated things around for 1 release after deprecation.
64 - IMP is now much more selective about when it invalidates the dependency graph. See [Dependencies](http://github.com/salilab/imp/wiki/Dependencies) for more information. This change should make evaluation of isolated restraints much faster in certain situations where they were unexpectedly slow before.
65 - IMP::atom::Selection has been completely rewritten as it was very brittle. The set of particles returned may change in some cases, in some cases because it was buggy before, in some cases because of new bugs.
66 - Reminder: the IMP_PROTECTED macros didn't work out well, and are now deprecated. If you had Python implementations on top of IMP base classes that implement protected virtual methods, you may need to remove a leading `_` on the method name, if you get `Swig director pure virtual method called IMP::kernel::PairScore::do_get_inputs` messages.
67 - The generated `cmake` files are no longer stored in the repository. Instead `tools/build/setup_cmake.py` is run after checkouts and other git events that change the repository tree (assuming you have run `setup_git.py`).
68 - Generation of documentation using `doxygen` has been refactored. It is now done on a per-module basis, via targets like `IMP.core-doc`. The main advantage is that changes to the doc for a module can be tested comparatively quickly, just by building that module's docs. On the down side, docs are no longer quite so heavily interconnected, so dependencies only work to things that the module actually depends on.
69 - The restraint and score state statistics functions were removed from IMP::Model. They had been broken for quite a while, with no one complaining. Statistics can be added back easily if requested.
70 - Added an IMP-specific fork of `git-flow`. It handles things like `README.md` files when you start and finish feature branches and provides a tool to nicely update IMP and display the change log. The main commands of use are `git imp feature start <feature_name>`, `git imp feature finish <feature_name>`, and `git imp update`. You may want to remove the `git-flow` lines from your `.git/config` file as you may accidentally type `git flow` instead of `git imp`. You need to run `setup_git.py` to set things up.
71 - [RMF](http://salilab.github.com/rmf) is now included as a git submodule rather than copied into the IMP repository. You should rerun `setup_git.py` to make sure submodule stuff is initialized.
72 
73 
74 # For IMP 2.0 and earlier # {#changelog_2_0}
75 ## Spring 2013
76 - Modules and applications now have a _Maintainer_ in their `README.md`, giving the github id of the person to whom issues should be assigned.
77 - `setup_git.py` supports the `--module` flag which will set up git hooks and things for a git repository that contains a module.
78 - To clean up for the release, the module dependencies are now described in a file called `dependencies.py` and the module docs in a `README.md`, both in the main module directory.
79 - IMP-wide support for progress bars was added with the IMP::base::set_progress_display() function and helpers. These are only displayed when the IMP::base::get_log_level() is IMP::base::PROGRESS.
80 
81 ## Winter 2012-2013
82 - Scons support was removed. Use cmake to build IMP, it is way better.
83 - Examples are run with a `--test` argument when IMP is built with internal checks. Expensive examples should check this flag and shorten what they do in order to try to test all their code without taking too long.
84 - The class IMP::core::NonRigidMember was added to allow particles that are not rigid but whose coordinates are specified via internal coordinates in some IMP::algebra::Reference3D that is part of an IMP::core::RigidBody.
85 - The IMP_BIG_ENDIAN and IMP_LITTLE_ENDIAN preprocessor symbols are deprecated in favor of the BOOST_BIG_ENDIAN and BOOST_LITTLE_ENDIAN symbols.
86 - Support for asymmetric moves was added to IMP::core::MonteCarlo. To do this, IMP::core::MonteCarloMover was added and IMP::core::Mover and IMP::core::MoverBase were deprecated and implemented in terms of the new class. This should require few or no changes in code that uses Monte Carlo support or implements movers (although movers should move to IMP::core::MonteCarlo). All IMP::core::MonteCarloMover objects keep track of statistics (number of moves and number of accepted moves), rather than that being done in the IMP::core::SerialMover. In addition, the poorly defined move probability was removed from IMP::core::MonteCarlo.
87 - IMP::base::WarningContext now outputs warnings immediately. This change was needed as the previous behavior resulted in occasional core dumps when the libraries for log support were unloaded before the libraries where static IMP::base::WarningContexts were declared. And there was no easy way to detect such problems.
88 - You can now (probably) build IMP with [CMake on IMP wiki](https://github.com/salilab/imp/wiki/Cmake).
89 - The maximum logging level and check level can now be controlled independently of the build mode. To, for example, enable progress level logging in a fast build, add maxlog="PROGRESS" to your config. The maximum check level for `release` has been reduced to IMP::USAGE as that speeds things up a bit.
90 - The way applications are structured and specified has been regularized and simplified. Python files are automatically copied/installed and binary executables are compiled from each found `.cpp` file linked with any `.cpp` files contained in a subdirectory called `lib`. Nothing needs to be put into the SConscript file.
91 - The Python constants like IMP.algebra.has_cgal went away as swig autogenerates ones like IMP.algebra.IMP_ALGEBRA_HAS_IMP_CGAL. While the latter are a bit uglier, the constants aren't used much and having them be auto generated is nice.
92 - There have been some major changes to the build system. The main one is that the SConscripts in the directories below the module directory aren't really used. They are being removed from the repository. Now everything really is off of file locations (eg all test_* in test is a test, each *.cpp in bin becomes a program etc). This greatly simplifies the build system, which has, historically been a disaster. You can now define dependencies by dropping files into a dependency subdirectory in your module, no need to mess with the SConscript.
93 - Building IMP now always requires specifying a `repository` argument. This was always required for out of source builds, which is what one should be doing, but is now required for in source builds to, so as to make accidentally polluting your source with an in-source build harder. Use `repository="."` in that case.
94 - The HDF5 functionality in RMF was reorganized. Specifically, the headers were moved into `RMF/HDF5`, the Python functionality into `RMF_HDF5` and the code into namespace `RMF::HDF5` and all mentions of `HDF5` or `hdf5` in the class and function names were removed.
95 - Support for IMP-wide command line flags have been added to IMP::base in the base/flags.h file. They provide a simple command line parsing interface that can be used from C++ and Python. In addition, various functionality in IMP is automatically exposed on the command line when those functions are used. For example, one can control logging, checks or profiling. See IMP/base/flags.h for (some) more info.
96 - OpenMP support in IMP is officially released. All tests pass. But there has been little specific testing so far.
97 - Access to attributes using IMP::ParticleIndex and the IMP::Model now works from Python. See IMP::Model::add_attribute() and kin.
98 - IMP::ParticleKey and IMP::ParticlesKey were renamed to IMP::ParticleIndexKey and IMP::ParticleIndexesKey respectively as that is what they store. Typedefs were provided to support old code.
99 - Indexes have been added to the docs connecting classes with all the methods that return them, examples that use them and methods that take them. And all methods that are used in examples with the examples they are used in. Please check them out and report issues and ways to improve things. You can find links on the main page.
100 - The docs for a modules/biological systems/applications should now be found in an `overview.dox` in the module `doc` folder. Modules in IMP svn have been updated. For external modules, you can just move a `overview.dox` from that was previously generated into your `doc` folder and (eventually) remove the lines from your `doc/SConscript`. This makes it easier to use the full range of doxygen markup, as well as removes the need to escape doxygen markup for Python.
101 - Examples have now been simplified into full blown doxygen examples. This involves merging the `.py` and `.readme` files (putting `\#\#` in front of each line of the `.readme`) and adding a `## \\example module/examplename.py` line at the begginning. You can use `./tools/updaters/update_examples.py modules/mymodule` to update a module that was not already updated.
102 - IMP::base::FailureHandler has been removed as it wasn't used.
103 - Handling of data and includes has been simplified. All appropriate files in the corresponding directories are linked into build/installed. This is only likely to be a problem if you had broken headers sitting around `include`. If so, just comment them out, or move them some place nicer.
104 - Modules now must be in a folder called `modules`, which must have an `description.py` file.
105 - The build system should now be a little better about cleaning up after itself.
106 - How headers/doc files/data/examples
107 - The IMP_PROTECTED macros didn't work out well, and are now deprecated. Sorry. If you had Python implementations on top of IMP base classes that implement protected virtual methods, you may need to remove a leading "_" on the method name.
108 - Nice version numbers will now be generated if you use git. You need to rerun
109 tools/git/developer_tools/init_git if you have an existing clone.
110 
111 ## Fall 2012
112 - 11/9: RMF is now an external library shipped with IMP. IMP will build it and install it automatically if you have cmake version 2.8 or higher installed.
113 - 11/9: Updated support macros for IMP::Restraint and IMP::ScoreState classes have been added (IMP_RESTRAINT_2() and IMP_SCORE_STATE_2()) that make it easier to return dependencies on things other than IMP::Particle and IMP::ScoreState objects. In addition, the dependency functions on scores and modifiers have been updated similarly and standardized. In general this should not cause backward compatibility problems unless you were overriding the IMP::ModelObject::do_get_inputs() in IMP::Restraint and using the IMP_RESTRAINT() macro. In that case update to the IMP_RESTRAINT_2() macro.
114 - 11/8: Support has been added for the C++11 keywords override (IMP_OVERRIDE) and final (IMP_FINAL). They allow you to tell the compiler to produce an error if the marked method does not override/implement a parent's method and if anything overrides a given method, respectively.
115 - 11/8: IMP::SingletonModifier::apply_indexes() and IMP::SingletonScore::evaluate_indexes() now require an upper and lower bound index (you can just pass 0 and the size of the array). We can make them option if there is a good reason.
116 - 11/8: IMP::SingletonDerivativeModifier and kin were merged into IMP::SingletonModifier and kin as the only difference, the presence of the IMP::DerivativeAccumulator (whose weight was always 1) wasn't very interested and the split added lots of complexity. If this has an impact on your code, let us know.
117 - 11/8; Evaluation with containers was greatly simplified, moving many methods on containers. We can add backwards compatibility versions if that is interesting.
118 - 11/7: Predicates, scores and modifiers written in Python need to update their methods for returning inputs and outputs. They should now have a method \c _do_get_outputs(self, m, particle_indexes) which should probably just return \c [m.get_particle(i) for in in particle_indexes] to return all the passed particles.
119 - 11/7: It is now preferred that IMP::Restraint and IMP::ScoreState descendents report dependencies directly using IMP::ModelObject::do_get_inputs() and IMP::ModelObject::do_get_outputs(). To do this, you should use the IMP_RESTRAINT_2() and IMP_CONSTRAINT_2() macros instead. Methods like IMP::Restraint::get_input_particles() are now deprectated. This change was made as the old mechanism introduced a lot of extra complication and made it so that there was no way to directly depend on something that was not a Particle or a Container.
120 - 11/3: IMP::container::InContainerPairFilter and friends now treat pairs as unordered. A flag was added to control this.
121 - 9/5: IMP::base::Object classes now have a method IMP::base::Object::clear_caches() that clears all cache data in the object. This is not universally implemented, but now provides a correct path for doing that. The IMP_LIST() type macros call that method when their contents changes.
122 ## Summer 2012
123 - 7/3: IMP_PERIODIC_OPTIMIZER_STATE() was superceeded by the class IMP::core::PeriodicOptimizerState as it is rather cleaner than the macro.
124 - 7/2: in order to make various base classes in IMP more Python friendly, macros IMP_PROTECTED_METHOD(), IMP_PROTECTED_CONSTRUCTOR() were added that properly expose such methods to Python. The standards checks now complain if \c protected is used an a class in the API.
125 - 6/24: Executables from \c module/bin are now put in \b build/module_bin/module. This removes a recurring source of errors in the build script due to the origin and destination directory have the same name in scons.
126 - 6/24: Benchmarks are now put int \c module/benchmark and build to \c build/benchmark/module to remove a recurring source of errors.
127 - 6/18: The IMP::benchmark module supports the GPerfTools profilers when available. Benchmark executables (things in \c bin whose name starts with \c benchmark_) that use the IMP_BENCHMARK() macro have command line flags to turn on and cpu and memory profiling.
128 - 6/12: The naming rules for .i files that are in module \c pyext directories changed. They should now be \c IMP_modulename.name.i instead of \c IMP_modulename_name.i. This is to better support underscores in names.
129 ## Winter 2011/2012
130 - 20/4: A method, IMP::atom::read_pdb(IMP::base::TextInput, int, IMP::atom::Hierarchy), was added to load coordinates from a pdb file into an existing IMP::atom::Hierarchy.
131 - 4/4: the filter types were superceeded by the predicate types. You will only see a difference if you develop a filter class (eg IMP::PairFilter -derived class) or directly call methods on filters (specifically IMP::PairFilter::get_contains()).
132 - 29/3: IMP::Particle::get_has_model() has been changed to IMP::ModelObject::get_is_part_of_model() to be consistent with other classes.
133 - 28/3: IMP::core::Mover changed slightly, adding an extra method IMP::core::Mover::get_output_particles() and requiring the IMP::Model be passed to the constructor. All movers in IMP SVN were updated without any difficulty. This allows movers to use information contained in the dependency graph amongst particles so they can, for example, weight moves based on scores.
134 - 26/3: IMP::SingletonContainerInput etc were added. Methods that take these as their arguments can be passed either containers or lists of particles (or tuples), as convenient. All methods that take IMP::SingletonContainer objects should eventually move over to taking this (changing just requires changing the argument from a pointer to an Input).
135 - 22/3: Over the last week or so, which IMP headers include which other heads have been substantially simplified. This may result in compilation errors for code outside of \c svn that depended on IMP headers including other headers. In general, you want to explicitly include the header defining each thing you use.
136 - 15/3: The vector used throughout IMP is now exposed at IMP::base::Vector and what it does it documented.
137 - 10/3: IMP::domino::RestraintCache was introduced to provide a documented centeralized place to handle restraint evaluation and caching in DOMINO. In the switch various bugs involving maximum scores and IMP::RestraintSet objects were fixed.
138 - 10/3: Scoring functions in IMP are now implemented in IMP::ScoringFunction objects. All restraint evaluation is handled by them and they can cache various useful information to aid in accelerating restraint evaluation. Backward compatibility interfaces have mostly been provided, please complain if some important interface went away. This has greatly simplified the code as well as fixed various bugs in various types of restraint evaluation (particularly in the handling of maximum scores on IMP::Restraint and IMP::RestraintSet objects.
139 - 29/2: The macros IMP_NAMED_TUPLE_1(),IMP_NAMED_TUPLE_2(),IMP_NAMED_TUPLE_3() were added for easy generation of simply struct for use in passing and returning values. The generated structs support comparison, output, hashing and have constructors. Use the macros instead of a boost::tuple or a a POD struct.
140 - 16/2: Restraints now are evaluated with the correct weights when evaluated by themselves as opposed to always returning their weight as seen by the model as a whole.
141 - 15/2: The IMP::algebra grid support was rearranged and simplified. Most of the changes should be transparent. However, the IMP::algebra::grids namespace got folded into IMP::algebra, which might break some code. And various (obscure) constructors of IMP::algebra::GridD were removed. All code in svn has been changed as needed.
142 - 3/2: The IMP::domino HDF5 container has been revamped. This involves splitting it into a write version (IMP::domino::WriteHDF5AssignmentContainer) and a read version (IMP::domino::ReadHDF5AssignmentContainer).
143 - 3/2: IMP::domino::WriteAssignmentContainer and IMP::domino::ReadAssignmentContainer were added to do direct binary file writing. This is faster than the HDF5 versions.
144 - 3/2: The installation instructions have been revamped and the developer instruction, in particular, have been greatly simplified.
145 - 24/1: \c tools/show-changes has been added that shows the changes in the history log since you last updated.
146 - 24/1: \c tools/make-source has been added that adds a source/header pair to a module
147 - 24/1: principal components analysis in IMP::algebra was generalized to work in any dimension. This required renaming the class to IMP::algebra::PrincipalComponentAnalysisD.
148 - 24/1: the output of the IMP::algebra::PrincipalComponentAnalysisD::show() was changed to reflect the standards (values produce compact, single line output on show). The old show has been moved to IMP::multifit
149 - 19/1: IMP::container::ConsecutivePairContainer had IMP::container::ExclusiveConsecutivePairContainer split off of it to make the two operating mode clearer and so that there could be a clear IMP::container::ExclusiveConsecutivePairFilter to use.
150 - IMP::algebra::Grid::apply was added to provide faster access to all (or, later, part of a grid). It can be an order of magnitude or more faster than using the iterators when doing simple operations.
151 - the scons config options \c pretty and \c color were added (defaulting to True). When they are true, build commands are mostly suppressed and a much briefer description of what is being done is printed out (in color). Note that \c color mode and compilation in emacs don't get along too well.
152 - IMP::algebra::ParabolicFit was renamed to IMP::algebra::ParabolicFit2D (a backwards compatibility typedef is currently provided)
153 - IMP::algebra::LinearFit was renamed to IMP::algebra::LinearFit2D. It now supports error bars on the y-values.
154 ## Fall 2011
155 - IMP::compatibility::checked_vector was renamed to IMP::compatibility::vector and made available to IMP as IMP::vector. Typedefs should use this type (IMP::vector).
156 - Various IMP::algebra plural typedefs which had been using std::vector (since they never were updated), have now been moved to IMP::vector.
157 - IMP::statistics::HistogramD now supports display with \c matplotlib.
158 - IMP::statistics::HistogramD superceeds IMP::statistics::Histogram
159 - predicate base classes have been added: IMP::SingletonPredicate, IMP::PairPredicate etc. These take particles and return an integer. Current functionality using them includes IMP::core::PredicateSingletonScore that uses a predicate to choose which score to apply.
160 - the core generic restraint and score state support was moved to the kernel to avoid breaking various scores outside of IMP svn.
161 - the IMP::display module was refactored and moved up to be a dependency of IMP::core and IMP::atom rather than vice versa. The main observable results are that you should now use IMP::atom::HierarchyGeometry, IMP::atom::SelectionGeometry, IMP::atom::HierarchiesGeometry, IMP::core::XYZRGeometry, IMP::atom::BondGeometry etc instead of finding them in IMP::display. This change means that, display can be used internally when testing and debugging functionality in IMP::core and IMP::atom and that tests that use IMP::display don't need to build all of IMP::atom.
162 - Decomposition of restraints now results in restraints that are faster to evaluate, using the generic restraint mechanism in IMP kernel.
163 - IMP::algebra::get_unit_bounding_box_d() was changed to return a bounding box with radius 1 to be consistent with IMP::algebra::get_unit_sphere_d()
164 - A general purpose scheme to associate data with tuples of hierarchy nodes was added to the RMF format. This deprecates the special purpose bond support.
165 - the way various types of geometry is stored in RMF files was changed, breaking backwards compatibility.
166 ## Summer 2011
167 - some functionality from the kernel has been spun off into a new module IMP.base. You probably won't notice anything. The only significant changes are that functions that accept or return IMP::base::TextInput and IMP::base::TextOutput must declare them with the \c base qualifier (eg base::TextInput) so that swig is happy.
168 - the source for the kernel has been moved from \c kernel to \c modules/kernel. This is unlikely to effect anyone.
169 - IMP::core::ExcludedVolumeRestraint now supports filters
170 - IMP::domino::HDF5AssignmentTable now caches internally, which makes it several times faster than before.
171 - you can now pick which Python to use with the \c python argument to scons.
172 - the units for BD diffusion coefficients changed to be consistent with other IMP units.
173 - IMP::domino::get_interaction_graph() now takes an IMP::RestraintsTemp, like other functions
174 - The assert failure handling function was documented and renamed to IMP::handle_error() so it is easier to find when you want to use gdb.
175 - to work around various issues with ref counting pointers and compiler eccentricities, we added emulation of the C++0x \c nullptr. You should prefer that to \c NULL in IMP code that you want to run cross platform.
176 - IMP::IntsList, IMP::FloatsList and IMP::StringsList have been added to replace the various scattered solutions for passing such types.
177 - IMP::Restraint::get_decomposition() and IMP::Restraint::get_current_decomposition() changed to return a single Restraint, instead of a list. This makes it easier to propagate the weight and maximum reliably.
178 - IMP now supports usage of restraints without adding them to the IMP::Model scoring function. To do this, do IMP::Restraint::set_model(), passing the model. The restraint can then be evaluated.
179 - IMP::domino::DominoSampler does not use the IMP::domino::OptimizeRestraints restraint optimization by default. Instead, if it is asked to create the IMP::domino::RestraintScoreSubsetFilterTable, it decomposes the restraints first (via IMP::create_decomposition()). This avoids several bugs and very fragile code.
180 - the IMP::core::DiameterRestraint was ignoring the radii of the particles involved and so was giving artifically low scores. It now is on the actual diameter of this molecule.
181 - the IMP::core::MonteCarlo optimizers now support incremental evaluation. This can be a lot faster when only a few particles are moved each step.
182 - all the plural types in IMP have moved to bounds checked vectors when using debug builds with gcc. If you get a non-imp error about an invalid access, it is probably some code that walks off the end of an array. Please report it.
183 - The IMP::core::MoverBase was changed to move it off of the IMP::SingletonContainer. This resulted in the IMP::core::BallMover and IMP::core::NormalMover having new constructors. Now create them from a list of particles, a list of float keys and a radius/standard deviation. This removes some complexity and inefficiencies as well is removes some scope for errors.
184 - Temp and non-temp decorator lists have been merged in C++. This was done to simplifity code since no one was using the non-temp variants. Now all decorator lists are temp (non-reference counted) variants.
185 - restraints and restraint sets are now evaluated only using "canonical" weights. That is, each restraint has one weight for the model (the total over all the restraint sets it is contained in and will always be evaluated with that weight). This allows the evaluation of simple restraints to be faster.
186 - The IMP_LIST() macros have been changed slightly. If your usage needs to take action upon addition, removal or changes to the list, use the IMP_LIST_ACTION() variant in your header. The IMP_LIST_IMPL() macro no longer takes the actions, and the last three (generally empty arguments) will have to be removed from the call to get it to work. This is needed to move towards more flexible and efficient passing of lists of values.
187 - IMP::domino uses the new IMP::Model::evaluate_if_good() support to accelerate computations
188 - IMP::core::MonteCarlo can use the IMP::Model::evaluate_if_good() support to more quickly reject
189  very bad conformations. See IMP::core::MonteCarlo::set_maximum_difference().
190 - IMP::core::ExcludedVolumeRestraint has been rewritten to be faster. It is especially
191  faster when used with IMP::Model::evaluate_if_good()
192 - a new evaluation mode IMP::Model::evaluate_if_good() and IMP::Model::evaluate_if_below() has been added. It allows restraints to shortcut score computation when the score can be shown to be worse than a maximum value.
193 - as part of moving towards more efficient use of evaluate_if_good() various deprecated methods have been removed from IMP::core::ExcludedVolumeRestraint and IMP::core::RigidClosePairsFinder.
194 - incremental evaluation support was removed from IMP. The reason for doing this was that the code was complicated, created overhead even when incremental support was not used and was not commonly used. Further, decomposing the restraints and using the dependency graph yields similar results and is more transparent.
195 - the RMF helper binaries have been moved to their own application so that they get installed.
196 - IMP::display::Writer has been revised to better support writers that write multiple frames to a single file and ones that write binary data. The noticeable changes are that the existing IMP::display::Writer instances must be created with a file name. And the IMP::display::WriteOptimizerState just takes a writer rather than a write and a file name template. IMP::display::Writer::set_frame() has been added so that you can directly control the frame being written.
197 
198 ## Spring 2011
199 - An interactive mode has been added to IMP::domino::DominoSampler. The interactive mode is useful for understanding domino sampling runs and distributing domino comptutations across a cluster.
200 - Functions IMP::domino::set_assignments() and IMP::domino::get_assignments() were added which support
201  writing subset assignments to data fields in hdf5 files. These can be used to helping to distribute
202  domino on a cluster as well as debugging the sampling process.
203 - a Python function IMP.show_graphviz() has been added that attempts to render a graph with \c dot and then open the pdf.
204 - The Python functions IMP.show_altgraph() and IMP.get_networkx_graph() have been added to provide alternatives for quick viewing of IMP graphs. Unfortunately, they still pale compared to graphviz.
205 - IMP.atom.create_cover() was added to facilitate creating a summary particle for part of a hierarchy in order to accelerate restraints.
206 - IMP.hdf5 was renamed to IMP.rmf, the proposed name of the file format that it supports. That also better separates the hdf5 support from the file format support.
207 - The old I/O functions have been marked as deprecated in favor of IMP.hdf5. You may need to compile with deprecated="yes" if you use them.
208 - The Python graph interface now has a remove_vertex method.
209 - One can now access the model restraint evaluation statistics programmatically using IMP::Model::get_restaint_statistics(). Restraint statistics can be logged to a file during optimization using IMP::core::WriteRestraintScoreStatisticsOptimizerState.
210 - IMP::domino::DominoSampler now allows you to specify the tree on which merges occur directly. Also, you now need to specify the merge tree rather than the JunctionTree if you want to do non-loopy inference and specify something about how it is done. Sorry, it makes the code a lot easier.
211 - Preliminary symmetry support has been added via the IMP::core::TransformationSymmetry and IMP::core::TransformationAndReflectionSymmetry classes.
212 
213 ## Winter 2011
214 - There now is a common base class IMP::atom::Simulation for IMP::atom::BrownianDynamics and IMP::atom::MolecularDynamics. In merging them there were several minor changes made to both. The most noticeable may be that the function for setting the maximum time step length is now IMP::atom::Simulation::set_maximum_time_step(). The last time step length can be extracted by IMP::atom::Simulation::get_last_time_step()
215 - IMP::core::MonteCarlo::set_temperature() was renamed to IMP::core::MonteCarlo::set_kt() as that is what it is doing.
216 - A new module IMP.hdf5 has been added to provide more general support for saving and loading IMP::atom::Hierarchy structures to files. Multiple conformations of each hierarchy can be saved as well as information about geometry and restraints (although these can't be read at the moment, so they are not so useful).
217 - IMP::algebra::grids::GridD now supports dense grids in arbitrary dimension through use of IMP::algebra::grids::DenseGridStorageD.
218 - IMP::Optimizer now can use a list of restraint sets to compute the score rather than the complete Model score.
219 - each IMP::Restraint now has its own weight. This is lightly tested.
220 - A new log level IMP::PROGRESS has been added. The idea is that IMP::Sampler::get_sample() calls and other expensive loops can show a boost progress meter at this log level to give some idea when things are moving forward.
221 - IMP::domino::TrivialParticleStates renamed to IMP::domino::IndexParticleStates to be less judgmental
222 - IMP::domino::CompoundParticleStates and IMP::domino::RecursiveParticleStates added
223 - IMP::domino::DominoSampler now supports maximum scores on IMP::RestraintSets (untested).
224 - the name of the clustering methods have been changed to create_ from get_ since they create objects.
225 - the names of the recently added metric based clustering support has been changed to Metric rather than Distance.
226 - IMP now has the ability to have certain tests designated as expensive and to skip those tests when test-fast is run. The motivation for this is that the tests take a really long time making it impractical to run before every commit. And it is hard to tell which tests have not been run when running with the necessary multiple build processes. My thought is that tests that take about a second or less on a debug build should be left along (this is probably >95% of the tests), but the few that take longer should be marked as expensive. To do that, rename the test to expensive_text_XXX.py (from test_XXX.py) and add expensive_python_tests= env.IMPModuleGetExpensivePythonTests() to the IMPModuleTest call in the test SConscript.
227 - the fuction IMP::display::create_restraint_geometry() was added to do what its name says.
228 - runtime dimensional geometric objects have been added. These include IMP::algebra::VectorKD, IMP::algebra::BoundingBoxKD and IMP::algebra::SphereKD. The IMP::statistics::Embedding classes now use IMP::algebra::VectorKD instead of Floats. The sparse grids also support variable dimensions as to the nearest neighbor searches.
229 - IMP::atom::DopePairScore has been added to IMP.
230 - IMP::atom::CHARMMStereochemistryRestraint provides a high-level simplified
231 interface to the bonded part of the CHARMM forcefield.
232 - IMP modules are now built by first combining all the .cpp files into one, and then building that file. This greatly accelerates building of a module from scratch as build time is dominated by parsing headers. This does change the semantics of .cpp files as they see headers included by and functions declared by an arbitrary subset of other .cpp files. For now they are still required to be able to be compiled separately. To get the only behavior back either globally or on a per-module basis, see the percppcompilation parameter to scons.
233 - Instructions and scripts have been added for building modules and things externally to the IMP build. See the installation guide.
234 - IMP::atom::CHARMMParameters can now automatically map CHARMM-style atom and
235 residue naming to PDB-style, so CHARMM topology files can be used unmodified.
236 - IMP::atom::CHARMMTopology::add_sequence() provides a simple way to generate a topology from a string of amino acid one-letter codes.
237 - IMP::atom::CHARMMTopology::add_coordinates() will generate atomic Cartesian coordinates from CHARMM internal coordinate information.
238 - IMP::atom::CHARMMTopology::add_missing_atoms() and
239 IMP::atom::remove_charmm_untyped_atoms() can now be used to ensure that atoms
240 read from a PDB file match the CHARMM topology.
241 - building of deprecated functionality is now false by default
242 - the IMP_COMPARISONS(), IMP_COMPARISONS_1(), IMP_COMPARISONS_2() macros now take the name of the class as an additional (first) argument. This avoids the formerly needed, \c This typedef and makes them more consistent with the other macros in IMP.
243 - modules can now be built externally to the IMP svn in addition to applications and biological systems. To do so, create a directory with your module in a subdir containing links to the IMP SConscript file and scons_tools and a config.py that has information needed to run IMP (eg an appropriate \c pythonpath, \c ldpath).
244 - removed IMP::algebra::GridD::get_index(VectorD) as it wasn't very safe (in that vectors coordinates can get rounded between the IMP::algebra::GridD::get_has_index() and IMP::algebra::GridD::get_index() calls. Use IMP::algebra::GridD::get_nearest_index() or IMP::algebra::GridD::get_extended_index() or IMP::algebra::GridD::operator[]() instead.
245 - renamed IMP::domino::ParticleStatesTable::get_particles() to IMP::domino::ParticleStatesTable::get_subset() as it is more useful to be able to get the subset containing all the particles.
246 - rename IMP::restrainer::Restraint::print_all_restraints() to IMP::restrainer::Restraint::show_all_restraints() to be consistent with the rest of IMP.
247 - renamed IMP::atom::get_conect_record_string() to IMP::atom::get_pdb_conect_record_string() to make clearer what it is.
248 - class and method names are now spell checked. Add missing words to spelling_exceptions in the module test call.
249 - the plural names (eg IMP.Particles()) have been removed from the Python side as they are just Python lists.
250 - biological systems can now include internal modules. These provide a conventient place to put application specific C++ and Python code. See the example system for more info.
251 - IMP_VALUES() now includes IMP_OUTPUT_OPERATOR() so you no longer need two namespace macros for each value.
252 - the function IMP::core::Harmonic::k_from_standard_deviation was renamed to IMP::core::Harmonic::get_k_from_standard_deviation() to conform to the standards.
253 - the IMP::atom::PDBSelector and IMP::atom::Mol2Selector became IMP::Object classes. All this
254  means is that they need to be created with \c new in C++ code. It also means that one is
255  no longer prohibited from storing them (not that there is much use in doing that).
256 - the standards tests have been improved to test more useful aspects. Now class and function names are checked some as well as all modules have the checks for show and plural types. The error messages should explain how to fix things.
257 - IMP::core::RigidBody::lazy_set_reference_frame() was renamed to IMP::core::RigidBody::set_reference_frame_lazy() to fit with the standards better.
258 - the transform based methods on referene frame which have been deprecated for a while were removed
259 - the hierarchy visiting and searching functions have been renamed to better fit the IMP naming scheme as we don't expect they were used outside of the IMP source.
260 - IMP::atom::NonhydrogenMol2Selector was renamed IMP::atom::NonHydrogenMol2Selector to be consistent with the PDB version
261 
262 ## Fall 2010
263 - IMP::display::PlaneGeometry was added to display planes
264 - the optimize methods on optimizers was moved to a "non-virtual interface". Usage has not changed, but optimizers should implement IMP::Optimizer::do_optimize() instead of IMP::Optimizer::optimize() to
265 benifit from better checking.
266 - the two-vector constructor for IMP::algebra::Plane3D now expects the second vector to be a unit vector as otherwise one could switch the order around without noticing.
267 - the io functions in the kernel have been cleaned up a bit (the old ones are there for backwards compatibility). See IMP::write_particles(), IMP::write_particles_binary(), IMP::write_particles_to_buffer() and IMP::read_particles(), IMP::read_particles_binary(), IMP::read_particles_from_buffer()
268 - IMP::core::WriteModelOptimizerState is going away as it duplicated IMP::WriteParticlesOptimizerState.
269 - the IMP::algebra::Grid3D has been changed to make it support any (fixed) dimension when used with sparse storage. The template arguments have also been changed to remove a redundant one. See IMP::algebra::GridD.
270 - the biological systems specification has been improved a little adding ability to run some rudamentary tests to make sure the scripts are ok and to not require that everything be run from the svn directory.
271 - A new method IMP::atom::create_compatible_rigid_body() which creates a rigid body from a hierarchy which has the same internal coordinates as another rigid body. A way to make the rigid body construction more canonical would be nice (so we don't need this function), but I'm not sure how to do that.
272 - Logging has been improved to better report the name of methods producing the log messages
273 - a macro IMP_FUNCTION_LOG has been added which should be added to the start of non-member functions which produce significant logging output.
274 - IMP::algebra::get_distance(const Rotation3D&,const Rotation3D&) was changed to use the Euclidean distance in R4 as that seems better behaved than the prior metric.
275 - IMP.domino2 was renamed to IMP.domino and the old IMP.domino was moved
276 - the documentation for classes and some methods now includes a list of all examples which use the class. Please report any incorrect links or phantom classes appearing in the docs. Unfortunately, functions have to be added individually. Please request any functions of particular interest.
277 - applications and biological systems now have their own documentatin pages
278 - IMP::atom::Hierarchy requires radii on its leaves
279 - IMP::atom::read_pdb add radii to the atoms
280 - IMP::helper was merged into IMP::restrainer as all the functionality there was primarily to provide support for restrainer
281 - IMP::domino2::SubsetEvaluatorTable was removed. Pass the model and IMP::domino2::ParticleStatesTable to the IMP::domino2::RestraintScoreSubsetFilterTable instead.
282 - IMP::atom::Selection was added to allow specification of parts of IMP::atom::Hierarchy using biological sorts of names. A few functions to create restraints from them were added too.
283 - a new example was added in the kernel to show IMP used on a biological system
284 - IMP::display::PymolWriter now supports adding labels to things
285 - IMP::display::PairRestraintGeometry and IMP::display::ConnectivityRestraintGeometry were added to aid in visualizing those restraints.
286 - IMP::bullet was added with an optimizer to use hard body physics to resolve local collisions.
287 - IMP::atom::setup_as_rigid_body() has been deprecated and replaced by IMP::atom::create_rigid_body(). The latter creates the rigid body as a separtate particle so that the molecular hierarchy doesn't have to worry about having its bounding sphere large enough to enclose all the members.
288 - IMP::core::KClosePairsPairScore was added to have count based cutoffs for close pair scoring.
289 - IMP::algebra::get_surface_area_and_volume() was added to compute the two numbers for a set of balls
290 
291 ## Summer 2010
292 - The IMP::core::RigidDistancePairScore and IMP::core::ClosePairsPairScore have been revised to remove certain inconsistencies and ambiguities and to make them faster. Existing code using them will need to be minorly tweaked to work.
293 - Javi added his 2D EM scoring functionality as IMP::em2D
294 - some new ways to speed up scons have been added. See IMP::core::HarmonicDistancePairScore, IMP::core::SoftSpherePairScore and, for C++ users, the generic restraint support IMP::container::create_restraint() and IMP::core::create_restraint(). These each offer between 2x and 1.2x speedup when using simple scores (like harmonics on distances). In addition, a function IMP::container::get_slack_estimate() has been added which will estimate the correct slack to use with a IMP::container::ClosePairContainer. This will be extended to support IMP::core::ExcludedVolumeRestraint eventually.
295 - support for dense and sparse grids have been added to IMP::algebra. See the IMP::algebra module page (I'm still working on how to make the docs clearer).
296 - all write functions now have associated IMP::OptimizerState and IMP::FailureHandler classes. For examples, see IMP::WriteOptimizerState, IMP::WriteBinaryOptimizerState, IMP::WriteFailureHandler, IMP::atom::WritePDBOptimizerState etc.
297 - functions IMP::write_binary_model(), IMP::read_binary_model() and IMP::read_configurations() have been added to support space and filesystem efficient storage of model configurations. Multiple configuration can be written to a single file. This functionality requires NetCDF be installed (NetCDF is a standard library for reading and writing binary data).
298 - domino2 has been added. It provides a simpler interface on Keren's domino optimize as well as a number of new optimization and hooks for customizing the optimization process
299 - a better explaination of how to use reference counted pointers has been added to IMP::Pointer.
300 - all simple, planar polygons are now supported for display when CGAL is present
301 
302 ## Week of April 1, 2010
303 
304 - All plural objects in Python are now simply Python lists rather than C++ recreations of Python lists. This makes compilation of the wrappers much, much, much faster. The visible changes are
305  - types are not checked until the lists are passed to C++
306  - passing std::vector types by pointer and storing passed std::vector types by pointer will not work (but should never have been done anyway from code exposed to Python)
307  - swig has issues with some overloads (not always for obvious reasons). These are being sorted out. None are commonly used.
308  - get_particles() on a plural object doesn't work in Python (and is not needed in C++). Implicit conversions will always work.
309 
310 - All containers need to know the model at time of construction. If, after updating, you get an error on a container constructor, just add the model as the first argument. This also means that emtpy lists of particles in the constructors cause check failures. We can figure out a work around if this is too annoying.
311 
312 ## Week of March 13, 2010
313 - function get_rotation_in_radians_about_axis() was renamed to get_rotation_about_axis() as it didn't parse and we don't have the "in radians" elsewhere.
314 
315 - Added IMP::algebra::ReferenceFrame3D. As part of the cleanup, IMP::core::RigidBody::set_reference_frame() replaces set_transformation(). And the reference-frame related transformation construction functions were replaced. IMP::algebra::get_rotation_from_x_y_axes() was added to aid in the construction of reference frames (and replaces the algebra function taking three vectors).
316 
317 ## Week of March 6, 2010
318 - Publications now have a description field to give browsers an indication of what is in the publication to aid selection of what to read/cite.
319 
320 
321 ## Week of Feb 27, 2010
322 - IMP::algebra::decompose_rotation_into_axis_angle() was renamed to IMP::algebra::get_angle_and_axis().
323 
324 - renamed IMP::atom::bond() and IMP::atom::unbond() to IMP::atom::create_bond() and IMP::atom::destroy_bond() to be more consistent with things
325 
326 - renamed IMP::core::root() to IMP::core::get_root()
327 
328 
329 ## Week of Feb 21, 2010
330 
331 - IMP::Object::set_was_owned() was changed to IMP::Object::set_was_used() as that better reflects what the flag means.
332 - various more interpolation and endian methods had their names fixed (by adding \c get_)
333 - the function get_mean() on vectors was removed as it duplicated IMP::algebra::get_centroid()
334 - build_Transformation3D_from_transformation3D was replaced by IMP.algebra.get_transformation_3d()
335 - IMP::algebra::almost_equal() is now IMP::algebra::get_are_almost_equal() to fit the naming conventions.
336 - 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
337  - 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>).
338  - 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.
339  Some good sed strings are
340  - "s\#random_vector_in_unit_sphere()\#get_random_vector_in(IMP.algebra.get_unit_sphere_3d())\#g"
341  - "s\#random_vector_in_unit_box()\#get_random_vector_in(IMP.algebra.get_unit_bounding_box_3d())\#g"
342  - "s\#random_vector_on_unit_sphere()\#get_random_vector_on(IMP.algebra.get_unit_sphere_3d())\#g"
343  - "s\#random_vector_on_unit_box()\#get_random_vector_on(IMP.algebra.get_unit_bounding_box_3d())\#g"
344  - "s\#random_vector_in_box(\#get_random_vector_in(\#g"
345  - "s\#random_vector_on_box(\#get_random_vector_on(\#g"
346  - "s\#random_vector_in_sphere(\#get_random_vector_in(\#g"
347  - "s\#random_vector_on_sphere(\#get_random_vector_on(\#g"
348  - "s\#grid_cover\#get_grid_surface_cover\#g"
349  - "s\#uniform_coverr\#get_uniform_surface_cover\#g"
350  .
351 - Spheres in IMP::algebra are now supported in general dimensions. See IMP::algebra::SphereD.
352 - Many methods in IMP::algebra were renamed to be more consistent with other methods or general conventions. Most of these simply involved adding \c get_ as a prefix and/or add a \c _3d suffix when they did not take any arguments.
353  - build_Rotation2D_from_Vector2D became IMP::algebra::get_rotation_to_x_axis()
354  - most of the Rotation3D and Transformation3D functions (in addition, IMP::algebra::get_identity_rotation_3d() and IMP::algebra::get_identity_transformation_3d() added the \c _3d so we can add 2D versions at some point)
355  - IMP::algebra::Transformation3D::get_transformed() and IMP::algebra::Rotation3D::get_rotated(). Replacing \c ".transform(" worked in the IMP code base.
356  - IMP::algebra::get_distance(), this also carries over to the IMP::core::get_distance()
357  The following global replacements are probably safe (in sed expressions)
358  - "s\#core.distance(\#core.get_distance\#g"
359  - "s\#algebra.distance(\#algebra.get_distance\#g"
360  - "s\#\.transform(\#.get_transformed(\#g" Only in C++
361  - "s\#\.rotate(\#.get_rotated(\#g" Only in C++
362  - "s\#rotation_from\#get_rotation_from\#g"
363  - "s\#rotation_in\#get_rotation_in\#g"
364  - "s\#identity_rotation(\#get_indentity_rotation_3d("
365  - "s\#::distance(\#::get_distance(\#g"
366  .
367 - 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.
368 - 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.
369 - 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()
370 
371 ## Week of Feb 14, 2010
372 
373 - The IMP::atom::Bond types were rearranged to reconcile the protein-centric classification with ligand support.
374 
375 - IMP::atom::Atom no longer has charge since we have IMP::atom::Charged.
376 
377 - IMP::atom::read_mol2() and IMP::atom::write_mol2() were added
378 
379 - IMP::atom::Selector and descendents renamed to IMP::atom::PDBSelector since we will soon have Mol2Selectors. In addition, the IMP::atom::IgnoreAlteriativesSelector is now IMP::atom::NonAlternativeSelector to keep the name positive, like the others. In the IMP body, all instances of the string Selector were for PDBSelectors and so sed was safe to use.
380 
381 - IMP::atom::read_pdb() lost the "ignore_alternatives" argument. Instead, all of the provided selectors, other than IMP::atom::AllSelector ignore alternatives internally. Code that uses the IMP::atom::AllSelector should probably change to the IMP::atom::NonAlternativeSelector.
382 
383 - IMP::example renamed (from examples)
384 
385 - The IMP_USAGE_CHECK() macro lost the (unused) third argument.
386 
387 ## Week of February 3, 2010
388 
389 - The model io code as moved into the kernel so it is now IMP::write_model() and IMP::read_model()
390 
391 - Remove the version_info argument from the implementation macros. Instead, just pick up the module version info automatically.
392 
393 - Add a function Object::get_type_name() and Object::get_module() to get the respective bits of information about each object.
394 
395 - Change Object::show() to be a non-virtual wrapper which prints the object name and other info before passing control off to Object::do_show().
396 
397 - The containers were moved to IMP.container. See that module page for a full list of what moved. In the process, the backwards compatability functions were removed from IMP::container::PairsRestraint and kin.
398 
399 - IMP.atom.create_protein() now returns the created protein
400 
401 - the simplify functions have been moved from IMP.helper. They are now IMP.atom.create_simplified_along_backbone().
402 
403 - IMP.helper.clone() has been renamed to IMP.atom.create_clone()
404 
405 - IMP.misc.ConnectingPairContainer has been moved to IMP.core.ConnectingPairContainer
406 
407 - The locations for pixels in IMP::em::DensityMap have been moved to the center of the corresponding voxel from the lower left corner.
408 
409 - IMP::em::get_transformed(), IMP::em::get_resampled() and IMP::em::get_density() have been added.
410 
411 - The documentation has been majorly cleaned up and simplified. Please look around and see if you like it. There are now two main pages, the introduction and the developers guide, rather than the previous plethora of pages.
412 
413 - IMP::algebra::Cone3D::get_bounding_sphere() has been removed since it was not of general use, not returning the bounding sphere you would expect and was trivial to implement.
414 
415 - IMP::algebra::projection() was removed since it didn't actually project onto the segment and the name didn't follow the normal conventions. And it wasn't used.
416 
417 - Most geometry now has namespace methods IMP::algebra::get_bounding_box(), IMP::algebra::get_surface_area(), IMP::algebra::get_volume().
418 
419 ## Week of January 22, 2010
420 
421 - A generic geometry layer has been added (see \ref genericgeometry). Using it, IMP::atom::rmsd(),
422  IMP::algebra::alignment_taking_first_to_second() and the new IMP::atom::native_overlap() all
423  can work on either collections of either IMP::core::XYZ particles or IMP::algebra::Vector3Ds.
424 
425 - Deprecated functionality has been removed from IMP.core. For those still using it, IMP::core::ClosePairsScoreState was replaced by IMP::core::ClosePairContainer and IMP::core::CloseBipartitePairsScoreState was replaced by IMP::core::CloseBipartitePairContainer.
426 
427 - The macros for Scores changed slightly. Scores not in IMP svn which use the IMP_*_SCORE macros now have to implement the get_is_changed() function outside of the class declaration and scores which use the IMP_SIMPLE_*_SCORE now don't have to implement the functions to get interactions and used particles.
428 
429 - Rename IMP::core::MinimumPairScoreRestraint (and kin, Maximum, Singleton, Triplet and Quad) to IMP::core::MinimumPairRestraint.
430 
431 - Add IMP::core::MinumumPairScore (and kin).
432 
433 ## Week of January 1, 2010
434 
435 - IMP::em is now using Particles to resample density maps and for fitting restraints. The previous ParticleAccessPoint mechanism is removed.
436 
437 - IMP::UsageException and IMP::InternalException are now reserved for their respective
438  checks (and cannot be thrown by IMP_THROW()). This makes the distinction between API
439  exceptions (which are thrown in any build mode and should be documented and tested)
440  and helper exceptions which are only thrown when checks are turned on (and hence
441  should not be documented) clearer.
442 
443 - IMP::core::RestraintSet moved to IMP::RestraintSet. The restraint sets now simply define a tree
444  with weights which the model traverses as opposed to being an opaque IMP::Restraint themselves.
445  This means that incremental evaluation of restraints in restraint sets now works and that
446  restraints in restraint sets can be individually evaluated. Existing working usage should not
447  have changed (so \c sed should manage updates just fine), but the internal
448  implementation is completely new, so pay attention.
449 
450 - IMP now has a text i/o layer consisting of IMP::TextInput and IMP::TextOutput. These classes are
451  convertible to C++ streams and implicitly constructable from both streams and file paths. As a result,
452  functions that take them will work when called with a string for a file path, a Python file or a
453  C++ stream.
454 
455 - The IMP.examples module now documents how to use the needed aspects of scons and SWIG.
456 
457 - The IMP.examples module is used as the basis for new modules created by the make-module script, so those include more documentation and are tested.
458 
459 - Module overview pages are now generated from the information passed in the SConscript file, rather than from the (now removed) modulename.dox file. See the examples file for an example of the things you can do there.
460 
461 - boost program options is now a checked for dependency.
462 
463 - The IMP::Model now uses dependency information from IMP::ScoreStates to automatically reorder the IMP::ScoreStates so that they are evaluated in the right order. Also, IMP::Model::evaluate() on a subset of the restraints now only updates the needed score states, not all of them.
464 
465 - Functions on rigid bodies no longer provide the IMP::core::RigidMemberRefiner as a default as it is, pretty much always, the wrong thing to use. That class may go away without notice in the future and is no longer documented.
466 
467 - the IMP::helper::create_simple_connectivity_on_rigid_bodies() and IMP::helper::create_simple_excluded_volume_on_rigid_bodies() now both take an IMP::Refiner as an (optional) final argument. This makes it so they can be used with the rigid bodies created from molecular hierarchies. This code still needs to be updated and the docs don't reflect what the code was or is doing, so use with caution (see notes in the header file).
468 
469 - The IMP::helper create* functions now all take non-Object inputs as const& to make clear what is input and that there are no memory management gotchas.
470 
471 - a new base class IMP::Constraint has been added for constraints. Various
472 other classes have been renamed to be consistent.
473 
474 ## Week of December 11
475 
476 - The interface of IMP::PairScore changed slightly to make the function signatures more uniform across various methods. Now all methods that take a pair of IMP::Particle objects take a const IMP::ParticlePair&. Previously some took that, some took an IMP::ParticlePair and some took two IMP::Particle*s. If you have an implementation of an IMP::PairScore outside of svn, you will have to update your function signatures (the compiler will tell you where). Backward compatible IMP::PairScore::evaluate() methods have been provided, so simple users of pair scores shouldn't see a difference.
477 
478 - IMP::core::PairRestraint takes a IMP::ParticlePair in the constructor instead of two IMP::Particle*s. A backwards compatible constructor can be added if needed.
479 
480 - IMP::ParticlePair::first and second went away since no one claimed to be using it and it complicated the implementation.
481 
482 - The generic restraints/score states/scores infrastructure has been extended to triplets and quads (for angles and torsion angles).
483 
484 ## Week of December 4
485 
486 - IMP now makes use of Boost.Filesystem to manipulate paths. Things may not work well on systems where boost libs are not available which does not support posix paths. But libless boost installs generally don't exist outside of our test systems.
487 
488 - new functions like IMP::core::get_example_path(filename) and IMP::core::get_data_path(filename) allow one to easily find a data file named 'filename' for the examples and library internal data.
489 
490 - The IMP::display module has been revamped in order to support non-linear geometry. VRML support has been dropped. CMM support will be dropped unless someone requests it (as IMP::display::ChimeraWriter does all it does and more).
491 
492 ## Week of November 19
493 
494 - imp.xcodeproj was moved into tools and updated accordingly
495 
496 - the bin directory finally went away
497 
498 - IMP::display::ChimeraWriter now supports the latest version of Chimera
499 
500 - IMP::display::CGOWriter was renamed to IMP::display::PymolWriter as it can do more than just CGO.
501 
502 - IMP::VectorOfRefCounted::operator[] can now be used for assignments just like a normal vector. No more need to use the IMP::VectorOfRefCounted::set() method.
503 
504 - the IMP::atom::Hierarchy constructor from an IMP::Particle* is now explicit (as were the ther decorator constructors)
505 
506 
507 ## Week of November 12
508 
509 - All exception types are now mapped to equivalent classes in Python. The
510 class hierarchy is similar (e.g. IMP::ModelException derives from IMP::Exception
511 in both C++ and Python) so all IMP exceptions can be caught in Python using
512 "except IMP.Exception". For convenience, the IMP::IOException,
513 IMP::ValueException and IMP::IndexException classes in Python also derive from
514 the similarly-named standard Python classes (IOError, ValueError and IndexError
515 respectively).
516 
517 ## week of October 29 Update
518 
519 - You can now add members to rigid bodies via IMP::core::RigidBody::add_member(). These members can be other rigid bodies (although this functionality is only lightly tested).
520 
521 - The code to get bounding volumes for IMP::atom::Hierarchy has been moved to the atom module, as as the clone and destroy code. They can be found at IMP::atom::clone(), IMP::atom::destroy(), IMP::atom::get_bounding_box().
522 
523 - Added IMP::core::VolumeRestraint.
524 
525 - Several functions have been added to helper in creating restraints. They are create_simple_connectivity_on_rigid_bodies(), create_simple_connectivitiy_on_molecules(), create_simple_distance(), create_simple_diameter(), create_simple_em_fit(), and create_simple_excluded_volume_on_rigid_bodies(). Functions load_em_density_map() and set_rigid_bodies() are added as well. See IMP::helper for more information.
526 
527 
528 - IMP::ScoreStates are further hidden. Namely, IMP::core::RigidBody constructs the needed score states internally, doing away with the need for the create functions (which have been done away with). In addition there are new decorators IMP::core::Cover and IMP::core::Centroid which manage their respective score states, further doing away with more create methods. The hierarchy-based create method for rigid bodies has been moved to the atom module and is called IMP::atom::rigid_body_setup_hierarchy().
529 
530 - IMP::em::read_map() will figure out the file type to use automatically from the extension. Other such methods should follow suite.
531 
532 - A class IMP::core::StructureSet has been added to provide a convenient way to manage solutions of optimization runs.
533 
534 - IMP::core::RigidBodyMover now takes its angle argument in radians and is documented as such.
535 
536 - IMP::core::ClosePairsScoreState and IMP::core::CloseBipartitePairsScoreState have been replaced by IMP::core::ClosePairContainer and IMP::core::CloseBipartitePairContainer. The score states have been marked as deprecated and are mostly still there, but are more limited than they were.
537 
538 - IMP::core::AllPairsPairContainer has been renamed to IMP::core::AllPairContainer and a bipartite version has been added.
539 
540 - All containers now keep track of what they looked like on the previous time step.
541 
542 - The IMP::core::ListPairContainer and IMP::core::ListSingletonContainer have had their interface reduced a bit in order to make implementing change tracking easier.
543 
544 - The set of exceptions has been simplified to go along with simplification of the checks. We now have IMP::InternalException and IMP::UsageException which are thrown by the respective checks (and the former is thrown by IMP_FAILURE()). When you want to to pass an exception back to Python use one of IMP::ValueException or IMP::IndexException or IMP::IOException. There is also a new macro, IMP_THROW() to be used when you want to throw an exception with a nice error message. Please look at code you have worked on and make sure that the exceptions make sense given the new clarifications.
545 
546 - An IMP::ModelException is now thrown when IMP::Particle attributes attain invalid values. This exception can be caught to recover from failures of IMP::core::ConjugateGradients or difficult restraints.
547 
548 ## Week of October 15
549 
550 - The set of functions needed to get meta information about IMP::Restraint and IMP::ScoreState objects has hopefully stabilized. Sorry about the thrashing. If you have restraints or score states not in SVN, see the corresponding IMP_RESTRAINT type macros, the IMP::Interaction class and base classes for what exactly you need to implement.
551 
552 ## Week of October 8
553 
554 - IMP::Interaction was modified to split IMP::interaction::get_used_particles() into IMP::interaction::get_read_particles() and IMP::interaction::get_write_particles(). This makes it possible to check for IMP::ScoreState objects being in an inconsistent order (so that the input to one is updated after it is read). Later, we will be able to automatically order the score states ensure that there are no problems.
555 
556 - IMP::atom::Hierarchy has been modifier to get rid of the IMP::atom::Hierarchy::Type. Instead, all types are contained in the decorators. IMP::atom::get_by_type() was also updated to reflect this.
557 
558 - IMP_check() and IMP_assert() have been
559 replaced with IMP_USAGE_CHECK() and IMP_INTERNAL_CHECK()
560 respectively. Hopefully this makes it clearer when to use
561 which. IMP::set_check_level() has been revised accordingly (to use
562 IMP::USAGE and IMP::USAGE_AND_INTERNAL). Also, IMP_failure() and
563 IMP_not_implemented() have been renamed to IMP_FAILURE() and
564 IMP_NOT_IMPLEMENTED() to make all macros be all caps. To update
565 external code,
566  - replace IMP.EXPENSIVE with IMP.USAGE_AND_INTERNAL
567  - replace IMP.CHEAP with IMP.USAGE
568  - replace IMP_assert and IMP_check as above.
569 
570 ## Week of October 1
571 - IMP::ScoreState and IMP::Restraint now better track the set of particles that they use and the dependencies between the particles. To this end, a new base class IMP::Interaction has been added with methods to get the inter-particle interactions and the set of particles used.
572 
573 - .cpp, .h, .py and SConscript files which contain the string "DO NOT COMMIT" will be rejected on checkin. Use this to make experimental or debugging changes you are making so you don't accidentally commit them.
574 
575 - The search module is no longer built by default and is not longer supported. It will get moved out of svn shortly.
576 
577 - IMP::ScoreState objects now also have IMP::Interacting::get_interacting_particles() methods. Soon IMP::PairScore and IMP::SingletonScore objects will too.
578 
579 ## Week of September 27
580 
581 - Some support for gather statistics has been added to IMP::Model (see IMP::Model::set_gather_statistics()). If requested, an API can be provided so that the individual data points can be returned to programs.
582 
583 - A class IMP::core::RigidBodyDistancePairScore has been added which provides accelerated computations for the distance between two rigid bodies.
584 
585 - The SWIG input files were renamed from swig.i to swig.i-in to aid in dependency tracking.
586 
587 - rigid bodies now have two sets of particles associated with them in the various places they are used. One is the IMP::core::RigidBodyMember particles, as was previously the case. The other is defined through a refiner (and could be the RigidBodyMember particles if a IMP::core::RigidMembersRefiner is used). The idea is that you sometimes want some particles which are transformed along with the rigid body, but which are not really part of the representation of the rigid body. Examples would include marker points or multiresolution representations of proteins.
588 
589 ## Week of September 20
590 
591 - all \c .i files have been renamed to start with \c IMP_ to help make dependency tracking easier.
592 
593 - static builds (builds with \c static=True) build both the static and dynamic libraries and just static executables
594 
595 - the \c profile build target has been removed as \c static=True does the important bit of what is needed. Just do \c linkflags=['-pg'] to add the needed link flag for \c gprof.
596 
597 - Restraints should now implement IMP::Restraint::unprotected_evaluate() instead of IMP::Restraint::evaluate(). The latter can now be called outside of IMP::Model::evaluate() and will return the right answer always.
598 
599 - \c bin/imppy.sh no longer works, as was previously warned. Use \c tools/imppy.sh instead. The bin directory will go away eventually, for now the script just tells you to use the tools version.
600 
601 ## Week of August 30
602 
603 - A new score IMP::core::BoundingBox3DSingletonScore has been added to keep particles
604  in a box.
605 
606 - str should now work better in Python when applied to IMP::Object objects and a few others. Objects
607  should use the new IMP_SHOWABLE and IMP_SHOWABLE_INLINE macros instead of declaring show
608  functions directory to make it so that they work in Python. It is now a bug to \c print or \c str
609  to not return something useful in Python for any IMP object.
610 
611 ## Week of August 23
612 
613 - each module now has a version, eg IMP::get_module_version_info() which is also returned by the various restraions of the module. The Python code checkes that loaded libraries have the expected version numbers to try to provide better messages when runtime linking problems occur.
614 
615 - the various bounding_box methods have been renamed to ::get_bounding_box() to be more consistent with the other names.
616 
617 - Python documentation is now parsed by doxygen
618 
619 ## Week of August 15
620 
621 - The Object::get_version_info() result now includes the SVN revision info when building from SVN. This means you can use it to more easily tell exactly what a built version of IMP was built from.
622 
623 ## Week of August 8
624 
625 - Treatment of hetatoms in hierarchies (and hence pdbs) is now documented. See IMP::atom::Hierarchy. This involved broadening IMP::atom::Residue to handle ligands and having IMP::atom::Hierarchy::LIGAND, IMP::atom::Hierarchy::AMINOACID and IMP::atom::Hierarchy::NUCLEICACID be handled by IMP::atom::Residue.
626 
627 - IMP::atom::read_pdb() currently drops HOH ATOM records on the floor. We should add a IMP::atom::Water decorator if anyone wants to handle them (since they aren't atoms and don't have elements).
628 
629 - IMP::atom::Mass() has been added for decorating particles with mass. IMP::atom::Atom mass has been moved to that.
630 
631 - The scheme for generating atom types is now fully specified. See the IMP::atom::AtomType documentation.
632 
633 - IMP::atom::Atom and IMP::atom::Residue have been somewhat restructured. Some of the helper functions have been renamed to be more descriptive or removed (if they duplicated other easily accessible functionality). get_residue_index() has been removed (since you can just call get_index() on the return result of the IMP::atom::get_residue()). IMP::atom::get_chain() now returns an IMP::atom::Chain. root() was renamed to IMP::atom::get_root() for consistency.
634 
635 - SWIG files are now generated from a file called swig.i in the pyext directory. This file only has to contain module-specific commands such as lines to wrap headers and instantiate module templates. No more boilerplate.
636 
637 - The contents of bin are moving to tools since the two directories both contained assorted development tools
638  (not all of which were executable). For now, bin/imppy.sh will still work, but that will go away soon.
639 
640 - IMP::Decorator::show() now just takes the stream (it used to take a prefix also, which was often ignored).
641  Anyone who implemented a decorator will have to delete the second argument of their show function.
642 
643 ## Week of August 1
644 
645 - Containers now have methods IMP::SingletonContainer::evaluate(), IMP::PairContainer::evaluate(),
646  IMP::SingletonContainer::apply() and IMP::PairContainer::apply(). Using these can be significantly
647  faster than looping over the particles externally. Similarly, there is IMP::SingletonScore::evaluate(),
648  IMP::PairScore::evaluate(), IMP::SingletonModifier::apply(), IMP::PairModifier::apply().
649 
650 - The decorator functions have been renamed to IMP::Decorator::setup_particle(), IMP::Decorator::decorate_particle()
651  and IMP::Decorator::particle_is_instance(). A shell script \c tools/update-decorators is provided which
652  updates the names in all code in subdirectories of the current directory. Please backup things first.
653 
654 - a function, IMP::Restraint::safe_evaluate() has been added to be used
655  when requesting the value of restraints outside of the IMP::Model::evaluate().
656 
657 ## Week of July 18
658 
659 - The atom::BondPairContainer has been renamed to atom::BondPairFilter
660  since it wasn't a real container. A real atom::BondPairContainer has
661  been added.
662 
663 - Out of source builds mostly works. To do an out of source build, make a link
664  to \c scons_tools and \c SConstruct from the source directory in the build
665  directory and then add the line \command{repository="../path_to_src_dir"} in
666  the \c config.py in the build directory. Then running \c scons in the build
667  directory will put generated files there. This allows you to make both a
668  \c release and \c fast build off of the same set of sources. Proper docs
669  will be added soon.
670 
671 - The SConscript setup for a module has been greatly simplified so it should
672  be easy enough for users to maintain their own module and updates to the
673  build system shouldn't involve changes to user SConscripts any more. This does
674  mean that any non-svn modules need to be updated. Look at IMP.core or another
675  module and copy what is there. Again, proper docs will be added soon.
676 
677 
678 ## Week of July 11
679 
680 - Per Javi's suggestion, the conventions have been split into \ref
681  devguide_conventions "Coding conventions" and \ref introduction_conventions
682  "API conventions" and linked from the main page.
683 
684 - benchmarks got moved to their own module, IMP::benchmark and will
685  now be tracked over time
686 
687 ## Week of July 4
688 
689 - FilteredListSingletonContainer and FilteredPairSingletonContainer
690  went away as there was too much hard to factor code shared with
691  IMP::core::ListSingletonContainer and IMP::core::PairSingletonContainer. The
692  IMP::core::ClosePairsScoreState is now handled by a list of filters
693  on the class itself. That is, do
694  IMP::core::ClosePairsScoreState::add_close_pair_filter() to add a
695  filter.
696 
697 - Hooks have been added to allow actions to be taken on an assertion
698  or check failure. See IMP::HandleFailure and its descendants for
699  more details.
700 
701 - IMP::display::CGOWriter has been much improved and now allows
702  provides lots of display-time control and easy building of
703  animations.
704 
705 - Generic optimizer states have been added
706  (IMP::core::SingletonsOptimizerState and
707  IMP::core::PairsOptimizerState).
708 
709 ## Week of June 15
710 
711 - box distributions (IMP::algebra::random_vector_on_box(),
712  IMP::algebra::random_vector_in_box()) take bounding boxes
713 
714 - IMP::em::DensityMap are now IMP::Object objects. Some current
715  allocations on the stack may need to be changed (since ref counted
716  objects can't be stack allocated).
717 
718 - IMP::em::DensityMap::Read() is now deprecated (as is
719  IMP::em::DensityMap::Write) as they violated a slew of
720  conventions. Use IMP::em::read_map() and IMP::em::write_map()
721  instead.
722 
723 
724 ## Week of June 8
725 
726 - new methods IMP::atom::add_radii() and IMP::atom::add_bonds();
727 
728 - Hierarchys to IMP::atom::Hierarchies
729 
730 - IMP::Particles has been changed to a new type. It no longer plays
731  quite so well with Python lists (you can't create one from an
732  arbitrary Python list).
733 
734 - The containers for multiple decorators have been revised to make them
735  more useful. See IMP::Decorators. You can now implicitly convert,
736  for %example, a IMP::core::XYZs to an IMP::Particles (as well as use
737  IMP::Decorators::get_particles()). All methods that take a
738  collection of particles with a certain type now instead take a
739  IMP::Decorators.
740 
741 - A method that has expectations about the particles it takes should
742  take decorators rather than particles. That is, anything which
743  expects IMP::core::XYZ particles, should take an IMP::core::XYZs
744  instead of IMP::Particles.
745 
746 - IMP_LIST() now takes an extra argument (the name of the plural
747  container)
748 
749 - In C++ IMP::Decorator objects are implicitly convertible to
750  IMP::Particle* objects. Unfortunately, making this work in Python is
751  problematic.
752 
753 - More methods take and return decorators rather than
754  IMP::Particles. This means it is clearer what their expectations are
755  and what they produce.
756 
757 ## Week of May 15
758 
759 - The IMP::helper module was added and various functionality moved
760  there. See its documentation page for a list of what is there.
761 
762 - IMP::algebra::SphericalCoords was renamed to
763  IMP::algebra::SphericalVector3D to be consistent with other algebra
764  classes.
765 
766 - IMP::algebra::Rotation2D is now IMP::InvalidDefault to be consistent
767  with the other similar classes.
768 
769 - We are trying to be a bit more specific about what is expected from
770  a IMP::atom::Hierarchy. Towards that end, there are two methods for
771  extracting a representation from a hierarchy,
772  IMP::atom::get_detailed_representation(), and
773  IMP::atom::get_simplified_representation()
774 
775 - A method has been added to produce a simplified copy of an
776  IMP::atom::Hierarchy. The method is still a bit crude and could
777  benefit from other people inspecting the output and saying how it
778  should be improved.
779 
780 - There is now an IMP::algebra::BoundingBoxD (and
781  IMP::algebra::BoundingBox3D) to track bounding boxes. There are
782  methods like IMP::algebra::bound_box(Sphere3D) which gets the
783  bounding box of a sphere.
784 
785 - Each IMP::Object has its own log level. If
786  IMP::Object::set_log_level() is called with a value other than
787  IMP::DEFAULT, the value is used for code within and called by the
788  object. To support this in your objects you need to add
789  IMP_OBJECT_LOG to the start of each major method. It has been added
790  to some of the core objects.
791 
792 ## Week of May 8
793 
794 - IMP::atom::MolecularHierarchy has been renamed to
795  IMP::atom::Hierarchy. Use \command{sed -i.old
796  "s\#MolecularHierarchy\#Hierarchy\#g" my_files}
797 
798 - the long-deprecated Name(Decorator) was removed
799 
800 - The decorator suffix has been removed from decorator names.
801 
802 - Unit conventions have been established and documented for distance,
803  energy, force and angle.
804 
805 - there is a function IMP::atom::create_protein() to create a coarse
806  grained protein. The function is crude so far, but the idea is that
807  we should have standard ways of generating such things so that
808  everyone can benefit from best practices.
809 
810 - a class IMP::atom::BondGraph has been added so Boost.Graph
811  algorithms can be used with bond graphs
812 
813 - the IMP-specific doxygen commands have been documented.
814 
815 - the doxygen commands unstable{name} and untested{name} have been
816  added to doxygen to be used for marking methods and functions as
817  likely to change or not well tested. Pass the name of the class or
818  method as name.
819 
820 - bonds can now be added to molecular hierarchies automatically see
822 
823 ## Week of May 1
824 
825 - There is a IMP::Rotation2D
826 
827 - You can now extract fixed Euler ZYZ angles from a
828  IMP::Rotation3D. This code can serve as a template for extracting
829  other Euler angle conventions if they are needed.
830 
831 - IMP::algebra::rotation_between_two_vectors() changed to
832  IMP::algebra::rotation_taking_first_to_second() to make it clear
833  which direction the rotation goes.
834 
835 ## Week of April 27
836 
837 - IMP::Decorator derived objects are now convertible to bool. So code
838 like \code if (d) { blah } \endcode works.
839 
840 - IMP::Decorator::cast now returns a null decorator (\c
841  DecoratorName()) rather than throwing an exception. This might make
842  it actually useful.
843 
844 - New IMP::statistics module for statistical methods
845  (e.g. clustering).
846 
847 ## Week of April 20
848 
849 - Support for taking advantage of rigid bodies in collision detection
850  has been added via the IMP::core::RigidClosePairsFinder.
851 
852 - All IMP::core::ClosePairsScoreState-related functinality has been
853  optimized and should be noticeably faster.
854 
855 - The EMBED project has been merged into the IMP::em module. Thus, it
856  is no longer necessary to obtain EMBED separately to build IMP::em.
857 
858 - All C++ methods which work with std::istream or std::ostream
859  arguments should now be usable from Python: any Python file-like
860  object can be used.
861 
862 - The SWIG interface now ties in to the reference counting mechanism
863  used in the C++ code, for all classes derived from
864  IMP::RefCounted. So, for %example, deleting a Python object should
865  not free the underlying C++ object if another C++ object holds a
866  reference to it, and unrefing a C++ object should not delete it if a
867  Python object still holds a reference to it. There should be no
868  further need to manually keep references to Python objects to
869  prevent things from being prematurely cleaned up. This should be
870  transparent to the user; please report any problems.
871 
872 - IMP::atom::AtomDecorator no longer inherits from
873  IMP::core::XYZDecorator.
874 
875 ## Week of April 13
876 
877 - The decorators IMP::atom::AtomDecorator, IMP::atom::ChainDecorator,
878  IMP::atom::ResidueDecorator etc. now inhertic from
879  IMP::atom::MolecularHierarchyDecorator. This means they can set
880  their IMP::atom::MolecularHierarchyDecorator::Type properly and
881  saves a lot of typing in the common case. We can always make
882  hierarchy decorators zero memory overhead if we find that the cost
883  matters.
884 
885 - The base classes IMP::Comparable, IMP::NullDefault,
886  IMP::ValidDefault and IMP::UninitializedDefault were added to
887  document what the default constructors do for various objects in
888  IMP.
889 
890 ## Week of April 6
891 
892 - IMP::Object now defines pure virtual methods
893  IMP::Object::get_version_info() and IMP::Object::show(). All
894  non-abstract classes which inherit from IMP::Object must implement
895  them. Doing this means they are more uniformly implemented and are
896  documented in one place.
897 
898 - IMP::Object is now reference counted (the only objects this changes
899  are IMP::Model and IMP::Optimizer). As a result optimizers and
900  IMP::Model objects must be created on the heap.
901 
902 - IMP::RefCounted has had its name changed and no longer inherits from
903  IMP::Object. This makes it easier to use independently.
904 
905 - the docs for reference counting (IMP::RefCounted) and and IMP::Decorator
906  have been improved
907 
908 - running doxygen produces no warnings. Let's try to keep it that
909  way. Run \command{scons doc > /dev/null} before you check in large
910  blocks of new code to make sure that you didn't introduce warnings.
911 
912 - Helper classes have been added to make SingletonModifier and
913  PairModifier objects look like functors for C++ and Python. This
914  makes it so you can use \c map in Python and \c for_each in C++. See
915  IMP::SingletonFunctor and IMP::PairFunctor for more information.
916 
917 - The recent changes page has moved to a doxygen page to make it
918  easier to link changes back to the relevant source code.
919 
920 ## Week of March 20:
921 
922 - create_rigid_body(), create_rigid_bodies(), create_centroid()
923  etc. now require you to add the score state to the model
924  yourself. Whether the rigid body is enforced or not can be
925  controlled by adding or removing the returned IMP::ScoreState.
926 
927 - All previously deprecated code has been removed. This includes
928  indexes in particles, the no-argument constructor for particles and
929  the functionality that was moved from core to atom.
930 
931 - The IMP::core::RigidBodyDecorator and
932  IMP::core::RigidMemberDecorator have been simplified by removing the
933  traits classes. There is now only one type of rigid body and it
934  stores the list of member particles internally.
935 
936 - IMP::core::NameDecorator has been deprecated as IMP::Particles have
937  built in names (use IMP::Particle::get_name(),
938  IMP::Particle::set_name()).
939 
940 - IMP::atom::ChainDecorator has been added
941 
942 ## Week of March 13:
943 
944 - A new IMP::display::Writer, IMP::display::ChimeraWriter has been
945  added which exports geometry to native Chimera constructs. It
946  probably should be used instead of bild and cmm for most purposes as
947  it combines the best of both types.
948 
949 - compose() for transformation is now a free function so
950  compose(rotation, vector) will work via promotions.
951 
952  - the geometry classes have been cleaned up and are now more
953  consistent with IMP standards (and more likely to do what their
954  names/comments suggest). See IMP::algebra::Sphere3D,
955  IMP::algebra::Cylinder3D, IMP::algebra::Segment3D,
956  IMP::algebra::Plane3D etc.
957 
958 - ParticleRefiner has been renamed to IMP::Refiner since the Particle
959  was long and unnecessary.
Restraints create_decomposition(const RestraintsTemp &rs)
Return the decomposition of a list of restraints.
BoundingBoxD<-1 > BoundingBoxKD
Typedef for Python.
Definition: BoundingBoxD.h:176
void report(std::string benchmark, std::string algorithm, double time, double check)
Report a benchmark result in a standard way.
IMP::base::Vector< IMP::base::Pointer< Container > > Containers
IMP::kernel::PairModifier PairModifier
Transformation2D get_transformation_aligning_pair(const Vector2Ds &set_from, const Vector2Ds &set_to)
#define IMP_WEIGHTED_GRAPH(Name, directionality, VertexData, ShowVertex)
Define a graph object in IMP.
Definition: graph_macros.h:102
A Monte Carlo optimizer.
Definition: MonteCarlo.h:45
SphereD< 3 > Sphere3D
Typedef for Python.
Definition: SphereD.h:87
VectorD< D > get_random_vector_on(const BoundingBoxD< D > &bb)
Generate a random vector on a box with uniform density.
IMP::kernel::ModelObject ModelObject
void show_timings(TextOutput out)
Chain get_chain(Hierarchy h)
double get_mean(const cv::Mat &mat, const cvIntMat &mask)
#define IMP_COMPARISONS_2(Name, f0, f1)
Implement comparison in a class using field as the variable to compare.
Key< 6, true > ParticleIndexesKey
The type used to identify a particle attribute in the Particles.
#define IMP_SHOWABLE_INLINE(Name, how_to_show)
Declare the methods needed by an object that can be printed.
algebra::Sphere3D get_bounding_sphere(const Hierarchy &h)
Rotation3D get_rotation_from_x_y_axes(const Vector3D &x, const Vector3D &y)
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
base::Vector< VectorD< D > > get_uniform_surface_cover(const SphereD< D > &s, unsigned int n)
Generate a set of vectors which covers a sphere uniformly.
IMP::base::Vector< IMP::base::Pointer< Object > > Objects
A list of objects.
Definition: types.h:61
Ints get_index(const kernel::ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
IMP::kernel::ScoreState ScoreState
ParticlesTemp get_output_particles(const ModelObjectsTemp &mos)
Return all the output particles for a given ModelObject.
IMP::base::Vector< Strings > StringsList
Standard way to pass a bunch of Strings values.
Definition: types.h:58
IMP::kernel::PairScore PairScore
A member of a rigid body, it has internal (local) coordinates.
Definition: rigid_bodies.h:368
IMP::kernel::DerivativeAccumulator DerivativeAccumulator
IMP::base::Vector< IMP::base::Pointer< RestraintSet > > RestraintSets
Stores a 2D rotation matrix.
Definition: Rotation2D.h:36
IMP::kernel::SingletonContainer SingletonContainer
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
#define IMP_FINAL
Have the compiler report an error if anything overrides this method.
Hierarchy create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=false)
Hierarchy create_clone(Hierarchy d)
Clone the Hierarchy.
void set_log_level(LogLevel l)
Set the current global log level.
#define IMP_FUNCTION_LOG
Beginning logging for a non-member function.
Definition: log_macros.h:306
IMP::kernel::Constraint Constraint
Display a Selection.
Definition: Selection.h:324
IMP::base::Vector< IMP::base::Pointer< PDBSelector > > PDBSelectors
Definition: pdb.h:47
#define IMP_GRAPH(Name, directionality, VertexData, EdgeData, ShowVertex)
Define a graph object in IMP.
Definition: graph_macros.h:29
#define IMP_OBJECT_LOG
Set the log level to the object's log level.
Definition: log_macros.h:297
void add_radii(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
ParticlesTemp get_particles(kernel::Model *m, const ParticleIndexes &ps)
#define IMP_DECORATOR_METHODS(Name, Parent)
IMP::base::Vector< IMP::base::WeakPointer< Restraint > > RestraintsTemp
double get_slack_estimate(const kernel::ParticlesTemp &ps, double upper_bound, double step, const kernel::RestraintsTemp &restraints, bool derivatives, Optimizer *opt, ClosePairContainer *cpc)
Object used to hold a set of restraints.
double get_volume(const Cone3D &g)
Definition: Cone3D.h:64
IMP::kernel::ScoringFunction ScoringFunction
Sample best solutions using Domino.
Definition: DominoSampler.h:32
IMP::base::Vector< IMP::base::Pointer< Restraint > > Restraints
IMP::kernel::SingletonPredicate SingletonPredicate
void set_progress_display(std::string description, unsigned int steps)
Set up the progress bar with the passed description.
#define IMP_BASE_SMALL_ORDERED_SET
Macro to support platform independent declaration of a small ordered set.
#define IMP_SHOWABLE(Name)
base::Array< 2, base::WeakPointer< Particle >, Particle * > ParticlePair
IMP::kernel::Optimizer Optimizer
ParticlesTemp get_input_particles(const ModelObjectsTemp &mos)
Return all the input particles for a given ModelObject.
IMP::base::Vector< Floats > FloatsList
Standard way to pass a bunch of Floats values.
Definition: types.h:54
#define IMP_COMPARISONS(Name)
Implement comparison in a class using a compare function.
void destroy_bond(Bond b)
Destroy the bond connecting two particles.
virtual double evaluate(const kernel::ParticlePair &vt, DerivativeAccumulator *da) const
Compute the score and the derivative if needed.
ScoreStates maintain invariants in the Model.
Score particles based on how far outside a box they are.
DensityMap * read_map(std::string filename, MapReaderWriter *reader)
Read a density map from a file and return it.
LogLevel get_log_level()
Get the currently active global log level.
Definition: log.h:94
InteractionGraph get_interaction_graph(ScoringFunctionAdaptor rs, const ParticleStatesTable *pst)
Rotation3D get_rotation_about_axis(const Vector3D &axis, double angle)
Generate a Rotation3D object from a rotation around an axis.
A decorator for a point particle that has an electrostatic charge.
Definition: Charged.h:31
A class to store an fixed array of same-typed values.
Definition: Array.h:33
IMP::base::Vector< IMP::base::Pointer< ScoreState > > ScoreStates
Hierarchy read_pdb(base::TextInput input, kernel::Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Abstract class for scoring object(s) of type ParticlePair.
IMP::algebra::Transformation3D get_transformation_aligning_first_to_second(const Vector3DsOrXYZs0 &source, const Vector3DsOrXYZs1 &target)
Compute the rigid transform bringing the first point set to the second.
IMP::kernel::Container Container
IMP::kernel::SingletonModifier SingletonModifier
const VectorD< C::DIMENSION > & get_vector_geometry(const C &g)
Definition: VectorD.h:418
#define IMP_VALUES(Name, PluralName)
Define the type for storing sets of values.
Definition: value_macros.h:23
base::Vector< VectorD< 3 > > Vector3Ds
Definition: VectorD.h:397
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
void read_particles_from_buffer(const base::Vector< char > &buffer, const ParticlesTemp &particles, const FloatKeys &keys)
load found attributes into the particles
Accelerated computation of the distance between two rigid bodies.
double get_distance(const Plane3D &pln, const Vector3D &p)
Return the distance between a plane and a point in 3D.
Definition: Plane3D.h:71
Simple Brownian dynamics simulator.
void transform(Hierarchy h, const algebra::Transformation3D &tr)
Transform a hierarchy. This is aware of rigid bodies.
core::XYZR create_cover(const Selection &s, std::string name=std::string())
The standard decorator for manipulating molecular structures.
Simple molecular dynamics optimizer.
Display an IMP::SingletonContainer of IMP::atom::Hierarchy particles as balls.
A decorator for wrapping a particle representing a molecular bond.
A decorator for a particle representing an atom.
Definition: atom/Atom.h:234
void write_map(DensityMap *m, std::string filename, MapReaderWriter *writer)
Write a density map to a file.
Bond create_bond(Bonded a, Bonded b, Int t)
Connect the two wrapped particles by a bond.
base::Vector< char > write_particles_to_buffer(const ParticlesTemp &particles, const FloatKeys &keys)
return a binary buffer with the data
IMP::kernel::Refiner Refiner
#define IMP_DECORATOR_SETUP_0(Name)
A base class for classes which perturb particles.
IMP::kernel::Model Model
BoundingBoxD< 3 > get_bounding_box(const Cone3D &g)
Definition: Cone3D.h:64
double evaluate(bool tf, bool warn=true)
bool get_are_almost_equal(const double a, const double b, const double epsilon)
Compares two values (intended for doubles)
Key< 3, true > ParticleIndexKey
The type used to identify a particle attribute in the Particles.
std::string show_graphviz(Graph g)
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
A restraint is a term in an IMP ScoringFunction.
VectorD< D > get_random_vector_in(const BoundingBoxD< D > &bb)
Generate a random vector in a box with uniform density.
double get_surface_area(const Cone3D &g)
Definition: Cone3D.h:64
double get_density(const DensityMap *m, const algebra::Vector3D &v)
Hierarchy read_mol2(base::TextInput mol2_file, kernel::Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
Out gather(H h, F f, Out out)
Gather all the particles in the hierarchy that meet some criteria.
FloatPair get_surface_area_and_volume(const algebra::Sphere3Ds &ss)
void write_mol2(Hierarchy rhd, base::TextOutput file_name)
Write a ligand hierarchy as a mol2 file.
Display a Bond particle as a segment.
Abstract predicate function.
Class to handle individual model particles.
void handle_error(const char *msg)
Rotation2D get_rotation_to_x_axis(const Vector2D &v)
Definition: Rotation2D.h:100
Vector3D get_transformed(const Vector3D &o) const
transform
A decorator for a particle that is part of a rigid body but not rigid.
Definition: rigid_bodies.h:498
An axis-aligned bounding box.
Definition: BoundingBoxD.h:27
IMP::kernel::Sampler Sampler
Vector3D get_centroid(const Vector3Ds &ps)
Returns the centroid of a set of vectors.
Definition: Vector3D.h:56
IMP::base::Vector< Ints > IntsList
Standard way to pass a bunch of Ints values.
Definition: types.h:56
Class to represent a 3D point in spherical coordinates.
Transformation3D get_identity_transformation_3d()
Return a transformation that does not do anything.
networkx::DiGraph get_networkx_graph(Graph g)
#define IMP_THROW(message, exception_name)
Throw an exception with a message.
Definition: check_macros.h:50
void show_altgraph(Graph g)
A decorator for a residue.
Definition: Residue.h:134
Transformation3D get_transformation_3d(const Transformation2D &t2d)
Builds a 3D transformation from a 2D one.
Display a plane as truncated to a bounding box.
base::Index< ParticleIndexTag > ParticleIndex
void show(Hierarchy h, std::ostream &out=std::cout)
Print out a molecular hierarchy.
IMP::base::Vector< Float > Floats
Standard way to pass a bunch of Float values.
Definition: types.h:47
IMP::kernel::Particle Particle
VectorD< 3 > Vector3D
Definition: VectorD.h:395
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
Rotation3D get_identity_rotation_3d()
Return a rotation that does not do anything.
Definition: Rotation3D.h:236
Hierarchy create_protein(kernel::Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
Create a coarse grained molecule.
Prevent a set of particles and rigid bodies from inter-penetrating.
#define IMP_LIST(protection, Ucname, lcname, Data, PluralData)
A macro to provide a uniform interface for storing lists of objects.
#define IMP_USAGE_CHECK(expr, message)
A runtime test for incorrect usage of a class or method.
Definition: check_macros.h:170
IMP::kernel::PairContainer PairContainer
virtual double do_optimize(unsigned int ns)=0
override this function to do actual optimization
Sphere3Ds get_simplified_from_volume(Sphere3Ds in, double maximum_allowed_error_angstroms)
IMP::kernel::OptimizerState OptimizerState
#define IMP_COMPARISONS_1(Name, field)
Implement comparison in a class using field as the variable to compare.
void apply(const SingletonModifier *sm) const
Apply a SingletonModifier to the contents.
IMP::kernel::Decorator Decorator
A decorator for a rigid body.
Definition: rigid_bodies.h:75
double get_rmsd_transforming_first(const Transformation3D &tr, const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Calculate the root mean square deviation between two sets of 3D points.
Dynamically build a histogram embedded in D-dimensional space.
Definition: HistogramD.h:27
IMP::kernel::SingletonScore SingletonScore
VectorD<-1 > VectorKD
Definition: VectorD.h:411
IMP::kernel::Restraint Restraint
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
IMP::kernel::RestraintSet RestraintSet
SphereD<-1 > SphereKD
Typedef for Python.
Definition: SphereD.h:87
Select hierarchy particles identified by the biological name.
Definition: Selection.h:62
Applies a list of movers one at a time.
Definition: SerialMover.h:23
Represent a sphere in D-dimensions.
Definition: SphereD.h:25
DensityMap * get_resampled(DensityMap *input, double scaling)
Get a resampled version of the map.
kernel::Restraint * create_restraint(Score *s, Container *c, std::string name=std::string())
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.
Display an IMP::atom::Hierarchy particle as balls.
Perform more efficient close pair finding when rigid bodies are involved.
Class for storing model, its restraints, constraints, and particles.
Definition: kernel/Model.h:73
Display an IMP::core::XYZR particle as a ball.
Definition: XYZR.h:149
ConnollySurfacePoints get_connolly_surface(const algebra::Sphere3Ds &spheres, double density, double probe_radius)
#define IMP_LIST_IMPL(Class, Ucname, lcname, Data, PluralData)
This should go in a .cpp file for the respective class.