4 # 2.21.0 - 2024-06-13 # {#changelog_2_21_0}
5 - The
new IMP::spatiotemporal module can be used to assist in building stepwise
6 spatiotemporal models, such as those we used to compute our model of
8 - The
new IMP::nestor module performs nested sampling-based optimization of
10 - This is the last version of IMP to support Python 2. Please port your
11 workflows to Python 3.
13 been removed; pass a list of chain IDs instead.
14 - The IMP::pmi::get_is_canonical
function has been removed; PMI no longer
15 supports the older PMI1-style hierarchies.
16 - .deb packages
for IMP
for Ubuntu LTS,
for both amd64 and arm64 architectures,
17 are now provided by an
19 - Many runtime checks on the VectorD and Array (e.g. used by ParticleIndexPair)
20 classes have now been moved to compile-time checks, which makes restraint
21 evaluation significantly faster in release builds, without sacrificing
24 # 2.20.2 - 2024-04-04 # {#changelog_2_20_2}
25 - Add support
for building ARM64 .deb packages.
26 - Bugfix: fix use of nested classes with latest SWIG.
27 - Bugfix: allow building with Boost 1.84.
28 - Bugfix: minor documentation corrections.
30 # 2.20.1 - 2024-01-16 # {#changelog_2_20_1}
31 - Bugfix: fix `soap_score` crash when scoring multiple models with an
32 orientation-dependent SOAP score.
33 - Bugfix: allow building with SWIG 4.2.
34 - Bugfix: various fixes
for Python 3.12.
36 # 2.20.0 - 2023-12-21 # {#changelog_2_20_0}
37 - The Windows .exe installer now supports Python 3.7 through 3.12.
38 - RPM packages
for IMP
for RedHat Linux (and clones such as Alma or Rocky)
39 and
for Fedora are now provided by the
41 Dependencies such as RMF and python-ihm are now packaged separately so that
42 they can be updated independently of IMP itself.
43 - We no longer provide packages
for Ubuntu 18.04 LTS (Bionic Beaver), as it
44 reached end of life in May 2023.
46 FASTA and PDB residue numbering, and the UniProt accession (
if known) of
47 the sequence. This information is also stored in RMF files.
48 - PMI
's FASTA file reader now reads the UniProt accession for each sequence,
50 - IMP::atom::ChainPDBSelector now takes a list of chain IDs, rather than a
51 single string, so that it can select chains with multi-character IDs.
52 When working with mmCIF files, it will now select based on the author-provided
53 chain ID, if available, for consistency with the naming of IMP::atom::Chain
55 - The IMP::rmf::load_frame and IMP::rmf::save_frame functions now warn if they
56 are called before links to IMP objects have been made (as this is a noop).
57 - IMP::saxs::Restraint has seen performance improvements, and will now use a
58 GPU for speedup if IMP is built with CUDA support.
59 - IMP::saxs::Restraint will now report an error if it is given invalid
60 particles; previously they would be silently ignored.
61 - The IMP::mmcif module has been rewritten to work with modern RMF files
62 and IMP::sampcon output.
63 - The `multi_foxs` command line tool now provides the same `--offset` option
65 - Model attributes can now use sparse rather than vector storage. This reduces
66 memory usage for attributes that are used by a minority of particles.
67 - Previous releases would erroneously allow a single Python string to be
68 passed to any method that wants a list of strings. This would split the
69 string into a list of single-character strings, which is often not was
70 intended. Such methods now require an explicit list (or tuple) of strings.
71 - The `IMP_NOEXCEPT` pre-C++11 compatibility macro has been removed; use
72 the C++ `noexcept` keyword instead.
73 - The CMake `IMP_PER_CPP_COMPILATION` and `IMP_CUDA` variables can now be set
74 to `ALL` to build all IMP modules one .cpp at a time, or with CUDA support,
76 - PMI no longer supports old PMI1-style hierarchies. The
77 IMP::pmi::get_is_canonical function, which detects PMI2-style hierarchies,
78 should thus be assumed to always return true, and has been deprecated.
79 - Windows builds now require MS Visual Studio 2017 or later.
80 - IMP::algebra::Rotation3D::get_derivative(),
81 IMP::algebra::Rotation3D::get_gradient(),
82 IMP::algebra::get_gradient_of_composed_with_respect_to_first(), and
83 IMP::algebra::get_gradient_of_composed_with_respect_to_second() have been
84 removed; instead use IMP::algebra::Rotation3D::get_gradient_of_rotated(),
85 IMP::algebra::Rotation3D::get_jacobian_of_rotated(),
86 IMP::algebra::get_jacobian_of_composed_wrt_first(), and
87 IMP::algebra::get_jacobian_of_composed_wrt_second(), respectively.
88 - The IMP::core::IncrementalScoringFunction class has been removed. Use
89 IMP::core::MonteCarlo::set_score_moved or
90 IMP::ScoringFunction::evaluate_moved instead.
91 - The IMP::em2d::CenteredMat and IMP::em2d::Fine2DRegistrationRestraint
92 classes, which are used only internally, have been removed.
93 - The base_utility.h and base_static.h headers have been removed; use utility.h
94 and static.h instead, respectively.
95 - The vector_property_map.h compatibility header has been removed;
96 use Boost's boost/property_map/property_map.hpp header instead.
98 # 2.19.0 - 2023-06-22 # {#changelog_2_19_0}
99 - Most IMP Value and Object types can now be serialized (or pickled in Python).
100 For example,
this can be used to save the current state of an
IMP::Model
101 or an IMP.pmi.macros.ReplicaExchange
object to be restored later or passed
102 to a separate process. Building IMP from source code now requires the
104 - Information on most IMP restraints, sampling protocols, input files and
105 analysis/clustering is now stored in the RMF file. Ultimately
this can be
106 used to generate an IHM mmCIF file directly from the RMF.
107 - IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint now
108 requires the `linker` argument, which specifies the chemistry of the linker.
109 - IMP.pmi.macros.ReplicaExchange0 has been removed.
110 Use IMP.pmi.macros.ReplicaExchange instead.
111 - The undocumented IMP::core::ConjugateGradients::set_threshold() method is
112 now deprecated; use set_gradient_threshold() instead.
113 - Rigid body members are now handled correctly by IMP::atom::destroy(),
114 and can be removed from their rigid body with a new
115 IMP::core::RigidBody::remove_member() method.
116 - The IMP::em2d::CenteredMat and IMP::em2d::Fine2DRegistrationRestraint
117 classes have been moved to the IMP::em2d::internal namespace, as they
118 are implementation details.
119 - Windows builds now require MS Visual Studio 2015 or later (for full C++11
120 support). The following macro for pre-C++11 environments is no longer
121 needed and is deprecated: `IMP_NOEXCEPT`.
122 - The following pre-C++11 compatibility macros and headers are removed:
123 `IMP_NULLPTR`, `IMP_NULLPTR_T`, `IMP_OVERRIDE`, `IMP_FINAL`, `IMP_UNIQUE_PTR`,
124 `IMP_FOREACH`, `IMP/
nullptr.h`, and `IMP/nullptr_macros.h`.
125 - The deprecated IMP::em::emreal type has been removed.
126 - The deprecated IMP::isd::Weight::get_nstates_key() method has been removed.
127 - The deprecated IMP.npc.npc_restraints module has been removed. Use
128 IMP.pmi.restraints.npc or IMP.pmi1.restraints.npc instead.
129 - The deprecated IMP::core::{Singleton,Pair,Triplet,Quad}Constraint constructors
131 removed. Use the constructors that take a Model and
ParticleIndex (etc.)
134 # 2.18.0 - 2022-12-15 # {#changelog_2_18_0}
135 - The Windows .exe installer now supports Python 3.11.
136 - The IMP::em::emreal type is deprecated; use plain `
double` instead.
138 so can be written to or read from a stream in C++ using the
139 Boost.Serialization library, or pickled in Python.
140 - IMP::atom::CHARMMTopology::add_sequence() now allows for full residue names
141 to be specified, to simplify construction of structures of DNA or RNA.
142 - IMP::atom::CHARMMTopology::create_hierarchy() now supports construction of
143 more than 26 chains, assigning them multi-character chain IDs.
144 -
Objects that contain lists of other objects now provide a list-like
object
145 in Python to simplify management of the list (e.g. IMP::RestraintSet now
146 contains a `restraints` member in Python which is a list of the IMP::Restraint
148 - The NPC-specific PMI restraints in the IMP.npc.npc_restraints module (which
149 only work with PMI1) are now provided in IMP.pmi.restraints.npc (for current
150 PMI) and IMP.pmi1.restraints.npc (for the old PMI1). IMP.npc.npc_restraints
151 itself is deprecated.
152 - IMP.pmi.macros.ReplicaExchange0 has been renamed to
153 IMP.pmi.macros.ReplicaExchange; the old name is still present but deprecated.
154 - The obsolete `sample_objects` and `crosslink_restraints` arguments to
155 IMP.pmi.macros.ReplicaExchange have been removed.
156 - Passing anything other than Monte Carlo movers in the
157 `monte_carlo_sample_objects` argument to IMP.pmi.macros.ReplicaExchange
159 - The IMP.sampcon module can now provide inputs for the PrISM method, and has
160 improved support for symmetry groups (requires pyRMSD 4.3.2 or later).
161 - Bugfix: move-aware scoring (see IMP::core::MonteCarlo::set_score_moved())
162 should now work correctly with nested
RestraintSets and/or non-default
164 - Bugfix: IMP::em::DensityMap::add() now invalidates any previously-calculated
165 RMS, so that followup calculations (e.g. of cross correlation) now work
167 - Bugfix: all C++ code now uses the same IMP random number generator, so
168 that resetting the seed now yields a consistent sequence of random numbers.
170 # 2.17.0 - 2022-06-23 # {#changelog_2_17_0}
172 as
this can be quite computationally expensive. If in doubt, call
174 - The IMP::em::CoarseCC class has been removed. Use similarly-named free
175 functions instead to calculate coarse cross correlation.
176 - The Windows .exe installer no longer supports Python 2 (it works with
177 Python 3.6 through 3.10).
178 - Binary packages are now provided for Ubuntu 22.04 LTS, Jammy Jellyfish
179 and RedHat Enterprise Linux 9 (and variants, such as Rocky or Alma).
180 - IMP now requires a C++11 compiler and SWIG 3 (or later) to build. Most
181 recent compilers should support C++11, such as gcc, clang
182 or MS Visual Studio 2012 or later. Various IMP macro and header workarounds
183 for pre-C++11 environments are thus no longer needed and are deprecated:
184 `IMP_NULLPTR`, `IMP_NULLPTR_T`, `IMP_OVERRIDE`, `IMP_FINAL`, `IMP_UNIQUE_PTR`,
185 `IMP_FOREACH`, `IMP/
nullptr.h`, and `IMP/nullptr_macros.h`.
186 - The IMP::core::IncrementalScoringFunction class is now deprecated. Use
187 IMP::core::MonteCarlo::set_score_moved or
188 IMP::ScoringFunction::evaluate_moved instead.
189 - A new application of IMP is now available:
190 - [Integrative modeling of nanobody binding modes to the SARS-CoV-2 Spike protein](https:
192 # 2.16.0 - 2021-12-16 # {#changelog_2_16_0}
193 - OpenCubicSpline now
throws a ValueException
for out-of-range values, to
194 be consistent with ClosedCubicSpline (previously it threw ModelException).
195 - SAXS tools (such as `compute_rg`, `foxs`) can now read input structures
197 - Most IMP functions that return arrays of integer or floating point values,
198 or lists of ParticleIndexes, now return NumPy arrays if IMP is built with
199 NumPy. Code that adds lists or searches for particle pairs in a list may
200 need to be modified as NumPy arrays are slightly different from Python lists.
201 - IMP::pmi now handles MSE (selenomethionine) residues in input structures;
202 structure is read for such residues and they are considered equivalent to
203 regular MET in the FASTA sequence.
204 - The Windows .exe installer now supports Python 3.10.
205 - Scoring function evaluation can now be done more efficiently in some cases
206 by using information on which particles have moved since the last evaluation.
207 This behavior can be turned on (by default it is off) using
208 IMP::core::MonteCarlo::set_score_moved() or by setting the `score_moved`
209 parameter to IMP::pmi::macros::ReplicaExchange0.
210 - The orientation-dependent scoring function IMP::score_functor::OrientedSoap
211 now caches the system topology and so should be roughly twice as fast in
212 typical applications.
213 - IMP::pmi::macros::BuildSystem::add_state() now assigns multi-character
214 chain IDs by default, so that it is no longer limited to creating 62
216 - IMP::pmi::output::Output now reports a ValueError if asked to write out
217 a PDB file containing multi-character chain IDs, rather than silently
219 - The unused IMP::piecewise_linear_distribution class has been removed.
220 Use boost::piecewise_linear_distribution instead.
221 - The deprecated methods
222 IMP::{Singleton,Pair,Triplet,Quad}Predicate::get_value() have been removed.
223 Use the get_value_index() methods instead.
224 - The deprecated methods IMP::SingletonContainer::
get_particles(),
225 IMP::PairContainer::get_particle_pairs(),
226 IMP::TripletContainer::get_particle_triplets(), and
227 IMP::QuadContainer::get_particle_quads() have been removed. Use the
228 get_contents() method instead.
229 - The deprecated IMP::isd::Weight::get_number_of_states() method has been
230 removed. Use get_number_of_weights() instead.
231 - We no longer provide packages for Ubuntu 16.04 LTS (Xenial Xerus), as it
232 reached end of life in April 2021.
234 # 2.15.0 - 2021-06-02 # {#changelog_2_15_0}
235 - The [Homebrew](https:
236 - We no longer provide RPMs
for CentOS 6, since it has reached end of life.
237 - Python 2.6 is no longer supported; Python 2.7 is the oldest version of
238 Python that works with IMP (although Python 3 is recommended).
239 - IMP now requires Boost 1.53 or later; support
for Boost 1.41 has been dropped.
240 - IMP::em::FitRestraint::cast() has been removed. Use `get_from()` instead.
241 - The deprecated methods IMP::SingletonContainer::get_particle(),
242 IMP::PairContainer::get_particle_pair(),
243 IMP::TripletContainer::get_particle_triplet(), and
244 IMP::QuadContainer::get_particle_quad() have been removed. Use the
245 get_contents() method instead.
246 - The IMP::em::CoarseCC class is deprecated. Use similarly-named free
247 functions instead to calculate coarse cross correlation.
248 - A new numerically stable grid-based Bayesian scoring function,
249 IMP::em::FitRestraintBayesEM3D, has been added for cryo-EM data. Note that
250 this is still in development.
251 - The IMP::pmi::mmcif::ProtocolOutput constructor no longer takes a file
252 handle argument, and the IMP::pmi::mmcif::ProtocolOutput::flush() method
253 has been removed. Instead, use the python-ihm library to output mmCIF
255 - IMP can now be built using external (system) copies of the RMF and/or
256 python-ihm libraries, instead of those bundled with IMP itself; use the
257 `IMP_USE_SYSTEM_RMF` or `IMP_USE_SYSTEM_IHM` CMake variables.
258 - MRC file handling has been extended; MRC files not aligned with the xyz
259 axes (mapc/mapr/maps not 1,2,3) are now automatically transposed rather than
260 raising an exception, and the origin is now set from the
261 nxstart/nystart/nzstart fields if present and the file origin is zero.
262 - New applications of IMP are now available:
263 - [Integrative model of the γTuSC-Spc110 complex](https:
264 - [Integrative structure of the Smc5/6-Nse2/5/6 complex](https:
265 - IMP's copies of the old Template Numerical Toolkit (TNT) and
266 JAMA/C++ library have been removed from IMP::algebra::internal.
267 Use equivalent functionality in the Eigen library instead.
269 # 2.14.0 - 2020-12-02 # {#changelog_2_14_0}
270 - All IMP.parallel worker classes are now subclasses of IMP.parallel.Worker;
271 the old
class names still exist as aliases, but are deprecated.
272 - The IMP.kinematics module has had a major overhaul.
273 - The Windows .exe installer now supports Python 3.9, and has dropped support
275 - New applications of IMP are now available:
276 - [Integrative structures of the Nef-CD4-AP2 complex](https:
277 - [Integrative Modeling of Yeast Exocyst Complex](https:
278 - [Integrative threading of protein structure using secondary structure elements](https:
279 - Bugfix: fix near-infinite loop in FoXS JavaScript output when no models
281 - Bugfix: IMP.saxs.Restraint should now work correctly when some or all
282 particles are members of rigid bodies.
284 # 2.13.0 - 2020-05-14 # {#changelog_2_13_0}
285 - Ubuntu .deb packages now use Python 3 by default (install the imp-python2
286 package if you want to use Python 2) and support MPI (install the
287 imp-openmpi package if you want to use the IMP::mpi or IMP::spb modules).
288 - A binary package is now provided for Ubuntu 20.04 LTS, Focal Fossa.
289 - The new IMP::sampcon module implements the protocol described in
290 [Viswanath et al, 2017](https:
291 This can be used in analysis to estimate the highest precision at which
292 the sampling is exhaustive.
293 - RMF files, particularly those output by IMP::pmi, now contain more information
294 on the restraints used, such as restraint parameters, and links to
295 non-Cartesian particles containing restraint information, such as Gaussians
296 used to represent EM densities, or Bayesian nuisances. Much of this
297 information can now be shown in
300 - IMP modules that contain no C++ code can now be marked as "Python only"
301 in `dependencies.py`. IMP::test, IMP::mmcif, IMP::parallel, IMP::EMageFit,
302 IMP::pepdock, and IMP::saxs\_merge are so marked. This speeds up the build
303 since such modules do not need to be run through SWIG or compiled, and
304 saves space by eliminating their shared libraries.
305 - The `crosslink_restraints` argument to IMP.pmi.macros.ReplicaExchange0
306 is now ignored (and deprecated). All cross-link restraints are now
307 automatically added to RMF files.
308 - The `CrossLinkDataBase` argument to
309 IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
310 is deprecated. Use `database` instead.
311 - IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint now
312 takes a `linker` argument which can be used to specify the chemistry of
314 - IMP.pmi.output.Output now supports output of pseudo-atomic PDBs in mmCIF
315 format. This can be useful for quick visualization of output models that
316 contain a large number of chains in software that does not understand
317 the mmCIF IHM extension (for integrative models) or RMF.
318 - IMP.pmi now has improved support for RNA/DNA (previously all nucleic acid
319 residues were treated as RNA). IMP.pmi.topology.Molecule now takes an
320 `alphabet` argument which can be used to specify any of the alphabets
321 provided in the IMP.pmi.alphabets module (amino acids, RNA, or DNA) or a
323 - A new application of IMP is now available:
324 - [Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling](https:
325 - 'Object "foo" never used' warnings are now emitted only when IMP is run with
326 internal checks turned on, as these warnings are primarily intended for
327 IMP developers, not end users.
328 - Bugfix: fix infinite loop when reading some corrupt mol2 files.
330 # 2.12.0 - 2019-12-06 # {#changelog_2_12_0}
331 - The Windows .exe installer now supports Python 3.8, and has dropped support
333 - Packages are no longer provided for Ubuntu 14.04 (Trusty Tahr) since
334 it has reached end of life.
335 - The IMP distribution now includes the IMP::bayesianem module developed at
336 Institut Pasteur, Paris, for Bayesian handling of cryo-electron microscopy
337 density map data. See Bonomi et al. at https:
339 - The old IMP::pmi::representation::Representation class has been removed
340 from IMP.pmi. New applications should use IMP::pmi::topology::System instead.
341 - The IMP::pmi::restraints::crosslinking::ISDCrossLinkMS class for handling
342 crosslinking has been removed. Use
343 IMP::pmi::restraints::crosslinking::CrossLinkingMassSpectrometryRestraint
345 - The `rg` tool (part of the IMP::saxs module, used to compute radius of
346 gyration from a SAXS profile) is now called `compute_rg` for consistency
347 with other SAXS tools and to avoid conflicts with other packages.
348 - We now provide RPM packages for RedHat Enterprise Linux 8 (or compatible
349 operating systems such as CentOS 8).
350 - The RPM packages for RedHat Enterprise Linux 8 and for Fedora now use
351 Python 3 by default. If you need Python 2, install the IMP-python2 package
353 - IMP::algebra::Rotation3D::get_derivative(),
354 IMP::algebra::Rotation3D::get_gradient(),
355 IMP::algebra::get_gradient_of_composed_with_respect_to_first(), and
356 IMP::algebra::get_gradient_of_composed_with_respect_to_second() have been
357 deprecated and are superseded by
358 IMP::algebra::Rotation3D::get_gradient_of_rotated(),
359 IMP::algebra::Rotation3D::get_jacobian_of_rotated(),
360 IMP::algebra::get_jacobian_of_composed_wrt_first(), and
361 IMP::algebra::get_jacobian_of_composed_wrt_second(), respectively. By
362 default, the derivatives are now computed with respect to the unnormalized
363 quaternion and do not include the normalization operation.
364 - New methods are added to compute adjoint derivatives (reverse-mode
365 sensitivities) for compositions and actions of IMP::algebra::Rotation3D and
366 IMP::algebra::Transformation3D upon 3D vectors.
367 - Fixed a bug in nested rigid body derivative accumulation, where derivatives
368 with respect to quaternions were incorrectly projected to be orthogonal to
370 - Reimplemented rigid body derivative accumulation to use the new adjoint
371 methods. The many-argument versions of
372 IMP::core::RigidBody::add_to_derivatives(),
373 IMP::core::RigidBody::add_to_rotational_derivatives(), and
374 IMP::core::NonRigidMember::add_to_internal_rotational_derivatives(), which
375 previously pulled adjoints from member global reference frame to member
376 local reference frame and parent global reference frame are now deprecated.
377 Pullback functionality is now handled by
378 IMP::core::RigidBody::pull_back_members_adjoints().
379 - IMP::isd::Weight is now constrained to the unit simplex, and methods were
380 added for adding to its derivatives. IMP::isd::Weight::add_weight() no longer
381 resets all the weights to the barycenter of the unit simplex and instead
382 initializes the new weight to 0. IMP::isd::Weight::get_number_of_states()
383 and IMP::isd::Weight::get_nstates_key() were deprecated and superseded by
384 IMP::isd::Weight::get_number_of_weights() and
385 IMP::isd::Weight::get_number_of_weights_key(), respectively.
387 # 2.11.1 - 2019-07-18 # {#changelog_2_11_1}
388 - Bugfix: fix build system failures with CMake 3.12 and 3.13, and on Windows.
389 - Bugfix: IMP::atom::create_clone() now always copies mass, even of particles
391 - Bugfix: IMP::rmf::create_hierarchies() should no longer fail with
392 "The filename cannot be empty".
394 # 2.11.0 - 2019-06-25 # {#changelog_2_11_0}
395 - A number of new tutorials are now available covering a variety of topics
396 from modeling complexes with IMP::pmi to writing new C++ code. See
397 the [tutorial index](https:
399 - The build system has been updated to use new CMake functionality
400 (if available) to detect Python. If you have CMake 3.14 or later, this should
401 do a much better job of handling multiple Python installations (e.g. Macs
402 with Homebrew). It will default to using Python 3. To force use of Python 2,
403 pass `-DUSE_PYTHON2=on` to your CMake invocation.
404 - CMake files are now provided to make it straightforward to use IMP as
405 a library in other programs. See
406 [the tutorial](https:
408 - CMake files are now provided to build new IMP modules outside of the IMP
409 build tree (i.e. a module can be built against an IMP binary).
410 - The IMP::OptionParser class has been removed. Use IMP::ArgumentParser instead.
411 - The IMP::test::TempDir and IMP::test::RunInTempDir utility classes have been
412 removed. Use the IMP::test::temporary_directory and
413 IMP::test::temporary_working_directory context managers instead.
415 # 2.10.1 - 2019-02-26 # {#changelog_2_10_1}
416 - Add support for OpenCV 4.
417 - Fix IMP::isd `create_gmm.py` script to handle command line options correctly.
418 - Command line tools in the Mac and Ubuntu packages should now use system
419 Python (/usr/bin/python), not the first Python (e.g. Anaconda Python)
420 found in PATH (which might not be compatible with IMP's Python libraries).
422 # 2.10.0 - 2019-01-08 # {#changelog_2_10_0}
423 - Applications using IMP::pmi should now use the IMP::pmi::topology::System
424 class to set up the system (sometimes referred to as "PMI2"), rather than
425 the older IMP::pmi::representation::Representation class ("PMI1").
426 This new class is faster and produces standard IMP Hierarchy objects. The
427 old PMI1-style classes are deprecated in this release and will be removed
428 in the next one. For support of published studies using "PMI1", a legacy
429 IMP::pmi1 module is provided (to use it, simply replace all imports of
430 "IMP.pmi" with "IMP.pmi1"). This module will receive only minor bug fixes,
432 - All IMP Python command line tools now use
435 options, as optparse is deprecated in modern Python versions. The
436 IMP::OptionParser class, which extends optparse to add standard IMP options,
437 is now deprecated. Use the similar IMP::ArgumentParser class instead.
438 - The bundled copy of [python-ihm](https:
439 updated to the latest release. This supports faster (C-accelerated) reading
440 of mmCIF files, read and write support for BinaryCIF files, and support
441 for output of PMI2-style models. The new IMP::atom::read_mmcif function
442 allows reading a PDB file in mmCIF format, similarly to the existing
443 IMP::atom::read_pdb function.
444 - A new application of IMP is now available:
445 - [Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1](https:
446 - The deprecated IMP::isd::FNormal::density() method has been removed.
447 Use IMP::isd::FNormal::get_density() instead.
448 - Handling of quaternions (for example in the calculation of rotational
449 derivatives) is now faster and more numerically stable.
450 - IMP::mpi now includes a workaround for an OpenMPI failure when used
451 with Python, so previous hacks (building OpenMPI with the
452 `--disable-dlopen` flag, or using `sys.setdlopenflags` in Python)
453 should no longer be necessary.
455 # 2.9.0 - 2018-07-02 # {#changelog_2_9_0}
457 - The Windows .exe IMP installer no longer supports Python 2.6. Python 2.7,
458 3.4, 3.5, and 3.6 are supported by this installer.
459 - A binary package is now provided for Ubuntu 18.04 LTS, Bionic Beaver.
460 - The IMP::atom::setup_as_rigid_body() function has been removed.
461 Use IMP::atom::create_rigid_body() instead.
462 - Constructors for IMP::container classes, IMP::core::BallMover,
463 IMP::core::RigidBodyMover, and IMP::core::IncrementalScoringFunction taking
464 a RigidBody or Particles have been removed. Use constructors taking
465 ParticleIndexes instead.
466 - The IMP::core::ConnectivityRestraint::get_connected_pairs() method has been
467 removed. Use get_connected_index_pairs() instead.
468 - The stats() profiling method has been removed from
469 IMP::isd::GaussianProcessInterpolationRestraint and
470 IMP::isd::MultivariateFNormalSufficient. Use a third party package (such as
471 gperftools) for profiling instead.
472 - Scores in IMP.saxs (and FoXS) now use the chi-square value rather than chi.
473 - New applications of IMP are now available:
474 - [Modeling of the entire yeast nuclear pore complex](https:
475 [modeling of the flexible FG regions](https:
476 modeling of the individual [Nup133](https:
479 - [Modeling of the Ecm29-proteasome complex](https:
480 - The new modules IMP::npc and IMP::npctransport provide specialized
481 restraints and other functionality for modeling static nuclear pore complex
482 structures and transport through these structures, respectively, although
483 may also be useful for other modeling applications.
484 - IMP's mmCIF support for deposition of models in
486 now utilizes the [python-ihm](https:
487 a copy of which is included with IMP.
488 - RMF files now store additional metadata, such as the primary sequence of
489 each chain, software used, information on each restraint (such as fit values),
490 and provenance (classes derived from IMP::core::Provenance) that describes
491 transformations of the system, such as initial input from a PDB file,
492 sampling, clustering, and filtering.
493 - The new experimental IMP::mmcif module allows generating basic mmCIF files
494 directly from an IMP::Model and/or RMF files.
496 # 2.8.0 - 2017-08-16 # {#changelog_2_8_0}
497 - New applications of IMP are now available:
498 - [Modeling of the yeast Spindle Pole Body core](https:
499 - [Modeling of the SEA complex, a modulator of the TORC1 pathway](https:
500 - This will be the last release that includes packages for Ubuntu 12.04
501 (Precise Pangolin) since it has reached end of life. We will continue to
502 provide packages for newer Ubuntu LTS releases.
503 - The Anaconda and Windows .exe packages are now MPI-enabled. On Windows, in
504 order to use MPI, install [MS-MPI](https:
505 - IMP::em2d::PCAFitRestraint now uses binary PGM files as output, rather than
506 the less well supported text PGM format. (It can still read both text and
507 binary PGM files as input.)
508 - IMP::em::FitRestraint::cast() is deprecated. Use `get_from()` instead.
509 - The deprecated profiling (timing statistics) support has been removed.
510 A number of third party packages (such as gperftools) are available
511 for profiling and should be used instead.
512 - The new module IMP::spb provides specialized restraints, samplers, and
513 other objects to support modeling of the Spindle Pole Body (SPB). While
514 designed specifically for this system, they may be useful for modeling
517 # 2.7.0 - 2017-04-13 # {#changelog_2_7_0}
518 - New applications of IMP are now available:
519 - [Modeling of the yeast Mediator complex](https:
520 - [Modeling of the yeast and human TFIIH complex](https:
521 - [Modeling of complexes between the 26S proteasome and proteasome interacting proteins](https:
522 - [Human Complement modeling](https:
523 - [Modeling of a region of the fly genome](https:
524 - Memory and CPU performance improvements across the code, particularly
526 - Preview of mmCIF support for deposition of integrative models in
528 module for more details.
529 - This will be the last release that includes packages for RedHat Enterprise
530 Linux 5 (and variants, such as CentOS 5), since RHEL 5 has reached end
532 - The IMP::em::SurfaceShellDensityMap::binaries() method has been replaced
533 with the (correctly spelled) IMP::em::SurfaceShellDensityMap::binarize()
535 - IMP::multifit::WeightedExcludedVolumeRestraint no longer expects that the
536 IMP::core::RigidBody particles it acts on are also IMP::atom::Hierarchy
537 objects. Use an IMP::multifit::RigidLeavesRefiner in place of
538 IMP::core::LeavesRefiner to get the old behavior.
539 - IMP::modeller::MultipleBinormalRestraint has moved to the IMP::core
541 - The IMP::core::setup_as_rigid_body() method has been removed.
542 Use IMP::core::create_rigid_body() instead.
543 - IMP::test:TempDir and IMP::test::RunInTempDir are deprecated in favor
544 of similar functions that work as Python context managers
545 (IMP::test::temporary_directory() and IMP::test::temporary_working_directory()
548 # 2.6.2 - 2016-05-25 # {#changelog_2_6_2}
549 - Add support for SWIG 3.0.8.
550 - Add support for Ubuntu 16.04, Xenial Xerus.
551 - Minor documentation fixes.
552 - Bugfix: fix detection of termini in IMP::atom::Selection.
554 # 2.6.1 - 2016-04-14 # {#changelog_2_6_1}
555 - The 'cluster' binary is now called 'rmsd_cluster' to avoid conflicts with
556 other packages (e.g. graphviz also provides a 'cluster' binary).
557 - Minor bug fixes to PMI.
558 - Minor documentation fixes.
560 # 2.6.0 - 2016-03-28 # {#changelog_2_6_0}
561 - This release includes most of the functionality of PMI2. This is an improved
562 version of PMI that is faster than PMI1, more modular, and easier to use.
563 See IMP::pmi for more information.
564 - A new application of IMP is now available:
565 [Modeling of exosome complexes from cross-link MS data](http:
566 - The IMP::base and IMP::kernel namespaces have been removed (use the top-level
567 IMP namespace instead).
568 - The IMP::display::ChimeraWriter class has been removed (use IMP::rmf instead).
569 - IMP::Model no longer has an implicit scoring function. This means that
570 Model::evaluate() and Model::add_restraint() have been removed (use an
571 IMP::ScoringFunction instead). IMP::Optimizer and IMP::Sampler now also
572 require an IMP::ScoringFunction to be explicitly set before they are used.
573 - IMP::atom::Hierarchy::get_as_xxx() methods are deprecated; use regular
574 decorators instead. For example, instead of h.get_as_residue() use
575 Residue(h). If you want to check for validity first,
576 use Residue::get_is_setup(h).
577 - IMP::atom::Selection can now select by element.
578 - IMP::modeller::load_restraints_file() and IMP::modeller::read_pdb() have
579 been removed. Use the IMP::modeller::ModelLoader class instead.
580 - IMP::atom::PDBSelector subclasses are more flexible, with a new
581 IMP::atom::XorPDBSelector class, and can be combined using standard
582 Python operators, in similar fashion to sets (&, |, ^, -, ~ operators).
583 - The following modules that use FFTW (which is licensed under the GPL)
584 are themselves now also licensed under the GPL: IMP::EMageFit,
585 IMP::cnmultifit, IMP::em2d, IMP::integrative_docking, and IMP::multifit.
586 - Bugfix: sampled EM density maps should now handle resolution correctly; maps
587 generated by the fixed code agree well with those generated by EMAN. The old
588 radius-dependent kernel parameter code is no longer used.
590 # 2.5.0 - 2015-06-30 # {#changelog_2_5_0}
591 - Documentation has been revised and updated; the main manual now gives a
592 gentler introduction to IMP, with more technical details on the code
593 provided in a separate reference guide.
594 - The IMP::base and IMP::kernel namespaces are now deprecated. Functionality
595 in both base and kernel now lives in the top-level "IMP" namespace.
596 - IMP::atom::Selection::get_selected_particle_indexes() has a new
597 'with_representation' parameter. If turned on (the default), Selection
598 returns all representational (XYZ) particles that match the request -
599 for example, selecting a residue will typically return all of its atoms.
600 If turned off, Selection returns the highest matching particle instead -
601 so, in this case, the residue particle itself.
602 - All IMP::RAII objects (e.g. IMP::SetLogState) now support the context
603 manager protocol in Python (e.g. "with IMP.SetLogState() as s:")
604 - Several long-deprecated functions have been removed. These include:
605 - Several Restraint constructors that take Particles. Use equivalent
606 constructors that take an IMP::Model pointer and ParticleIndexes instead.
607 - IMP::core::MonteCarlo::get_number_of_forward_steps() (use
608 get_number_of_accepted_steps() instead).
609 - IMP::Model::remove_restraint(), IMP::Model::get_restraints(),
610 IMP::Model::get_number_of_restraints(), IMP::Model::get_restraints().
611 Store your restraints in an IMP::RestraintSet or use an
612 IMP::core::RestraintsScoringFunction. Related methods such as
613 IMP::Model::evaluate() will be removed in the next IMP release.
614 - IMP::Model::set_maximum_score() and related methods. Set the maximum
615 scores on the IMP::Restraint or IMP::RestraintSet directly, using
616 IMP::Restraint::set_maximum_score().
617 - IMP::Restraint::get_input_containers() and
618 IMP::Restraint::get_input_particles(). Use IMP::Restraint::get_inputs()
619 instead (similarly for get_outputs()).
620 - IMP::rmf::save_frame() no longer takes a frame index argument (it was
621 previously ignored anyway).
622 - Several functions have been deprecated in this release (and will be removed
623 in the next). These include several Restraint constructors that take Particle
624 or Particles objects (use constructors that take an IMP::Model and
625 ParticleIndex or ParticleIndexes instead); and add_particle*(),
626 set_particle*() and clear_particle*() in several Container objects (use add(),
627 set() and clear() with particle indexes instead).
628 - On platforms that support it, OpenMP is turned on by default. To speed up
629 some parts of IMP, call IMP::base::set_number_of_threads(). By default,
630 only a single thread is used.
631 - The RPM packages now include an -mpich subpackage that can be installed
632 to enable parallel computation, using the IMP.mpi module in concert
633 with the mpich library.
634 - We now provide packages for both of the currently-supported Ubuntu LTS
635 releases: Ubuntu 12.04 (Precise Pangolin) and Ubuntu 14.04 (Trusty Tahr).
636 - The default log level has changed from NONE to WARNING.
637 - A new command line tool, `multi_foxs`, allows for enumeration and scoring
638 of multi-state models against SAXS profiles.
639 - A new command line tool, `ligand_score_multiple`, acts similarly to the
640 existing `ligand_score` tool but scores each ligand pose generated by
641 docking software (such as PatchDock).
642 - New applications of IMP are now available:
643 - [Multi-state modeling of the histidine kinase, PhoQ](http:
644 - [Determination of the molecular architecture of the 40S⠢eIF1•eIF3 translation initiation complex](http://salilab.org/40S-eIF1-eIF3).
- IMP::domino::DiscreteSampler::set_restraints() now allows the set of
restraints used in DOMINO filtering to be controlled (previously, all
restraints in the IMP::Model were used).
- IMP::modeller::IMPRestraints now transfers an IMP::ScoringFunction into the
MODELLER score, not the implicit (and deprecated) score of the
entire IMP::Model.
- Bugfix #775: coordinates of voxels in EM maps were previously inconsistently
treated (they are supposed to be the centers of the voxels, but in some
cases they were the lower left edge). The fix may result in maps and their
bounding boxes appearing shifted by half the voxel size.
# 2.4.0 - 2015-02-27 # {#changelog_2_4_0}
- Python 3 is now supported. The Windows package now works out of the box
with Python 3.3 or 3.4; a `-python3` subpackage is provided for Ubuntu
and Fedora. (Apple does not yet provide Python 3 so the Mac package is not
built with Python 3 support, but if you install Python 3 you can compile
IMP from source to work with it.)
- A new command line tool, `rrt_sample`, allows for running rapidly exploring
random tree (RRT) based sampling, e.g. to sample conformations of multiple
domains connected by flexible linkers.
- Command line tools are now placed in the `bin` directory of modules (the
old `bin` directory, used for utility programs that are not installed, is
now called `utility`). The `applications` directory is removed.
- Several Python modules that were only used by EMageFit have been moved from
IMP::em2d to IMP::EMageFit.
- A new tutorial that uses the IMP::pmi module is now available (modeling of
the RNA Polymerase II stalk).
# 2.3.1 - 2014-12-01 # {#changelog_2_3_1}
- Minor bug fixes.
- Update to IMP::pmi to support the Nup84 and rnapolii biological systems.
# 2.3.0 - 2014-10-24 # {#changelog_2_3_0}
- 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.
- Binary installers for 64-bit Windows are now available.
- The `.py` extension has been removed from all Python applications, so that they are consistent with the C++ applications.
- 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.
- The integrative docking (idock) application now employs SOAP to improve the scoring.
- 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.
- 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.
# 2.2.1 - 2014-08-11 # {#changelog_2_2_1}
- Bugfix: PoseScore (see the ligand_score application) should now match that used by the Pose&Rank web server (http://salilab.org/poseandrank/)
# 2.2.0 - 2014-04-09 # {#changelog_2_2_0}
- 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.
- The Python support for grids was cleaned up. Hopefully this makes it more robust. If you were using a grid in Python that no longer exists, ping us, we can add it back.
- The generic geometry functions were simplified slightly and renamed to IMP::algebra::get_vector_geometry().
- The IMP::base::Flag class was added to simplify adding flags in C++.
- The `--log_level` and `--check_level` command line argument now take strings (eg VERBOSE) to specify their values, rather than cryptic (and a bit unstable) numbers.
- Command line options are now divided into normal and advanced ones. You do `--help_advanced` to show the advanced ones.
- Support for computing Connolly surfaces was added with IMP::algebra::get_connolly_surface(). In addition, there is now IMP::algebra::get_uniform_surface_cover(const IMP::algebra::Sphere3Ds&,double) to sample the surface of a collection of balls.
- IMP::atom::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.
- IMP::atom::get_rmsd(IMP::atom::Selection, IMP::atom::Selection, const IMP::algebra::Transformation3D&) was deprecated. Use IMP::atom::get_rmsd_transforming_first() instead.
- IMP::algebra::get_rmsd() and IMP::algebra::get_rmsd_transforming_first() were added.
- The family of macros IMP_BASE_[SMALL,LARGE]_[UNORDERED,ORDERED]_[MAP,SET] have been added (eg IMP_BASE_SMALL_ORDERED_SET ()). They provide platform and boost-version independent ways to take advantage of the best set/map for an application. In particular, they use boost::container::flat_set and kin when available.
- IMP::atom::State and IMP::atom::Representation decorators have been added to provide support for multiple states and multiple representation schemes. They are integrated with RMFs and IMP::atom::Selection. See atom/multiresolution.py and atom/multistate.py for examples.
- The container implementations has been cleaned up and simplified a bit. This should not change most usage.
- [RMF](http://salilab.github.io/rmf) has been updated. There are a few minor API changes, in addition to a new, faster format (`.rmf3`).
- [Eigen](#Eigen) is now included with IMP.
- The deprecated function IMP::kernel::Optimizer::set_restraints() was removed. Use IMP::kernel::Optimizer::set_scoring_function() instead.
- The deprecated constructor for IMP::kernel::ModelObject that does not take an IMP::kernel::Model was removed. This propagates to constructors IMP::kernel::Restraint, IMP::kernel::ScoreState and kin. Make sure you pass an IMP::kernel::Model as the first constructor argument. Related to this, deprecated functions like get_is_part_of_model(), set_model() were removed as they don't serve any purpose.
- The deprecated methods in IMP::kernel::Optimizer that pertain to attribute optimization were removed. Inherit from IMP::kernel::AttributeOptimizer instead if you want to use them in your optimizer.
- Some deprecated functionality was removed. If you encounter problems, replace IMP::base::OwnerPointer with IMP::base::PointerMember, find logging stuff in IMP/base/log.h, object in IMP/base/Object.h and random in IMP/base/random.h.
- IMP::atom::Chain now uses strings for the chain ids, to be consistent with changes in the PDB. PDB files are written using the first character of the chain string.
- Added orientation-dependent SOAP scoring (IMP::score_functor::OrientedSoap and IMP::atom::OrientedSoapPairScore). Orientation-dependent SOAP scores include those that score loops (SOAP-Loop), protein-peptide interfaces (SOAP-Peptide) and proteins (SOAP-Protein). The library files themselves are rather large (~1.5GB) and so are not included with IMP. They can be downloaded separately from http://salilab.org/SOAP/.
# 2.1.1 - 2013-11-04 # {#changelog_2_1_1}
- Added support for Mac OS 10.9
# 2.1.0 - 2013-10-24 # {#changelog_2_1_0}
- 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.
- 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.
- Class name OwnerPointer was switched to PointerMember, to denote more clearly a ref-counting pointer that is a class member.
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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`).
- 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.
- 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.
- 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.
- [RMF](https://github.com/salilab/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.
# For IMP 2.0 and earlier # {#changelog_2_0}
## Spring 2013
- Modules and applications now have a _Maintainer_ in their `README.md`, giving the github id of the person to whom issues should be assigned.
- `setup_git.py` supports the `--module` flag which will set up git hooks and things for a git repository that contains a module.
- 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.
- 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.
## Winter 2012-2013
- Scons support was removed. Use cmake to build IMP, it is way better.
- 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.
- 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.
- The IMP_BIG_ENDIAN and IMP_LITTLE_ENDIAN preprocessor symbols are deprecated in favor of the BOOST_BIG_ENDIAN and BOOST_LITTLE_ENDIAN symbols.
- 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.
- 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.
- You can now (probably) build IMP with [CMake on IMP wiki](https://github.com/salilab/imp/wiki/Cmake).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- OpenMP support in IMP is officially released. All tests pass. But there has been little specific testing so far.
- Access to attributes using IMP::ParticleIndex and the IMP::Model now works from Python. See IMP::Model::add_attribute() and kin.
- 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.
- 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.
- 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.
- 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 beginning. You can use `./tools/updaters/update_examples.py modules/mymodule` to update a module that was not already updated.
- IMP::base::FailureHandler has been removed as it wasn't used.
- 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.
- Modules now must be in a folder called `modules`, which must have a `description.py` file.
- The build system should now be a little better about cleaning up after itself.
- How headers/doc files/data/examples
- 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 "_" from the method name.
- Nice version numbers will now be generated if you use git. You need to rerun
tools/git/developer_tools/init_git if you have an existing clone.
## Fall 2012
- 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.
- 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.
- 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.
- 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.
- 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.
- 11/8; Evaluation with containers was greatly simplified, moving many methods on containers. We can add backwards compatibility versions if that is interesting.
- 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.
- 11/7: It is now preferred that IMP::Restraint and IMP::ScoreState descendants 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 deprecated. 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.
- 11/3: IMP::container::InContainerPairFilter and friends now treat pairs as unordered. A flag was added to control this.
- 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.
## Summer 2012
- 7/3: IMP_PERIODIC_OPTIMIZER_STATE() was superseded by the class IMP::core::PeriodicOptimizerState as it is rather cleaner than the macro.
- 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.
- 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.
- 6/24: Benchmarks are now put int \c module/benchmark and build to \c build/benchmark/module to remove a recurring source of errors.
- 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.
- 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.
## Winter 2011/2012
- 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.
- 4/4: the filter types were superseded 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()).
- 29/3: IMP::Particle::get_has_model() has been changed to IMP::ModelObject::get_is_part_of_model() to be consistent with other classes.
- 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.
- 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).
- 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.
- 15/3: The vector used throughout IMP is now exposed at IMP::base::Vector and what it does it documented.
- 10/3: IMP::domino::RestraintCache was introduced to provide a documented centralized place to handle restraint evaluation and caching in DOMINO. In the switch various bugs involving maximum scores and IMP::RestraintSet objects were fixed.
- 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.
- 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.
- 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.
- 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.
- 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).
- 3/2: IMP::domino::WriteAssignmentContainer and IMP::domino::ReadAssignmentContainer were added to do direct binary file writing. This is faster than the HDF5 versions.
- 3/2: The installation instructions have been revamped and the developer instruction, in particular, have been greatly simplified.
- 24/1: \c tools/show-changes has been added that shows the changes in the history log since you last updated.
- 24/1: \c tools/make-source has been added that adds a source/header pair to a module
- 24/1: principal components analysis in IMP::algebra was generalized to work in any dimension. This required renaming the class to IMP::algebra::PrincipalComponentAnalysisD.
- 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
- 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.
- 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.
- 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.
- IMP::algebra::ParabolicFit was renamed to IMP::algebra::ParabolicFit2D (a backwards compatibility typedef is currently provided)
- IMP::algebra::LinearFit was renamed to IMP::algebra::LinearFit2D. It now supports error bars on the y-values.
## Fall 2011
- 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).
- Various IMP::algebra plural typedefs which had been using std::vector (since they never were updated), have now been moved to IMP::vector.
- IMP::statistics::HistogramD now supports display with \c matplotlib.
- IMP::statistics::HistogramD supersedes IMP::statistics::Histogram
- 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.
- the core generic restraint and score state support was moved to the kernel to avoid breaking various scores outside of IMP svn.
- 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.
- Decomposition of restraints now results in restraints that are faster to evaluate, using the generic restraint mechanism in IMP kernel.
- 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()
- 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.
- the way various types of geometry is stored in RMF files was changed, breaking backwards compatibility.
## Summer 2011
- 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.
- the source for the kernel has been moved from \c kernel to \c modules/kernel. This is unlikely to effect anyone.
- IMP::core::ExcludedVolumeRestraint now supports filters
- IMP::domino::HDF5AssignmentTable now caches internally, which makes it several times faster than before.
- you can now pick which Python to use with the \c python argument to scons.
- the units for BD diffusion coefficients changed to be consistent with other IMP units.
- IMP::domino::get_interaction_graph() now takes an IMP::RestraintsTemp, like other functions
- 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.
- 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.
- IMP::IntsList, IMP::FloatsList and IMP::StringsList have been added to replace the various scattered solutions for passing such types.
- 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.
- 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.
- 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.
- the IMP::core::DiameterRestraint was ignoring the radii of the particles involved and so was giving artificially low scores. It now is on the actual diameter of this molecule.
- the IMP::core::MonteCarlo optimizers now support incremental evaluation. This can be a lot faster when only a few particles are moved each step.
- 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.
- 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.
- Temp and non-temp decorator lists have been merged in C++. This was done to simplify code since no one was using the non-temp variants. Now all decorator lists are temp (non-reference counted) variants.
- 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.
- 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.
- IMP::domino uses the new IMP::Model::evaluate_if_good() support to accelerate computations
- IMP::core::MonteCarlo can use the IMP::Model::evaluate_if_good() support to more quickly reject
very bad conformations. See IMP::core::MonteCarlo::set_maximum_difference().
- IMP::core::ExcludedVolumeRestraint has been rewritten to be faster. It is especially
faster when used with IMP::Model::evaluate_if_good()
- 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.
- 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.
- 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.
- the RMF helper binaries have been moved to their own application so that they get installed.
- 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.
## Spring 2011
- An interactive mode has been added to IMP::domino::DominoSampler. The interactive mode is useful for understanding domino sampling runs and distributing domino computations across a cluster.
- Functions IMP::domino::set_assignments() and IMP::domino::get_assignments() were added which support
writing subset assignments to data fields in hdf5 files. These can be used to helping to distribute
domino on a cluster as well as debugging the sampling process.
- a Python function IMP.show_graphviz() has been added that attempts to render a graph with \c dot and then open the pdf.
- 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.
- IMP.atom.create_cover() was added to facilitate creating a summary particle for part of a hierarchy in order to accelerate restraints.
- 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.
- 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.
- The Python graph interface now has a remove_vertex method.
- 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.
- 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.
- Preliminary symmetry support has been added via the IMP::core::TransformationSymmetry and IMP::core::TransformationAndReflectionSymmetry classes.
## Winter 2011
- 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()
- IMP::core::MonteCarlo::set_temperature() was renamed to IMP::core::MonteCarlo::set_kt() as that is what it is doing.
- 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).
- IMP::algebra::grids::GridD now supports dense grids in arbitrary dimension through use of IMP::algebra::grids::DenseGridStorageD.
- IMP::Optimizer now can use a list of restraint sets to compute the score rather than the complete Model score.
- each IMP::Restraint now has its own weight. This is lightly tested.
- 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.
- IMP::domino::TrivialParticleStates renamed to IMP::domino::IndexParticleStates to be less judgmental
- IMP::domino::CompoundParticleStates and IMP::domino::RecursiveParticleStates added
- IMP::domino::DominoSampler now supports maximum scores on IMP::RestraintSets (untested).
- the name of the clustering methods have been changed to create_ from get_ since they create objects.
- the names of the recently added metric based clustering support has been changed to Metric rather than Distance.
- 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.
- the function IMP::display::create_restraint_geometry() was added to do what its name says.
- 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.
- IMP::atom::DopePairScore has been added to IMP.
- IMP::atom::CHARMMStereochemistryRestraint provides a high-level simplified
interface to the bonded part of the CHARMM forcefield.
- 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.
- Instructions and scripts have been added for building modules and things externally to the IMP build. See the installation guide.
- IMP::atom::CHARMMParameters can now automatically map CHARMM-style atom and
residue naming to PDB-style, so CHARMM topology files can be used unmodified.
- IMP::atom::CHARMMTopology::add_sequence() provides a simple way to generate a topology from a string of amino acid one-letter codes.
- IMP::atom::CHARMMTopology::add_coordinates() will generate atomic Cartesian coordinates from CHARMM internal coordinate information.
- IMP::atom::CHARMMTopology::add_missing_atoms() and
IMP::atom::remove_charmm_untyped_atoms() can now be used to ensure that atoms
read from a PDB file match the CHARMM topology.
- building of deprecated functionality is now false by default
- 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.
- 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).
- 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.
- 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.
- rename IMP::restrainer::Restraint::print_all_restraints() to IMP::restrainer::Restraint::show_all_restraints() to be consistent with the rest of IMP.
- renamed IMP::atom::get_conect_record_string() to IMP::atom::get_pdb_conect_record_string() to make clearer what it is.
- class and method names are now spell checked. Add missing words to spelling_exceptions in the module test call.
- the plural names (eg IMP.Particles()) have been removed from the Python side as they are just Python lists.
- biological systems can now include internal modules. These provide a convenient place to put application specific C++ and Python code. See the example system for more info.
- IMP_VALUES() now includes IMP_OUTPUT_OPERATOR() so you no longer need two namespace macros for each value.
- 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.
- the IMP::atom::PDBSelector and IMP::atom::Mol2Selector became IMP::Object classes. All this
means is that they need to be created with \c new in C++ code. It also means that one is
no longer prohibited from storing them (not that there is much use in doing that).
- 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.
- IMP::core::RigidBody::lazy_set_reference_frame() was renamed to IMP::core::RigidBody::set_reference_frame_lazy() to fit with the standards better.
- the transform based methods on reference frame which have been deprecated for a while were removed
- 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.
- IMP::atom::NonhydrogenMol2Selector was renamed IMP::atom::NonHydrogenMol2Selector to be consistent with the PDB version
## Fall 2010
- IMP::display::PlaneGeometry was added to display planes
- 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
benefit from better checking.
- 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.
- 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()
- IMP::core::WriteModelOptimizerState is going away as it duplicated IMP::WriteParticlesOptimizerState.
- 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.
- the biological systems specification has been improved a little adding ability to run some rudimentary tests to make sure the scripts are ok and to not require that everything be run from the svn directory.
- 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.
- Logging has been improved to better report the name of methods producing the log messages
- a macro IMP_FUNCTION_LOG has been added which should be added to the start of non-member functions which produce significant logging output.
- 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.
- IMP.domino2 was renamed to IMP.domino and the old IMP.domino was moved
- 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.
- applications and biological systems now have their own documentation pages
- IMP::atom::Hierarchy requires radii on its leaves
- IMP::atom::read_pdb add radii to the atoms
- IMP::helper was merged into IMP::restrainer as all the functionality there was primarily to provide support for restrainer
- IMP::domino2::SubsetEvaluatorTable was removed. Pass the model and IMP::domino2::ParticleStatesTable to the IMP::domino2::RestraintScoreSubsetFilterTable instead.
- 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.
- a new example was added in the kernel to show IMP used on a biological system
- IMP::display::PymolWriter now supports adding labels to things
- IMP::display::PairRestraintGeometry and IMP::display::ConnectivityRestraintGeometry were added to aid in visualizing those restraints.
- IMP::bullet was added with an optimizer to use hard body physics to resolve local collisions.
- 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 separate particle so that the molecular hierarchy doesn't have to worry about having its bounding sphere large enough to enclose all the members.
- IMP::core::KClosePairsPairScore was added to have count based cutoffs for close pair scoring.
- IMP::algebra::get_surface_area_and_volume() was added to compute the two numbers for a set of balls
## Summer 2010
- 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 slightly tweaked to work.
- Javi added his 2D EM scoring functionality as IMP::em2D
- 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.
- 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).
- 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.
- 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).
- 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
- a better explanation of how to use reference counted pointers has been added to IMP::Pointer.
- all simple, planar polygons are now supported for display when CGAL is present
## Week of April 1, 2010
- 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
- types are not checked until the lists are passed to C++
- 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)
- swig has issues with some overloads (not always for obvious reasons). These are being sorted out. None are commonly used.
- get_particles() on a plural object doesn't work in Python (and is not needed in C++). Implicit conversions will always work.
- 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 empty lists of particles in the constructors cause check failures. We can figure out a work around if this is too annoying.
## Week of March 13, 2010
- 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.
- 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).
## Week of March 6, 2010
- 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.
## Week of Feb 27, 2010
- IMP::algebra::decompose_rotation_into_axis_angle() was renamed to IMP::algebra::get_angle_and_axis().
- renamed IMP::atom::bond() and IMP::atom::unbond() to IMP::atom::create_bond() and IMP::atom::destroy_bond() to be more consistent with things
- renamed IMP::core::root() to IMP::core::get_root()
## Week of Feb 21, 2010
- IMP::Object::set_was_owned() was changed to IMP::Object::set_was_used() as that better reflects what the flag means.
- various more interpolation and endian methods had their names fixed (by adding \c get_)
- the function get_mean() on vectors was removed as it duplicated IMP::algebra::get_centroid()
- build_Transformation3D_from_transformation3D was replaced by IMP.algebra.get_transformation_3d()
- IMP::algebra::almost_equal() is now IMP::algebra::get_are_almost_equal() to fit the naming conventions.
- the random vector generators have been cleaned up to remove redundant ones and make the names more consistent. They now have the form of either
- IMP::algebra::get_random_vector_in() or IMP::algebra::get_random_vector_on() where there is one argument describing the volume or shape (such as an IMP::algebra::SphereD<4>).
- or IMP::algebra::get_uniform_surface_cover() where the first argument is the primitive whose surface we are covering and the second is the number of points.
Some good sed strings are
- "s\#random_vector_in_unit_sphere()\#get_random_vector_in(IMP.algebra.get_unit_sphere_3d())\#g"
- "s\#random_vector_in_unit_box()\#get_random_vector_in(IMP.algebra.get_unit_bounding_box_3d())\#g"
- "s\#random_vector_on_unit_sphere()\#get_random_vector_on(IMP.algebra.get_unit_sphere_3d())\#g"
- "s\#random_vector_on_unit_box()\#get_random_vector_on(IMP.algebra.get_unit_bounding_box_3d())\#g"
- "s\#random_vector_in_box(\#get_random_vector_in(\#g"
- "s\#random_vector_on_box(\#get_random_vector_on(\#g"
- "s\#random_vector_in_sphere(\#get_random_vector_in(\#g"
- "s\#random_vector_on_sphere(\#get_random_vector_on(\#g"
- "s\#grid_cover\#get_grid_surface_cover\#g"
- "s\#uniform_coverr\#get_uniform_surface_cover\#g"
.
- Spheres in IMP::algebra are now supported in general dimensions. See IMP::algebra::SphereD.
- Many methods in IMP::algebra were renamed to be more consistent with other methods or general conventions. Most of these simply involved adding \c get_ as a prefix and/or add a \c _3d suffix when they did not take any arguments.
- build_Rotation2D_from_Vector2D became IMP::algebra::get_rotation_to_x_axis()
- most of the Rotation3D and Transformation3D functions (in addition, IMP::algebra::get_identity_rotation_3d() and IMP::algebra::get_identity_transformation_3d() added the \c _3d so we can add 2D versions at some point)
- IMP::algebra::Transformation3D::get_transformed() and IMP::algebra::Rotation3D::get_rotated(). Replacing \c ".transform(" worked in the IMP code base.
- IMP::algebra::get_distance(), this also carries over to the IMP::core::get_distance()
The following global replacements are probably safe (in sed expressions)
- "s\#core.distance(\#core.get_distance\#g"
- "s\#algebra.distance(\#algebra.get_distance\#g"
- "s\#\.transform(\#.get_transformed(\#g" Only in C++
- "s\#\.rotate(\#.get_rotated(\#g" Only in C++
- "s\#rotation_from\#get_rotation_from\#g"
- "s\#rotation_in\#get_rotation_in\#g"
- "s\#identity_rotation(\#get_identity_rotation_3d("
- "s\#::distance(\#::get_distance(\#g"
.
- IMP::algebra::Vector3D and IMP::algebra::Vector3Ds were replaced by the expanded (non-typedef) version in functions parsed by SWIG as the current situation was extremely brittle. For the moment, you should not use the typedefs in definitions that swig sees. Sorry.
- IMP::algebra::Sphere3DPatch was renamed to IMP::algebra::SpherePatch3D to be consistent with the other geometry and allow us to support higher dimensions in the future.
- rigid_align_first_to_second was renamed to IMP::algebra::get_transformation_aligning_first_to_second() and build_Transformation2D_from_point_sets was renamed to IMP::algebra::get_transformation_aligning_pair()
## Week of Feb 14, 2010
- The IMP::atom::Bond types were rearranged to reconcile the protein-centric classification with ligand support.
- IMP::atom::Atom no longer has charge since we have IMP::atom::Charged.
- IMP::atom::read_mol2() and IMP::atom::write_mol2() were added
- IMP::atom::Selector and descendants 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.
- 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.
- IMP::example renamed (from examples)
- The IMP_USAGE_CHECK() macro lost the (unused) third argument.
## Week of February 3, 2010
- The model io code as moved into the kernel so it is now IMP::write_model() and IMP::read_model()
- Remove the version_info argument from the implementation macros. Instead, just pick up the module version info automatically.
- Add a function Object::get_type_name() and Object::get_module() to get the respective bits of information about each object.
- 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().
- The containers were moved to IMP.container. See that module page for a full list of what moved. In the process, the backwards compatibility functions were removed from IMP::container::PairsRestraint and kin.
- IMP.atom.create_protein() now returns the created protein
- the simplify functions have been moved from IMP.helper. They are now IMP.atom.create_simplified_along_backbone().
- IMP.helper.clone() has been renamed to IMP.atom.create_clone()
- IMP.misc.ConnectingPairContainer has been moved to IMP.core.ConnectingPairContainer
- The locations for pixels in IMP::em::DensityMap have been moved to the center of the corresponding voxel from the lower left corner.
- IMP::em::get_transformed(), IMP::em::get_resampled() and IMP::em::get_density() have been added.
- 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.
- 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.
- 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.
- Most geometry now has namespace methods IMP::algebra::get_bounding_box(), IMP::algebra::get_surface_area(), IMP::algebra::get_volume().
## Week of January 22, 2010
- A generic geometry layer has been added (see \ref genericgeometry). Using it, IMP::atom::rmsd(),
IMP::algebra::alignment_taking_first_to_second() and the new IMP::atom::native_overlap() all
can work on either collections of either IMP::core::XYZ particles or IMP::algebra::Vector3Ds.
- 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.
- 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.
- Rename IMP::core::MinimumPairScoreRestraint (and kin, Maximum, Singleton, Triplet and Quad) to IMP::core::MinimumPairRestraint.
- Add IMP::core::MinumumPairScore (and kin).
## Week of January 1, 2010
- IMP::em is now using Particles to resample density maps and for fitting restraints. The previous ParticleAccessPoint mechanism is removed.
- IMP::UsageException and IMP::InternalException are now reserved for their respective
checks (and cannot be thrown by IMP_THROW()). This makes the distinction between API
exceptions (which are thrown in any build mode and should be documented and tested)
and helper exceptions which are only thrown when checks are turned on (and hence
should not be documented) clearer.
- IMP::core::RestraintSet moved to IMP::RestraintSet. The restraint sets now simply define a tree
with weights which the model traverses as opposed to being an opaque IMP::Restraint themselves.
This means that incremental evaluation of restraints in restraint sets now works and that
restraints in restraint sets can be individually evaluated. Existing working usage should not
have changed (so \c sed should manage updates just fine), but the internal
implementation is completely new, so pay attention.
- IMP now has a text i/o layer consisting of IMP::TextInput and IMP::TextOutput. These classes are
convertible to C++ streams and implicitly constructable from both streams and file paths. As a result,
functions that take them will work when called with a string for a file path, a Python file or a
C++ stream.
- The IMP.examples module now documents how to use the needed aspects of scons and SWIG.
- 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.
- 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.
- boost program options is now a checked for dependency.
- 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.
- 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.
- 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).
- 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.
- a new base class IMP::Constraint has been added for constraints. Various
other classes have been renamed to be consistent.
## Week of December 11
- 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.
- 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.
- IMP::ParticlePair::first and second went away since no one claimed to be using it and it complicated the implementation.
- The generic restraints/score states/scores infrastructure has been extended to triplets and quads (for angles and torsion angles).
## Week of December 4
- 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.
- 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.
- 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).
## Week of November 19
- imp.xcodeproj was moved into tools and updated accordingly
- the bin directory finally went away
- IMP::display::ChimeraWriter now supports the latest version of Chimera
- IMP::display::CGOWriter was renamed to IMP::display::PymolWriter as it can do more than just CGO.
- IMP::VectorOfRefCounted::operator[] can now be used for assignments just like a normal vector. No more need to use the IMP::VectorOfRefCounted::set() method.
- the IMP::atom::Hierarchy constructor from an IMP::Particle* is now explicit (as were the decorator constructors)
## Week of November 12
- All exception types are now mapped to equivalent classes in Python. The
class hierarchy is similar (e.g. IMP::ModelException derives from IMP::Exception
in both C++ and Python) so all IMP exceptions can be caught in Python using
"except IMP.Exception". For convenience, the IMP::IOException,
IMP::ValueException and IMP::IndexException classes in Python also derive from
the similarly-named standard Python classes (IOError, ValueError and IndexError
respectively).
## week of October 29 Update
- 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).
- 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().
- Added IMP::core::VolumeRestraint.
- Several functions have been added to helper in creating restraints. They are create_simple_connectivity_on_rigid_bodies(), create_simple_connectivity_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.
- 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().
- IMP::em::read_map() will figure out the file type to use automatically from the extension. Other such methods should follow suite.
- A class IMP::core::StructureSet has been added to provide a convenient way to manage solutions of optimization runs.
- IMP::core::RigidBodyMover now takes its angle argument in radians and is documented as such.
- 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.
- IMP::core::AllPairsPairContainer has been renamed to IMP::core::AllPairContainer and a bipartite version has been added.
- All containers now keep track of what they looked like on the previous time step.
- The IMP::core::ListPairContainer and IMP::core::ListSingletonContainer have had their interface reduced a bit in order to make implementing change tracking easier.
- 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.
- 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.
## Week of October 15
- 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.
## Week of October 8
- 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.
- 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.
- IMP_check() and IMP_assert() have been
replaced with IMP_USAGE_CHECK() and IMP_INTERNAL_CHECK()
respectively. Hopefully this makes it clearer when to use
which. IMP::set_check_level() has been revised accordingly (to use
IMP::USAGE and IMP::USAGE_AND_INTERNAL). Also, IMP_failure() and
IMP_not_implemented() have been renamed to IMP_FAILURE() and
IMP_NOT_IMPLEMENTED() to make all macros be all caps. To update
external code,
- replace IMP.EXPENSIVE with IMP.USAGE_AND_INTERNAL
- replace IMP.CHEAP with IMP.USAGE
- replace IMP_assert and IMP_check as above.
## Week of October 1
- 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.
- .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.
- The search module is no longer built by default and is not longer supported. It will get moved out of svn shortly.
- IMP::ScoreState objects now also have IMP::Interacting::get_interacting_particles() methods. Soon IMP::PairScore and IMP::SingletonScore objects will too.
## Week of September 27
- 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.
- A class IMP::core::RigidBodyDistancePairScore has been added which provides accelerated computations for the distance between two rigid bodies.
- The SWIG input files were renamed from swig.i to swig.i-in to aid in dependency tracking.
- 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.
## Week of September 20
- all \c .i files have been renamed to start with \c IMP_ to help make dependency tracking easier.
- static builds (builds with \c static=True) build both the static and dynamic libraries and just static executables
- 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.
- 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.
- \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.
## Week of August 30
- A new score IMP::core::BoundingBox3DSingletonScore has been added to keep particles
in a box.
- str should now work better in Python when applied to IMP::Object objects and a few others. Objects
should use the new IMP_SHOWABLE and IMP_SHOWABLE_INLINE macros instead of declaring show
functions directory to make it so that they work in Python. It is now a bug to \c print or \c str
to not return something useful in Python for any IMP object.
## Week of August 23
- each module now has a version, eg IMP::get_module_version_info() which is also returned by the various restraints of the module. The Python code checks that loaded libraries have the expected version numbers to try to provide better messages when runtime linking problems occur.
- the various bounding_box methods have been renamed to ::get_bounding_box() to be more consistent with the other names.
- Python documentation is now parsed by doxygen
## Week of August 15
- 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.
## Week of August 8
- 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.
- 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).
- IMP::atom::Mass() has been added for decorating particles with mass. IMP::atom::Atom mass has been moved to that.
- The scheme for generating atom types is now fully specified. See the IMP::atom::AtomType documentation.
- 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.
- 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.
- The contents of bin are moving to tools since the two directories both contained assorted development tools
(not all of which were executable). For now, bin/imppy.sh will still work, but that will go away soon.
- IMP::Decorator::show() now just takes the stream (it used to take a prefix also, which was often ignored).
Anyone who implemented a decorator will have to delete the second argument of their show function.
## Week of August 1
- Containers now have methods IMP::SingletonContainer::evaluate(), IMP::PairContainer::evaluate(),
IMP::SingletonContainer::apply() and IMP::PairContainer::apply(). Using these can be significantly
faster than looping over the particles externally. Similarly, there is IMP::SingletonScore::evaluate(),
IMP::PairScore::evaluate(), IMP::SingletonModifier::apply(), IMP::PairModifier::apply().
- The decorator functions have been renamed to IMP::Decorator::setup_particle(), IMP::Decorator::decorate_particle()
and IMP::Decorator::particle_is_instance(). A shell script \c tools/update-decorators is provided which
updates the names in all code in subdirectories of the current directory. Please backup things first.
- a function, IMP::Restraint::safe_evaluate() has been added to be used
when requesting the value of restraints outside of the IMP::Model::evaluate().
## Week of July 18
- The atom::BondPairContainer has been renamed to atom::BondPairFilter
since it wasn't a real container. A real atom::BondPairContainer has
been added.
- Out of source builds mostly works. To do an out of source build, make a link
to \c scons_tools and \c SConstruct from the source directory in the build
directory and then add the line \command{repository="../path_to_src_dir"} in
the \c config.py in the build directory. Then running \c scons in the build
directory will put generated files there. This allows you to make both a
\c release and \c fast build off of the same set of sources. Proper docs
will be added soon.
- The SConscript setup for a module has been greatly simplified so it should
be easy enough for users to maintain their own module and updates to the
build system shouldn't involve changes to user SConscripts any more. This does
mean that any non-svn modules need to be updated. Look at IMP.core or another
module and copy what is there. Again, proper docs will be added soon.
## Week of July 11
- Per Javi's suggestion, the conventions have been split into
"Coding conventions" and "API conventions" and linked from the main page.
- benchmarks got moved to their own module, IMP::benchmark and will
now be tracked over time
## Week of July 4
- FilteredListSingletonContainer and FilteredPairSingletonContainer
went away as there was too much hard to factor code shared with
IMP::core::ListSingletonContainer and IMP::core::PairSingletonContainer. The
IMP::core::ClosePairsScoreState is now handled by a list of filters
on the class itself. That is, do
IMP::core::ClosePairsScoreState::add_close_pair_filter() to add a
filter.
- Hooks have been added to allow actions to be taken on an assertion
or check failure. See IMP::HandleFailure and its descendants for
more details.
- IMP::display::CGOWriter has been much improved and now allows
provides lots of display-time control and easy building of
animations.
- Generic optimizer states have been added
(IMP::core::SingletonsOptimizerState and
IMP::core::PairsOptimizerState).
## Week of June 15
- box distributions (IMP::algebra::random_vector_on_box(),
IMP::algebra::random_vector_in_box()) take bounding boxes
- IMP::em::DensityMap are now IMP::Object objects. Some current
allocations on the stack may need to be changed (since ref counted
objects can't be stack allocated).
- IMP::em::DensityMap::Read() is now deprecated (as is
IMP::em::DensityMap::Write) as they violated a slew of
conventions. Use IMP::em::read_map() and IMP::em::write_map()
instead.
## Week of June 8
- new methods IMP::atom::add_radii() and IMP::atom::add_bonds();
- Hierarchys to IMP::atom::Hierarchies
- IMP::Particles has been changed to a new type. It no longer plays
quite so well with Python lists (you can't create one from an
arbitrary Python list).
- The containers for multiple decorators have been revised to make them
more useful. See IMP::Decorators. You can now implicitly convert,
for %example, a IMP::core::XYZs to an IMP::Particles (as well as use
IMP::Decorators::get_particles()). All methods that take a
collection of particles with a certain type now instead take a
IMP::Decorators.
- A method that has expectations about the particles it takes should
take decorators rather than particles. That is, anything which
expects IMP::core::XYZ particles, should take an IMP::core::XYZs
instead of IMP::Particles.
- IMP_LIST() now takes an extra argument (the name of the plural
container)
- In C++ IMP::Decorator objects are implicitly convertible to
IMP::Particle* objects. Unfortunately, making this work in Python is
problematic.
- More methods take and return decorators rather than
IMP::Particles. This means it is clearer what their expectations are
and what they produce.
## Week of May 15
- The IMP::helper module was added and various functionality moved
there. See its documentation page for a list of what is there.
- IMP::algebra::SphericalCoords was renamed to
IMP::algebra::SphericalVector3D to be consistent with other algebra
classes.
- IMP::algebra::Rotation2D is now IMP::InvalidDefault to be consistent
with the other similar classes.
- We are trying to be a bit more specific about what is expected from
a IMP::atom::Hierarchy. Towards that end, there are two methods for
extracting a representation from a hierarchy,
IMP::atom::get_detailed_representation(), and
IMP::atom::get_simplified_representation()
- A method has been added to produce a simplified copy of an
IMP::atom::Hierarchy. The method is still a bit crude and could
benefit from other people inspecting the output and saying how it
should be improved.
- There is now an IMP::algebra::BoundingBoxD (and
IMP::algebra::BoundingBox3D) to track bounding boxes. There are
methods like IMP::algebra::bound_box(Sphere3D) which gets the
bounding box of a sphere.
- Each IMP::Object has its own log level. If
IMP::Object::set_log_level() is called with a value other than
IMP::DEFAULT, the value is used for code within and called by the
object. To support this in your objects you need to add
IMP_OBJECT_LOG to the start of each major method. It has been added
to some of the core objects.
## Week of May 8
- IMP::atom::MolecularHierarchy has been renamed to
IMP::atom::Hierarchy. Use \command{sed -i.old
"s\#MolecularHierarchy\#Hierarchy\#g" my_files}
- the long-deprecated Name(Decorator) was removed
- The decorator suffix has been removed from decorator names.
- Unit conventions have been established and documented for distance,
energy, force and angle.
- there is a function IMP::atom::create_protein() to create a coarse
grained protein. The function is crude so far, but the idea is that
we should have standard ways of generating such things so that
everyone can benefit from best practices.
- a class IMP::atom::BondGraph has been added so Boost.Graph
algorithms can be used with bond graphs
- the IMP-specific doxygen commands have been documented.
- the doxygen commands unstable{name} and untested{name} have been
added to doxygen to be used for marking methods and functions as
likely to change or not well tested. Pass the name of the class or
method as name.
- bonds can now be added to molecular hierarchies automatically see
IMP::atom::add_bonds()
## Week of May 1
- There is a IMP::Rotation2D
- You can now extract fixed Euler ZYZ angles from a
IMP::Rotation3D. This code can serve as a template for extracting
other Euler angle conventions if they are needed.
- IMP::algebra::rotation_between_two_vectors() changed to
IMP::algebra::rotation_taking_first_to_second() to make it clear
which direction the rotation goes.
## Week of April 27
- IMP::Decorator derived objects are now convertible to bool. So code
like \code if (d) { blah } \endcode works.
- IMP::Decorator::cast now returns a null decorator (\c
DecoratorName()) rather than throwing an exception. This might make
it actually useful.
- New IMP::statistics module for statistical methods
(e.g. clustering).
## Week of April 20
- Support for taking advantage of rigid bodies in collision detection
has been added via the IMP::core::RigidClosePairsFinder.
- All IMP::core::ClosePairsScoreState-related functionality has been
optimized and should be noticeably faster.
- The EMBED project has been merged into the IMP::em module. Thus, it
is no longer necessary to obtain EMBED separately to build IMP::em.
- All C++ methods which work with std::istream or std::ostream
arguments should now be usable from Python: any Python file-like
object can be used.
- The SWIG interface now ties in to the reference counting mechanism
used in the C++ code, for all classes derived from
IMP::RefCounted. So, for %example, deleting a Python object should
not free the underlying C++ object if another C++ object holds a
reference to it, and unrefing a C++ object should not delete it if a
Python object still holds a reference to it. There should be no
further need to manually keep references to Python objects to
prevent things from being prematurely cleaned up. This should be
transparent to the user; please report any problems.
- IMP::atom::AtomDecorator no longer inherits from
IMP::core::XYZDecorator.
## Week of April 13
- The decorators IMP::atom::AtomDecorator, IMP::atom::ChainDecorator,
IMP::atom::ResidueDecorator etc. now inherit from
IMP::atom::MolecularHierarchyDecorator. This means they can set
their IMP::atom::MolecularHierarchyDecorator::Type properly and
saves a lot of typing in the common case. We can always make
hierarchy decorators zero memory overhead if we find that the cost
matters.
- The base classes IMP::Comparable, IMP::NullDefault,
IMP::ValidDefault and IMP::UninitializedDefault were added to
document what the default constructors do for various objects in
IMP.
## Week of April 6
- IMP::Object now defines pure virtual methods
IMP::Object::get_version_info() and IMP::Object::show(). All
non-abstract classes which inherit from IMP::Object must implement
them. Doing this means they are more uniformly implemented and are
documented in one place.
- IMP::Object is now reference counted (the only objects this changes
are IMP::Model and IMP::Optimizer). As a result optimizers and
IMP::Model objects must be created on the heap.
- IMP::RefCounted has had its name changed and no longer inherits from
IMP::Object. This makes it easier to use independently.
- the docs for reference counting (IMP::RefCounted) and and IMP::Decorator
have been improved
- running doxygen produces no warnings. Let's try to keep it that
way. Run \command{scons doc > /dev/null} before you check in large
blocks of new code to make sure that you didn't introduce warnings.
- Helper classes have been added to make SingletonModifier and
PairModifier objects look like functors for C++ and Python. This
makes it so you can use \c map in Python and \c for_each in C++. See
IMP::SingletonFunctor and IMP::PairFunctor for more information.
- The recent changes page has moved to a doxygen page to make it
easier to link changes back to the relevant source code.
## Week of March 20:
- create_rigid_body(), create_rigid_bodies(), create_centroid()
etc. now require you to add the score state to the model
yourself. Whether the rigid body is enforced or not can be
controlled by adding or removing the returned IMP::ScoreState.
- All previously deprecated code has been removed. This includes
indexes in particles, the no-argument constructor for particles and
the functionality that was moved from core to atom.
- The IMP::core::RigidBodyDecorator and
IMP::core::RigidMemberDecorator have been simplified by removing the
traits classes. There is now only one type of rigid body and it
stores the list of member particles internally.
- IMP::core::NameDecorator has been deprecated as IMP::Particles have
built in names (use IMP::Particle::get_name(),
IMP::Particle::set_name()).
- IMP::atom::ChainDecorator has been added
## Week of March 13:
- A new IMP::display::Writer, IMP::display::ChimeraWriter has been
added which exports geometry to native Chimera constructs. It
probably should be used instead of bild and cmm for most purposes as
it combines the best of both types.
- compose() for transformation is now a free function so
compose(rotation, vector) will work via promotions.
- the geometry classes have been cleaned up and are now more
consistent with IMP standards (and more likely to do what their
names/comments suggest). See IMP::algebra::Sphere3D,
IMP::algebra::Cylinder3D, IMP::algebra::Segment3D,
IMP::algebra::Plane3D etc.
- ParticleRefiner has been renamed to IMP::Refiner since the Particle
was long and unnecessary.
€ eIF1•eIF3 translation initiation complex](http://salilab.org/40S-eIF1-eIF3).
- IMP::domino::DiscreteSampler::set_restraints() now allows the set of
restraints used in DOMINO filtering to be controlled (previously, all
restraints in the IMP::Model were used).
- IMP::modeller::IMPRestraints now transfers an IMP::ScoringFunction into the
MODELLER score, not the implicit (and deprecated) score of the
entire IMP::Model.
- Bugfix #775: coordinates of voxels in EM maps were previously inconsistently
treated (they are supposed to be the centers of the voxels, but in some
cases they were the lower left edge). The fix may result in maps and their
bounding boxes appearing shifted by half the voxel size.
# 2.4.0 - 2015-02-27 # {#changelog_2_4_0}
- Python 3 is now supported. The Windows package now works out of the box
with Python 3.3 or 3.4; a `-python3` subpackage is provided for Ubuntu
and Fedora. (Apple does not yet provide Python 3 so the Mac package is not
built with Python 3 support, but if you install Python 3 you can compile
IMP from source to work with it.)
- A new command line tool, `rrt_sample`, allows for running rapidly exploring
random tree (RRT) based sampling, e.g. to sample conformations of multiple
domains connected by flexible linkers.
- Command line tools are now placed in the `bin` directory of modules (the
old `bin` directory, used for utility programs that are not installed, is
now called `utility`). The `applications` directory is removed.
- Several Python modules that were only used by EMageFit have been moved from
IMP::em2d to IMP::EMageFit.
- A new tutorial that uses the IMP::pmi module is now available (modeling of
the RNA Polymerase II stalk).
# 2.3.1 - 2014-12-01 # {#changelog_2_3_1}
- Minor bug fixes.
- Update to IMP::pmi to support the Nup84 and rnapolii biological systems.
# 2.3.0 - 2014-10-24 # {#changelog_2_3_0}
- 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.
- Binary installers for 64-bit Windows are now available.
- The `.py` extension has been removed from all Python applications, so that they are consistent with the C++ applications.
- 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.
- The integrative docking (idock) application now employs SOAP to improve the scoring.
- 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.
- 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.
# 2.2.1 - 2014-08-11 # {#changelog_2_2_1}
- Bugfix: PoseScore (see the ligand_score application) should now match that used by the Pose&Rank web server (http://salilab.org/poseandrank/)
# 2.2.0 - 2014-04-09 # {#changelog_2_2_0}
- 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.
- The Python support for grids was cleaned up. Hopefully this makes it more robust. If you were using a grid in Python that no longer exists, ping us, we can add it back.
- The generic geometry functions were simplified slightly and renamed to IMP::algebra::get_vector_geometry().
- The IMP::base::Flag class was added to simplify adding flags in C++.
- The `--log_level` and `--check_level` command line argument now take strings (eg VERBOSE) to specify their values, rather than cryptic (and a bit unstable) numbers.
- Command line options are now divided into normal and advanced ones. You do `--help_advanced` to show the advanced ones.
- Support for computing Connolly surfaces was added with IMP::algebra::get_connolly_surface(). In addition, there is now IMP::algebra::get_uniform_surface_cover(const IMP::algebra::Sphere3Ds&,double) to sample the surface of a collection of balls.
- IMP::atom::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.
- IMP::atom::get_rmsd(IMP::atom::Selection, IMP::atom::Selection, const IMP::algebra::Transformation3D&) was deprecated. Use IMP::atom::get_rmsd_transforming_first() instead.
- IMP::algebra::get_rmsd() and IMP::algebra::get_rmsd_transforming_first() were added.
- The family of macros IMP_BASE_[SMALL,LARGE]_[UNORDERED,ORDERED]_[MAP,SET] have been added (eg IMP_BASE_SMALL_ORDERED_SET ()). They provide platform and boost-version independent ways to take advantage of the best set/map for an application. In particular, they use boost::container::flat_set and kin when available.
- IMP::atom::State and IMP::atom::Representation decorators have been added to provide support for multiple states and multiple representation schemes. They are integrated with RMFs and IMP::atom::Selection. See atom/multiresolution.py and atom/multistate.py for examples.
- The container implementations has been cleaned up and simplified a bit. This should not change most usage.
- [RMF](http://salilab.github.io/rmf) has been updated. There are a few minor API changes, in addition to a new, faster format (`.rmf3`).
- [Eigen](#Eigen) is now included with IMP.
- The deprecated function IMP::kernel::Optimizer::set_restraints() was removed. Use IMP::kernel::Optimizer::set_scoring_function() instead.
- The deprecated constructor for IMP::kernel::ModelObject that does not take an IMP::kernel::Model was removed. This propagates to constructors IMP::kernel::Restraint, IMP::kernel::ScoreState and kin. Make sure you pass an IMP::kernel::Model as the first constructor argument. Related to this, deprecated functions like get_is_part_of_model(), set_model() were removed as they don't serve any purpose.
- The deprecated methods in IMP::kernel::Optimizer that pertain to attribute optimization were removed. Inherit from IMP::kernel::AttributeOptimizer instead if you want to use them in your optimizer.
- Some deprecated functionality was removed. If you encounter problems, replace IMP::base::OwnerPointer with IMP::base::PointerMember, find logging stuff in IMP/base/log.h, object in IMP/base/Object.h and random in IMP/base/random.h.
- IMP::atom::Chain now uses strings for the chain ids, to be consistent with changes in the PDB. PDB files are written using the first character of the chain string.
- Added orientation-dependent SOAP scoring (IMP::score_functor::OrientedSoap and IMP::atom::OrientedSoapPairScore). Orientation-dependent SOAP scores include those that score loops (SOAP-Loop), protein-peptide interfaces (SOAP-Peptide) and proteins (SOAP-Protein). The library files themselves are rather large (~1.5GB) and so are not included with IMP. They can be downloaded separately from http://salilab.org/SOAP/.
# 2.1.1 - 2013-11-04 # {#changelog_2_1_1}
- Added support for Mac OS 10.9
# 2.1.0 - 2013-10-24 # {#changelog_2_1_0}
- 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.
- 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.
- Class name OwnerPointer was switched to PointerMember, to denote more clearly a ref-counting pointer that is a class member.
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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`).
- 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.
- 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.
- 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.
- [RMF](https://github.com/salilab/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.
# For IMP 2.0 and earlier # {#changelog_2_0}
## Spring 2013
- Modules and applications now have a _Maintainer_ in their `README.md`, giving the github id of the person to whom issues should be assigned.
- `setup_git.py` supports the `--module` flag which will set up git hooks and things for a git repository that contains a module.
- 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.
- 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.
## Winter 2012-2013
- Scons support was removed. Use cmake to build IMP, it is way better.
- 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.
- 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.
- The IMP_BIG_ENDIAN and IMP_LITTLE_ENDIAN preprocessor symbols are deprecated in favor of the BOOST_BIG_ENDIAN and BOOST_LITTLE_ENDIAN symbols.
- 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.
- 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.
- You can now (probably) build IMP with [CMake on IMP wiki](https://github.com/salilab/imp/wiki/Cmake).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- OpenMP support in IMP is officially released. All tests pass. But there has been little specific testing so far.
- Access to attributes using IMP::ParticleIndex and the IMP::Model now works from Python. See IMP::Model::add_attribute() and kin.
- 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.
- 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.
- 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.
- 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 beginning. You can use `./tools/updaters/update_examples.py modules/mymodule` to update a module that was not already updated.
- IMP::base::FailureHandler has been removed as it wasn't used.
- 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.
- Modules now must be in a folder called `modules`, which must have a `description.py` file.
- The build system should now be a little better about cleaning up after itself.
- How headers/doc files/data/examples
- 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 "_" from the method name.
- Nice version numbers will now be generated if you use git. You need to rerun
tools/git/developer_tools/init_git if you have an existing clone.
## Fall 2012
- 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.
- 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.
- 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.
- 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.
- 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.
- 11/8; Evaluation with containers was greatly simplified, moving many methods on containers. We can add backwards compatibility versions if that is interesting.
- 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.
- 11/7: It is now preferred that IMP::Restraint and IMP::ScoreState descendants 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 deprecated. 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.
- 11/3: IMP::container::InContainerPairFilter and friends now treat pairs as unordered. A flag was added to control this.
- 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.
## Summer 2012
- 7/3: IMP_PERIODIC_OPTIMIZER_STATE() was superseded by the class IMP::core::PeriodicOptimizerState as it is rather cleaner than the macro.
- 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.
- 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.
- 6/24: Benchmarks are now put int \c module/benchmark and build to \c build/benchmark/module to remove a recurring source of errors.
- 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.
- 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.
## Winter 2011/2012
- 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.
- 4/4: the filter types were superseded 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()).
- 29/3: IMP::Particle::get_has_model() has been changed to IMP::ModelObject::get_is_part_of_model() to be consistent with other classes.
- 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.
- 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).
- 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.
- 15/3: The vector used throughout IMP is now exposed at IMP::base::Vector and what it does it documented.
- 10/3: IMP::domino::RestraintCache was introduced to provide a documented centralized place to handle restraint evaluation and caching in DOMINO. In the switch various bugs involving maximum scores and IMP::RestraintSet objects were fixed.
- 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.
- 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.
- 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.
- 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.
- 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).
- 3/2: IMP::domino::WriteAssignmentContainer and IMP::domino::ReadAssignmentContainer were added to do direct binary file writing. This is faster than the HDF5 versions.
- 3/2: The installation instructions have been revamped and the developer instruction, in particular, have been greatly simplified.
- 24/1: \c tools/show-changes has been added that shows the changes in the history log since you last updated.
- 24/1: \c tools/make-source has been added that adds a source/header pair to a module
- 24/1: principal components analysis in IMP::algebra was generalized to work in any dimension. This required renaming the class to IMP::algebra::PrincipalComponentAnalysisD.
- 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
- 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.
- 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.
- 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.
- IMP::algebra::ParabolicFit was renamed to IMP::algebra::ParabolicFit2D (a backwards compatibility typedef is currently provided)
- IMP::algebra::LinearFit was renamed to IMP::algebra::LinearFit2D. It now supports error bars on the y-values.
## Fall 2011
- 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).
- Various IMP::algebra plural typedefs which had been using std::vector (since they never were updated), have now been moved to IMP::vector.
- IMP::statistics::HistogramD now supports display with \c matplotlib.
- IMP::statistics::HistogramD supersedes IMP::statistics::Histogram
- 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.
- the core generic restraint and score state support was moved to the kernel to avoid breaking various scores outside of IMP svn.
- 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.
- Decomposition of restraints now results in restraints that are faster to evaluate, using the generic restraint mechanism in IMP kernel.
- 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()
- 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.
- the way various types of geometry is stored in RMF files was changed, breaking backwards compatibility.
## Summer 2011
- 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.
- the source for the kernel has been moved from \c kernel to \c modules/kernel. This is unlikely to effect anyone.
- IMP::core::ExcludedVolumeRestraint now supports filters
- IMP::domino::HDF5AssignmentTable now caches internally, which makes it several times faster than before.
- you can now pick which Python to use with the \c python argument to scons.
- the units for BD diffusion coefficients changed to be consistent with other IMP units.
- IMP::domino::get_interaction_graph() now takes an IMP::RestraintsTemp, like other functions
- 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.
- 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.
- IMP::IntsList, IMP::FloatsList and IMP::StringsList have been added to replace the various scattered solutions for passing such types.
- 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.
- 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.
- 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.
- the IMP::core::DiameterRestraint was ignoring the radii of the particles involved and so was giving artificially low scores. It now is on the actual diameter of this molecule.
- the IMP::core::MonteCarlo optimizers now support incremental evaluation. This can be a lot faster when only a few particles are moved each step.
- 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.
- 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.
- Temp and non-temp decorator lists have been merged in C++. This was done to simplify code since no one was using the non-temp variants. Now all decorator lists are temp (non-reference counted) variants.
- 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.
- 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.
- IMP::domino uses the new IMP::Model::evaluate_if_good() support to accelerate computations
- IMP::core::MonteCarlo can use the IMP::Model::evaluate_if_good() support to more quickly reject
very bad conformations. See IMP::core::MonteCarlo::set_maximum_difference().
- IMP::core::ExcludedVolumeRestraint has been rewritten to be faster. It is especially
faster when used with IMP::Model::evaluate_if_good()
- 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.
- 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.
- 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.
- the RMF helper binaries have been moved to their own application so that they get installed.
- 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.
## Spring 2011
- An interactive mode has been added to IMP::domino::DominoSampler. The interactive mode is useful for understanding domino sampling runs and distributing domino computations across a cluster.
- Functions IMP::domino::set_assignments() and IMP::domino::get_assignments() were added which support
writing subset assignments to data fields in hdf5 files. These can be used to helping to distribute
domino on a cluster as well as debugging the sampling process.
- a Python function IMP.show_graphviz() has been added that attempts to render a graph with \c dot and then open the pdf.
- 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.
- IMP.atom.create_cover() was added to facilitate creating a summary particle for part of a hierarchy in order to accelerate restraints.
- 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.
- 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.
- The Python graph interface now has a remove_vertex method.
- 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.
- 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.
- Preliminary symmetry support has been added via the IMP::core::TransformationSymmetry and IMP::core::TransformationAndReflectionSymmetry classes.
## Winter 2011
- 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()
- IMP::core::MonteCarlo::set_temperature() was renamed to IMP::core::MonteCarlo::set_kt() as that is what it is doing.
- 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).
- IMP::algebra::grids::GridD now supports dense grids in arbitrary dimension through use of IMP::algebra::grids::DenseGridStorageD.
- IMP::Optimizer now can use a list of restraint sets to compute the score rather than the complete Model score.
- each IMP::Restraint now has its own weight. This is lightly tested.
- 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.
- IMP::domino::TrivialParticleStates renamed to IMP::domino::IndexParticleStates to be less judgmental
- IMP::domino::CompoundParticleStates and IMP::domino::RecursiveParticleStates added
- IMP::domino::DominoSampler now supports maximum scores on IMP::RestraintSets (untested).
- the name of the clustering methods have been changed to create_ from get_ since they create objects.
- the names of the recently added metric based clustering support has been changed to Metric rather than Distance.
- 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.
- the function IMP::display::create_restraint_geometry() was added to do what its name says.
- 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.
- IMP::atom::DopePairScore has been added to IMP.
- IMP::atom::CHARMMStereochemistryRestraint provides a high-level simplified
interface to the bonded part of the CHARMM forcefield.
- 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.
- Instructions and scripts have been added for building modules and things externally to the IMP build. See the installation guide.
- IMP::atom::CHARMMParameters can now automatically map CHARMM-style atom and
residue naming to PDB-style, so CHARMM topology files can be used unmodified.
- IMP::atom::CHARMMTopology::add_sequence() provides a simple way to generate a topology from a string of amino acid one-letter codes.
- IMP::atom::CHARMMTopology::add_coordinates() will generate atomic Cartesian coordinates from CHARMM internal coordinate information.
- IMP::atom::CHARMMTopology::add_missing_atoms() and
IMP::atom::remove_charmm_untyped_atoms() can now be used to ensure that atoms
read from a PDB file match the CHARMM topology.
- building of deprecated functionality is now false by default
- 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.
- 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).
- 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.
- 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.
- rename IMP::restrainer::Restraint::print_all_restraints() to IMP::restrainer::Restraint::show_all_restraints() to be consistent with the rest of IMP.
- renamed IMP::atom::get_conect_record_string() to IMP::atom::get_pdb_conect_record_string() to make clearer what it is.
- class and method names are now spell checked. Add missing words to spelling_exceptions in the module test call.
- the plural names (eg IMP.Particles()) have been removed from the Python side as they are just Python lists.
- biological systems can now include internal modules. These provide a convenient place to put application specific C++ and Python code. See the example system for more info.
- IMP_VALUES() now includes IMP_OUTPUT_OPERATOR() so you no longer need two namespace macros for each value.
- 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.
- the IMP::atom::PDBSelector and IMP::atom::Mol2Selector became IMP::Object classes. All this
means is that they need to be created with \c new in C++ code. It also means that one is
no longer prohibited from storing them (not that there is much use in doing that).
- 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.
- IMP::core::RigidBody::lazy_set_reference_frame() was renamed to IMP::core::RigidBody::set_reference_frame_lazy() to fit with the standards better.
- the transform based methods on reference frame which have been deprecated for a while were removed
- 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.
- IMP::atom::NonhydrogenMol2Selector was renamed IMP::atom::NonHydrogenMol2Selector to be consistent with the PDB version
## Fall 2010
- IMP::display::PlaneGeometry was added to display planes
- 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
benefit from better checking.
- 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.
- 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()
- IMP::core::WriteModelOptimizerState is going away as it duplicated IMP::WriteParticlesOptimizerState.
- 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.
- the biological systems specification has been improved a little adding ability to run some rudimentary tests to make sure the scripts are ok and to not require that everything be run from the svn directory.
- 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.
- Logging has been improved to better report the name of methods producing the log messages
- a macro IMP_FUNCTION_LOG has been added which should be added to the start of non-member functions which produce significant logging output.
- 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.
- IMP.domino2 was renamed to IMP.domino and the old IMP.domino was moved
- 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.
- applications and biological systems now have their own documentation pages
- IMP::atom::Hierarchy requires radii on its leaves
- IMP::atom::read_pdb add radii to the atoms
- IMP::helper was merged into IMP::restrainer as all the functionality there was primarily to provide support for restrainer
- IMP::domino2::SubsetEvaluatorTable was removed. Pass the model and IMP::domino2::ParticleStatesTable to the IMP::domino2::RestraintScoreSubsetFilterTable instead.
- 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.
- a new example was added in the kernel to show IMP used on a biological system
- IMP::display::PymolWriter now supports adding labels to things
- IMP::display::PairRestraintGeometry and IMP::display::ConnectivityRestraintGeometry were added to aid in visualizing those restraints.
- IMP::bullet was added with an optimizer to use hard body physics to resolve local collisions.
- 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 separate particle so that the molecular hierarchy doesn't have to worry about having its bounding sphere large enough to enclose all the members.
- IMP::core::KClosePairsPairScore was added to have count based cutoffs for close pair scoring.
- IMP::algebra::get_surface_area_and_volume() was added to compute the two numbers for a set of balls
## Summer 2010
- 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 slightly tweaked to work.
- Javi added his 2D EM scoring functionality as IMP::em2D
- 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.
- 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).
- 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.
- 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).
- 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
- a better explanation of how to use reference counted pointers has been added to IMP::Pointer.
- all simple, planar polygons are now supported for display when CGAL is present
## Week of April 1, 2010
- 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
- types are not checked until the lists are passed to C++
- 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)
- swig has issues with some overloads (not always for obvious reasons). These are being sorted out. None are commonly used.
- get_particles() on a plural object doesn't work in Python (and is not needed in C++). Implicit conversions will always work.
- 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 empty lists of particles in the constructors cause check failures. We can figure out a work around if this is too annoying.
## Week of March 13, 2010
- 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.
- 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).
## Week of March 6, 2010
- 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.
## Week of Feb 27, 2010
- IMP::algebra::decompose_rotation_into_axis_angle() was renamed to IMP::algebra::get_angle_and_axis().
- renamed IMP::atom::bond() and IMP::atom::unbond() to IMP::atom::create_bond() and IMP::atom::destroy_bond() to be more consistent with things
- renamed IMP::core::root() to IMP::core::get_root()
## Week of Feb 21, 2010
- IMP::Object::set_was_owned() was changed to IMP::Object::set_was_used() as that better reflects what the flag means.
- various more interpolation and endian methods had their names fixed (by adding \c get_)
- the function get_mean() on vectors was removed as it duplicated IMP::algebra::get_centroid()
- build_Transformation3D_from_transformation3D was replaced by IMP.algebra.get_transformation_3d()
- IMP::algebra::almost_equal() is now IMP::algebra::get_are_almost_equal() to fit the naming conventions.
- the random vector generators have been cleaned up to remove redundant ones and make the names more consistent. They now have the form of either
- IMP::algebra::get_random_vector_in() or IMP::algebra::get_random_vector_on() where there is one argument describing the volume or shape (such as an IMP::algebra::SphereD<4>).
- or IMP::algebra::get_uniform_surface_cover() where the first argument is the primitive whose surface we are covering and the second is the number of points.
Some good sed strings are
- "s\#random_vector_in_unit_sphere()\#get_random_vector_in(IMP.algebra.get_unit_sphere_3d())\#g"
- "s\#random_vector_in_unit_box()\#get_random_vector_in(IMP.algebra.get_unit_bounding_box_3d())\#g"
- "s\#random_vector_on_unit_sphere()\#get_random_vector_on(IMP.algebra.get_unit_sphere_3d())\#g"
- "s\#random_vector_on_unit_box()\#get_random_vector_on(IMP.algebra.get_unit_bounding_box_3d())\#g"
- "s\#random_vector_in_box(\#get_random_vector_in(\#g"
- "s\#random_vector_on_box(\#get_random_vector_on(\#g"
- "s\#random_vector_in_sphere(\#get_random_vector_in(\#g"
- "s\#random_vector_on_sphere(\#get_random_vector_on(\#g"
- "s\#grid_cover\#get_grid_surface_cover\#g"
- "s\#uniform_coverr\#get_uniform_surface_cover\#g"
.
- Spheres in IMP::algebra are now supported in general dimensions. See IMP::algebra::SphereD.
- Many methods in IMP::algebra were renamed to be more consistent with other methods or general conventions. Most of these simply involved adding \c get_ as a prefix and/or add a \c _3d suffix when they did not take any arguments.
- build_Rotation2D_from_Vector2D became IMP::algebra::get_rotation_to_x_axis()
- most of the Rotation3D and Transformation3D functions (in addition, IMP::algebra::get_identity_rotation_3d() and IMP::algebra::get_identity_transformation_3d() added the \c _3d so we can add 2D versions at some point)
- IMP::algebra::Transformation3D::get_transformed() and IMP::algebra::Rotation3D::get_rotated(). Replacing \c ".transform(" worked in the IMP code base.
- IMP::algebra::get_distance(), this also carries over to the IMP::core::get_distance()
The following global replacements are probably safe (in sed expressions)
- "s\#core.distance(\#core.get_distance\#g"
- "s\#algebra.distance(\#algebra.get_distance\#g"
- "s\#\.transform(\#.get_transformed(\#g" Only in C++
- "s\#\.rotate(\#.get_rotated(\#g" Only in C++
- "s\#rotation_from\#get_rotation_from\#g"
- "s\#rotation_in\#get_rotation_in\#g"
- "s\#identity_rotation(\#get_identity_rotation_3d("
- "s\#::distance(\#::get_distance(\#g"
.
- IMP::algebra::Vector3D and IMP::algebra::Vector3Ds were replaced by the expanded (non-typedef) version in functions parsed by SWIG as the current situation was extremely brittle. For the moment, you should not use the typedefs in definitions that swig sees. Sorry.
- IMP::algebra::Sphere3DPatch was renamed to IMP::algebra::SpherePatch3D to be consistent with the other geometry and allow us to support higher dimensions in the future.
- rigid_align_first_to_second was renamed to IMP::algebra::get_transformation_aligning_first_to_second() and build_Transformation2D_from_point_sets was renamed to IMP::algebra::get_transformation_aligning_pair()
## Week of Feb 14, 2010
- The IMP::atom::Bond types were rearranged to reconcile the protein-centric classification with ligand support.
- IMP::atom::Atom no longer has charge since we have IMP::atom::Charged.
- IMP::atom::read_mol2() and IMP::atom::write_mol2() were added
- IMP::atom::Selector and descendants 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.
- 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.
- IMP::example renamed (from examples)
- The IMP_USAGE_CHECK() macro lost the (unused) third argument.
## Week of February 3, 2010
- The model io code as moved into the kernel so it is now IMP::write_model() and IMP::read_model()
- Remove the version_info argument from the implementation macros. Instead, just pick up the module version info automatically.
- Add a function Object::get_type_name() and Object::get_module() to get the respective bits of information about each object.
- 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().
- The containers were moved to IMP.container. See that module page for a full list of what moved. In the process, the backwards compatibility functions were removed from IMP::container::PairsRestraint and kin.
- IMP.atom.create_protein() now returns the created protein
- the simplify functions have been moved from IMP.helper. They are now IMP.atom.create_simplified_along_backbone().
- IMP.helper.clone() has been renamed to IMP.atom.create_clone()
- IMP.misc.ConnectingPairContainer has been moved to IMP.core.ConnectingPairContainer
- The locations for pixels in IMP::em::DensityMap have been moved to the center of the corresponding voxel from the lower left corner.
- IMP::em::get_transformed(), IMP::em::get_resampled() and IMP::em::get_density() have been added.
- 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.
- 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.
- 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.
- Most geometry now has namespace methods IMP::algebra::get_bounding_box(), IMP::algebra::get_surface_area(), IMP::algebra::get_volume().
## Week of January 22, 2010
- A generic geometry layer has been added (see \ref genericgeometry). Using it, IMP::atom::rmsd(),
IMP::algebra::alignment_taking_first_to_second() and the new IMP::atom::native_overlap() all
can work on either collections of either IMP::core::XYZ particles or IMP::algebra::Vector3Ds.
- 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.
- 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.
- Rename IMP::core::MinimumPairScoreRestraint (and kin, Maximum, Singleton, Triplet and Quad) to IMP::core::MinimumPairRestraint.
- Add IMP::core::MinumumPairScore (and kin).
## Week of January 1, 2010
- IMP::em is now using Particles to resample density maps and for fitting restraints. The previous ParticleAccessPoint mechanism is removed.
- IMP::UsageException and IMP::InternalException are now reserved for their respective
checks (and cannot be thrown by IMP_THROW()). This makes the distinction between API
exceptions (which are thrown in any build mode and should be documented and tested)
and helper exceptions which are only thrown when checks are turned on (and hence
should not be documented) clearer.
- IMP::core::RestraintSet moved to IMP::RestraintSet. The restraint sets now simply define a tree
with weights which the model traverses as opposed to being an opaque IMP::Restraint themselves.
This means that incremental evaluation of restraints in restraint sets now works and that
restraints in restraint sets can be individually evaluated. Existing working usage should not
have changed (so \c sed should manage updates just fine), but the internal
implementation is completely new, so pay attention.
- IMP now has a text i/o layer consisting of IMP::TextInput and IMP::TextOutput. These classes are
convertible to C++ streams and implicitly constructable from both streams and file paths. As a result,
functions that take them will work when called with a string for a file path, a Python file or a
C++ stream.
- The IMP.examples module now documents how to use the needed aspects of scons and SWIG.
- 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.
- 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.
- boost program options is now a checked for dependency.
- 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.
- 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.
- 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).
- 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.
- a new base class IMP::Constraint has been added for constraints. Various
other classes have been renamed to be consistent.
## Week of December 11
- 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.
- 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.
- IMP::ParticlePair::first and second went away since no one claimed to be using it and it complicated the implementation.
- The generic restraints/score states/scores infrastructure has been extended to triplets and quads (for angles and torsion angles).
## Week of December 4
- 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.
- 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.
- 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).
## Week of November 19
- imp.xcodeproj was moved into tools and updated accordingly
- the bin directory finally went away
- IMP::display::ChimeraWriter now supports the latest version of Chimera
- IMP::display::CGOWriter was renamed to IMP::display::PymolWriter as it can do more than just CGO.
- IMP::VectorOfRefCounted::operator[] can now be used for assignments just like a normal vector. No more need to use the IMP::VectorOfRefCounted::set() method.
- the IMP::atom::Hierarchy constructor from an IMP::Particle* is now explicit (as were the decorator constructors)
## Week of November 12
- All exception types are now mapped to equivalent classes in Python. The
class hierarchy is similar (e.g. IMP::ModelException derives from IMP::Exception
in both C++ and Python) so all IMP exceptions can be caught in Python using
"except IMP.Exception". For convenience, the IMP::IOException,
IMP::ValueException and IMP::IndexException classes in Python also derive from
the similarly-named standard Python classes (IOError, ValueError and IndexError
respectively).
## week of October 29 Update
- 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).
- 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().
- Added IMP::core::VolumeRestraint.
- Several functions have been added to helper in creating restraints. They are create_simple_connectivity_on_rigid_bodies(), create_simple_connectivity_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.
- 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().
- IMP::em::read_map() will figure out the file type to use automatically from the extension. Other such methods should follow suite.
- A class IMP::core::StructureSet has been added to provide a convenient way to manage solutions of optimization runs.
- IMP::core::RigidBodyMover now takes its angle argument in radians and is documented as such.
- 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.
- IMP::core::AllPairsPairContainer has been renamed to IMP::core::AllPairContainer and a bipartite version has been added.
- All containers now keep track of what they looked like on the previous time step.
- The IMP::core::ListPairContainer and IMP::core::ListSingletonContainer have had their interface reduced a bit in order to make implementing change tracking easier.
- 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.
- 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.
## Week of October 15
- 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.
## Week of October 8
- 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.
- 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.
- IMP_check() and IMP_assert() have been
replaced with IMP_USAGE_CHECK() and IMP_INTERNAL_CHECK()
respectively. Hopefully this makes it clearer when to use
which. IMP::set_check_level() has been revised accordingly (to use
IMP::USAGE and IMP::USAGE_AND_INTERNAL). Also, IMP_failure() and
IMP_not_implemented() have been renamed to IMP_FAILURE() and
IMP_NOT_IMPLEMENTED() to make all macros be all caps. To update
external code,
- replace IMP.EXPENSIVE with IMP.USAGE_AND_INTERNAL
- replace IMP.CHEAP with IMP.USAGE
- replace IMP_assert and IMP_check as above.
## Week of October 1
- 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.
- .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.
- The search module is no longer built by default and is not longer supported. It will get moved out of svn shortly.
- IMP::ScoreState objects now also have IMP::Interacting::get_interacting_particles() methods. Soon IMP::PairScore and IMP::SingletonScore objects will too.
## Week of September 27
- 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.
- A class IMP::core::RigidBodyDistancePairScore has been added which provides accelerated computations for the distance between two rigid bodies.
- The SWIG input files were renamed from swig.i to swig.i-in to aid in dependency tracking.
- 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.
## Week of September 20
- all \c .i files have been renamed to start with \c IMP_ to help make dependency tracking easier.
- static builds (builds with \c static=True) build both the static and dynamic libraries and just static executables
- 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.
- 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.
- \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.
## Week of August 30
- A new score IMP::core::BoundingBox3DSingletonScore has been added to keep particles
in a box.
- str should now work better in Python when applied to IMP::Object objects and a few others. Objects
should use the new IMP_SHOWABLE and IMP_SHOWABLE_INLINE macros instead of declaring show
functions directory to make it so that they work in Python. It is now a bug to \c print or \c str
to not return something useful in Python for any IMP object.
## Week of August 23
- each module now has a version, eg IMP::get_module_version_info() which is also returned by the various restraints of the module. The Python code checks that loaded libraries have the expected version numbers to try to provide better messages when runtime linking problems occur.
- the various bounding_box methods have been renamed to ::get_bounding_box() to be more consistent with the other names.
- Python documentation is now parsed by doxygen
## Week of August 15
- 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.
## Week of August 8
- 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.
- 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).
- IMP::atom::Mass() has been added for decorating particles with mass. IMP::atom::Atom mass has been moved to that.
- The scheme for generating atom types is now fully specified. See the IMP::atom::AtomType documentation.
- 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.
- 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.
- The contents of bin are moving to tools since the two directories both contained assorted development tools
(not all of which were executable). For now, bin/imppy.sh will still work, but that will go away soon.
- IMP::Decorator::show() now just takes the stream (it used to take a prefix also, which was often ignored).
Anyone who implemented a decorator will have to delete the second argument of their show function.
## Week of August 1
- Containers now have methods IMP::SingletonContainer::evaluate(), IMP::PairContainer::evaluate(),
IMP::SingletonContainer::apply() and IMP::PairContainer::apply(). Using these can be significantly
faster than looping over the particles externally. Similarly, there is IMP::SingletonScore::evaluate(),
IMP::PairScore::evaluate(), IMP::SingletonModifier::apply(), IMP::PairModifier::apply().
- The decorator functions have been renamed to IMP::Decorator::setup_particle(), IMP::Decorator::decorate_particle()
and IMP::Decorator::particle_is_instance(). A shell script \c tools/update-decorators is provided which
updates the names in all code in subdirectories of the current directory. Please backup things first.
- a function, IMP::Restraint::safe_evaluate() has been added to be used
when requesting the value of restraints outside of the IMP::Model::evaluate().
## Week of July 18
- The atom::BondPairContainer has been renamed to atom::BondPairFilter
since it wasn't a real container. A real atom::BondPairContainer has
been added.
- Out of source builds mostly works. To do an out of source build, make a link
to \c scons_tools and \c SConstruct from the source directory in the build
directory and then add the line \command{repository="../path_to_src_dir"} in
the \c config.py in the build directory. Then running \c scons in the build
directory will put generated files there. This allows you to make both a
\c release and \c fast build off of the same set of sources. Proper docs
will be added soon.
- The SConscript setup for a module has been greatly simplified so it should
be easy enough for users to maintain their own module and updates to the
build system shouldn't involve changes to user SConscripts any more. This does
mean that any non-svn modules need to be updated. Look at IMP.core or another
module and copy what is there. Again, proper docs will be added soon.
## Week of July 11
- Per Javi's suggestion, the conventions have been split into
"Coding conventions" and "API conventions" and linked from the main page.
- benchmarks got moved to their own module, IMP::benchmark and will
now be tracked over time
## Week of July 4
- FilteredListSingletonContainer and FilteredPairSingletonContainer
went away as there was too much hard to factor code shared with
IMP::core::ListSingletonContainer and IMP::core::PairSingletonContainer. The
IMP::core::ClosePairsScoreState is now handled by a list of filters
on the class itself. That is, do
IMP::core::ClosePairsScoreState::add_close_pair_filter() to add a
filter.
- Hooks have been added to allow actions to be taken on an assertion
or check failure. See IMP::HandleFailure and its descendants for
more details.
- IMP::display::CGOWriter has been much improved and now allows
provides lots of display-time control and easy building of
animations.
- Generic optimizer states have been added
(IMP::core::SingletonsOptimizerState and
IMP::core::PairsOptimizerState).
## Week of June 15
- box distributions (IMP::algebra::random_vector_on_box(),
IMP::algebra::random_vector_in_box()) take bounding boxes
- IMP::em::DensityMap are now IMP::Object objects. Some current
allocations on the stack may need to be changed (since ref counted
objects can't be stack allocated).
- IMP::em::DensityMap::Read() is now deprecated (as is
IMP::em::DensityMap::Write) as they violated a slew of
conventions. Use IMP::em::read_map() and IMP::em::write_map()
instead.
## Week of June 8
- new methods IMP::atom::add_radii() and IMP::atom::add_bonds();
- Hierarchys to IMP::atom::Hierarchies
- IMP::Particles has been changed to a new type. It no longer plays
quite so well with Python lists (you can't create one from an
arbitrary Python list).
- The containers for multiple decorators have been revised to make them
more useful. See IMP::Decorators. You can now implicitly convert,
for %example, a IMP::core::XYZs to an IMP::Particles (as well as use
IMP::Decorators::get_particles()). All methods that take a
collection of particles with a certain type now instead take a
IMP::Decorators.
- A method that has expectations about the particles it takes should
take decorators rather than particles. That is, anything which
expects IMP::core::XYZ particles, should take an IMP::core::XYZs
instead of IMP::Particles.
- IMP_LIST() now takes an extra argument (the name of the plural
container)
- In C++ IMP::Decorator objects are implicitly convertible to
IMP::Particle* objects. Unfortunately, making this work in Python is
problematic.
- More methods take and return decorators rather than
IMP::Particles. This means it is clearer what their expectations are
and what they produce.
## Week of May 15
- The IMP::helper module was added and various functionality moved
there. See its documentation page for a list of what is there.
- IMP::algebra::SphericalCoords was renamed to
IMP::algebra::SphericalVector3D to be consistent with other algebra
classes.
- IMP::algebra::Rotation2D is now IMP::InvalidDefault to be consistent
with the other similar classes.
- We are trying to be a bit more specific about what is expected from
a IMP::atom::Hierarchy. Towards that end, there are two methods for
extracting a representation from a hierarchy,
IMP::atom::get_detailed_representation(), and
IMP::atom::get_simplified_representation()
- A method has been added to produce a simplified copy of an
IMP::atom::Hierarchy. The method is still a bit crude and could
benefit from other people inspecting the output and saying how it
should be improved.
- There is now an IMP::algebra::BoundingBoxD (and
IMP::algebra::BoundingBox3D) to track bounding boxes. There are
methods like IMP::algebra::bound_box(Sphere3D) which gets the
bounding box of a sphere.
- Each IMP::Object has its own log level. If
IMP::Object::set_log_level() is called with a value other than
IMP::DEFAULT, the value is used for code within and called by the
object. To support this in your objects you need to add
IMP_OBJECT_LOG to the start of each major method. It has been added
to some of the core objects.
## Week of May 8
- IMP::atom::MolecularHierarchy has been renamed to
IMP::atom::Hierarchy. Use \command{sed -i.old
"s\#MolecularHierarchy\#Hierarchy\#g" my_files}
- the long-deprecated Name(Decorator) was removed
- The decorator suffix has been removed from decorator names.
- Unit conventions have been established and documented for distance,
energy, force and angle.
- there is a function IMP::atom::create_protein() to create a coarse
grained protein. The function is crude so far, but the idea is that
we should have standard ways of generating such things so that
everyone can benefit from best practices.
- a class IMP::atom::BondGraph has been added so Boost.Graph
algorithms can be used with bond graphs
- the IMP-specific doxygen commands have been documented.
- the doxygen commands unstable{name} and untested{name} have been
added to doxygen to be used for marking methods and functions as
likely to change or not well tested. Pass the name of the class or
method as name.
- bonds can now be added to molecular hierarchies automatically see
IMP::atom::add_bonds()
## Week of May 1
- There is a IMP::Rotation2D
- You can now extract fixed Euler ZYZ angles from a
IMP::Rotation3D. This code can serve as a template for extracting
other Euler angle conventions if they are needed.
- IMP::algebra::rotation_between_two_vectors() changed to
IMP::algebra::rotation_taking_first_to_second() to make it clear
which direction the rotation goes.
## Week of April 27
- IMP::Decorator derived objects are now convertible to bool. So code
like \code if (d) { blah } \endcode works.
- IMP::Decorator::cast now returns a null decorator (\c
DecoratorName()) rather than throwing an exception. This might make
it actually useful.
- New IMP::statistics module for statistical methods
(e.g. clustering).
## Week of April 20
- Support for taking advantage of rigid bodies in collision detection
has been added via the IMP::core::RigidClosePairsFinder.
- All IMP::core::ClosePairsScoreState-related functionality has been
optimized and should be noticeably faster.
- The EMBED project has been merged into the IMP::em module. Thus, it
is no longer necessary to obtain EMBED separately to build IMP::em.
- All C++ methods which work with std::istream or std::ostream
arguments should now be usable from Python: any Python file-like
object can be used.
- The SWIG interface now ties in to the reference counting mechanism
used in the C++ code, for all classes derived from
IMP::RefCounted. So, for %example, deleting a Python object should
not free the underlying C++ object if another C++ object holds a
reference to it, and unrefing a C++ object should not delete it if a
Python object still holds a reference to it. There should be no
further need to manually keep references to Python objects to
prevent things from being prematurely cleaned up. This should be
transparent to the user; please report any problems.
- IMP::atom::AtomDecorator no longer inherits from
IMP::core::XYZDecorator.
## Week of April 13
- The decorators IMP::atom::AtomDecorator, IMP::atom::ChainDecorator,
IMP::atom::ResidueDecorator etc. now inherit from
IMP::atom::MolecularHierarchyDecorator. This means they can set
their IMP::atom::MolecularHierarchyDecorator::Type properly and
saves a lot of typing in the common case. We can always make
hierarchy decorators zero memory overhead if we find that the cost
matters.
- The base classes IMP::Comparable, IMP::NullDefault,
IMP::ValidDefault and IMP::UninitializedDefault were added to
document what the default constructors do for various objects in
IMP.
## Week of April 6
- IMP::Object now defines pure virtual methods
IMP::Object::get_version_info() and IMP::Object::show(). All
non-abstract classes which inherit from IMP::Object must implement
them. Doing this means they are more uniformly implemented and are
documented in one place.
- IMP::Object is now reference counted (the only objects this changes
are IMP::Model and IMP::Optimizer). As a result optimizers and
IMP::Model objects must be created on the heap.
- IMP::RefCounted has had its name changed and no longer inherits from
IMP::Object. This makes it easier to use independently.
- the docs for reference counting (IMP::RefCounted) and and IMP::Decorator
have been improved
- running doxygen produces no warnings. Let's try to keep it that
way. Run \command{scons doc > /dev/null} before you check in large
blocks of new code to make sure that you didn't introduce warnings.
- Helper classes have been added to make SingletonModifier and
PairModifier objects look like functors for C++ and Python. This
makes it so you can use \c map in Python and \c for_each in C++. See
IMP::SingletonFunctor and IMP::PairFunctor for more information.
- The recent changes page has moved to a doxygen page to make it
easier to link changes back to the relevant source code.
## Week of March 20:
- create_rigid_body(), create_rigid_bodies(), create_centroid()
etc. now require you to add the score state to the model
yourself. Whether the rigid body is enforced or not can be
controlled by adding or removing the returned IMP::ScoreState.
- All previously deprecated code has been removed. This includes
indexes in particles, the no-argument constructor for particles and
the functionality that was moved from core to atom.
- The IMP::core::RigidBodyDecorator and
IMP::core::RigidMemberDecorator have been simplified by removing the
traits classes. There is now only one type of rigid body and it
stores the list of member particles internally.
- IMP::core::NameDecorator has been deprecated as IMP::Particles have
built in names (use IMP::Particle::get_name(),
IMP::Particle::set_name()).
- IMP::atom::ChainDecorator has been added
## Week of March 13:
- A new IMP::display::Writer, IMP::display::ChimeraWriter has been
added which exports geometry to native Chimera constructs. It
probably should be used instead of bild and cmm for most purposes as
it combines the best of both types.
- compose() for transformation is now a free function so
compose(rotation, vector) will work via promotions.
- the geometry classes have been cleaned up and are now more
consistent with IMP standards (and more likely to do what their
names/comments suggest). See IMP::algebra::Sphere3D,
IMP::algebra::Cylinder3D, IMP::algebra::Segment3D,
IMP::algebra::Plane3D etc.
- ParticleRefiner has been renamed to IMP::Refiner since the Particle
was long and unnecessary.
¢ IF1•eIF3 translation initiation complex](http://salilab.org/40S-eIF1-eIF3).
- IMP::domino::DiscreteSampler::set_restraints() now allows the set of
restraints used in DOMINO filtering to be controlled (previously, all
restraints in the IMP::Model were used).
- IMP::modeller::IMPRestraints now transfers an IMP::ScoringFunction into the
MODELLER score, not the implicit (and deprecated) score of the
entire IMP::Model.
- Bugfix #775: coordinates of voxels in EM maps were previously inconsistently
treated (they are supposed to be the centers of the voxels, but in some
cases they were the lower left edge). The fix may result in maps and their
bounding boxes appearing shifted by half the voxel size.
# 2.4.0 - 2015-02-27 # {#changelog_2_4_0}
- Python 3 is now supported. The Windows package now works out of the box
with Python 3.3 or 3.4; a `-python3` subpackage is provided for Ubuntu
and Fedora. (Apple does not yet provide Python 3 so the Mac package is not
built with Python 3 support, but if you install Python 3 you can compile
IMP from source to work with it.)
- A new command line tool, `rrt_sample`, allows for running rapidly exploring
random tree (RRT) based sampling, e.g. to sample conformations of multiple
domains connected by flexible linkers.
- Command line tools are now placed in the `bin` directory of modules (the
old `bin` directory, used for utility programs that are not installed, is
now called `utility`). The `applications` directory is removed.
- Several Python modules that were only used by EMageFit have been moved from
IMP::em2d to IMP::EMageFit.
- A new tutorial that uses the IMP::pmi module is now available (modeling of
the RNA Polymerase II stalk).
# 2.3.1 - 2014-12-01 # {#changelog_2_3_1}
- Minor bug fixes.
- Update to IMP::pmi to support the Nup84 and rnapolii biological systems.
# 2.3.0 - 2014-10-24 # {#changelog_2_3_0}
- 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.
- Binary installers for 64-bit Windows are now available.
- The `.py` extension has been removed from all Python applications, so that they are consistent with the C++ applications.
- 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.
- The integrative docking (idock) application now employs SOAP to improve the scoring.
- 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.
- 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.
# 2.2.1 - 2014-08-11 # {#changelog_2_2_1}
- Bugfix: PoseScore (see the ligand_score application) should now match that used by the Pose&Rank web server (http://salilab.org/poseandrank/)
# 2.2.0 - 2014-04-09 # {#changelog_2_2_0}
- 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.
- The Python support for grids was cleaned up. Hopefully this makes it more robust. If you were using a grid in Python that no longer exists, ping us, we can add it back.
- The generic geometry functions were simplified slightly and renamed to IMP::algebra::get_vector_geometry().
- The IMP::base::Flag class was added to simplify adding flags in C++.
- The `--log_level` and `--check_level` command line argument now take strings (eg VERBOSE) to specify their values, rather than cryptic (and a bit unstable) numbers.
- Command line options are now divided into normal and advanced ones. You do `--help_advanced` to show the advanced ones.
- Support for computing Connolly surfaces was added with IMP::algebra::get_connolly_surface(). In addition, there is now IMP::algebra::get_uniform_surface_cover(const IMP::algebra::Sphere3Ds&,double) to sample the surface of a collection of balls.
- IMP::atom::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.
- IMP::atom::get_rmsd(IMP::atom::Selection, IMP::atom::Selection, const IMP::algebra::Transformation3D&) was deprecated. Use IMP::atom::get_rmsd_transforming_first() instead.
- IMP::algebra::get_rmsd() and IMP::algebra::get_rmsd_transforming_first() were added.
- The family of macros IMP_BASE_[SMALL,LARGE]_[UNORDERED,ORDERED]_[MAP,SET] have been added (eg IMP_BASE_SMALL_ORDERED_SET ()). They provide platform and boost-version independent ways to take advantage of the best set/map for an application. In particular, they use boost::container::flat_set and kin when available.
- IMP::atom::State and IMP::atom::Representation decorators have been added to provide support for multiple states and multiple representation schemes. They are integrated with RMFs and IMP::atom::Selection. See atom/multiresolution.py and atom/multistate.py for examples.
- The container implementations has been cleaned up and simplified a bit. This should not change most usage.
- [RMF](http://salilab.github.io/rmf) has been updated. There are a few minor API changes, in addition to a new, faster format (`.rmf3`).
- [Eigen](#Eigen) is now included with IMP.
- The deprecated function IMP::kernel::Optimizer::set_restraints() was removed. Use IMP::kernel::Optimizer::set_scoring_function() instead.
- The deprecated constructor for IMP::kernel::ModelObject that does not take an IMP::kernel::Model was removed. This propagates to constructors IMP::kernel::Restraint, IMP::kernel::ScoreState and kin. Make sure you pass an IMP::kernel::Model as the first constructor argument. Related to this, deprecated functions like get_is_part_of_model(), set_model() were removed as they don't serve any purpose.
- The deprecated methods in IMP::kernel::Optimizer that pertain to attribute optimization were removed. Inherit from IMP::kernel::AttributeOptimizer instead if you want to use them in your optimizer.
- Some deprecated functionality was removed. If you encounter problems, replace IMP::base::OwnerPointer with IMP::base::PointerMember, find logging stuff in IMP/base/log.h, object in IMP/base/Object.h and random in IMP/base/random.h.
- IMP::atom::Chain now uses strings for the chain ids, to be consistent with changes in the PDB. PDB files are written using the first character of the chain string.
- Added orientation-dependent SOAP scoring (IMP::score_functor::OrientedSoap and IMP::atom::OrientedSoapPairScore). Orientation-dependent SOAP scores include those that score loops (SOAP-Loop), protein-peptide interfaces (SOAP-Peptide) and proteins (SOAP-Protein). The library files themselves are rather large (~1.5GB) and so are not included with IMP. They can be downloaded separately from http://salilab.org/SOAP/.
# 2.1.1 - 2013-11-04 # {#changelog_2_1_1}
- Added support for Mac OS 10.9
# 2.1.0 - 2013-10-24 # {#changelog_2_1_0}
- 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.
- 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.
- Class name OwnerPointer was switched to PointerMember, to denote more clearly a ref-counting pointer that is a class member.
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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`).
- 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.
- 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.
- 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.
- [RMF](https://github.com/salilab/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.
# For IMP 2.0 and earlier # {#changelog_2_0}
## Spring 2013
- Modules and applications now have a _Maintainer_ in their `README.md`, giving the github id of the person to whom issues should be assigned.
- `setup_git.py` supports the `--module` flag which will set up git hooks and things for a git repository that contains a module.
- 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.
- 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.
## Winter 2012-2013
- Scons support was removed. Use cmake to build IMP, it is way better.
- 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.
- 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.
- The IMP_BIG_ENDIAN and IMP_LITTLE_ENDIAN preprocessor symbols are deprecated in favor of the BOOST_BIG_ENDIAN and BOOST_LITTLE_ENDIAN symbols.
- 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.
- 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.
- You can now (probably) build IMP with [CMake on IMP wiki](https://github.com/salilab/imp/wiki/Cmake).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- OpenMP support in IMP is officially released. All tests pass. But there has been little specific testing so far.
- Access to attributes using IMP::ParticleIndex and the IMP::Model now works from Python. See IMP::Model::add_attribute() and kin.
- 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.
- 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.
- 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.
- 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 beginning. You can use `./tools/updaters/update_examples.py modules/mymodule` to update a module that was not already updated.
- IMP::base::FailureHandler has been removed as it wasn't used.
- 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.
- Modules now must be in a folder called `modules`, which must have a `description.py` file.
- The build system should now be a little better about cleaning up after itself.
- How headers/doc files/data/examples
- 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 "_" from the method name.
- Nice version numbers will now be generated if you use git. You need to rerun
tools/git/developer_tools/init_git if you have an existing clone.
## Fall 2012
- 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.
- 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.
- 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.
- 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.
- 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.
- 11/8; Evaluation with containers was greatly simplified, moving many methods on containers. We can add backwards compatibility versions if that is interesting.
- 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.
- 11/7: It is now preferred that IMP::Restraint and IMP::ScoreState descendants 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 deprecated. 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.
- 11/3: IMP::container::InContainerPairFilter and friends now treat pairs as unordered. A flag was added to control this.
- 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.
## Summer 2012
- 7/3: IMP_PERIODIC_OPTIMIZER_STATE() was superseded by the class IMP::core::PeriodicOptimizerState as it is rather cleaner than the macro.
- 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.
- 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.
- 6/24: Benchmarks are now put int \c module/benchmark and build to \c build/benchmark/module to remove a recurring source of errors.
- 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.
- 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.
## Winter 2011/2012
- 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.
- 4/4: the filter types were superseded 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()).
- 29/3: IMP::Particle::get_has_model() has been changed to IMP::ModelObject::get_is_part_of_model() to be consistent with other classes.
- 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.
- 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).
- 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.
- 15/3: The vector used throughout IMP is now exposed at IMP::base::Vector and what it does it documented.
- 10/3: IMP::domino::RestraintCache was introduced to provide a documented centralized place to handle restraint evaluation and caching in DOMINO. In the switch various bugs involving maximum scores and IMP::RestraintSet objects were fixed.
- 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.
- 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.
- 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.
- 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.
- 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).
- 3/2: IMP::domino::WriteAssignmentContainer and IMP::domino::ReadAssignmentContainer were added to do direct binary file writing. This is faster than the HDF5 versions.
- 3/2: The installation instructions have been revamped and the developer instruction, in particular, have been greatly simplified.
- 24/1: \c tools/show-changes has been added that shows the changes in the history log since you last updated.
- 24/1: \c tools/make-source has been added that adds a source/header pair to a module
- 24/1: principal components analysis in IMP::algebra was generalized to work in any dimension. This required renaming the class to IMP::algebra::PrincipalComponentAnalysisD.
- 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
- 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.
- 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.
- 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.
- IMP::algebra::ParabolicFit was renamed to IMP::algebra::ParabolicFit2D (a backwards compatibility typedef is currently provided)
- IMP::algebra::LinearFit was renamed to IMP::algebra::LinearFit2D. It now supports error bars on the y-values.
## Fall 2011
- 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).
- Various IMP::algebra plural typedefs which had been using std::vector (since they never were updated), have now been moved to IMP::vector.
- IMP::statistics::HistogramD now supports display with \c matplotlib.
- IMP::statistics::HistogramD supersedes IMP::statistics::Histogram
- 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.
- the core generic restraint and score state support was moved to the kernel to avoid breaking various scores outside of IMP svn.
- 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.
- Decomposition of restraints now results in restraints that are faster to evaluate, using the generic restraint mechanism in IMP kernel.
- 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()
- 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.
- the way various types of geometry is stored in RMF files was changed, breaking backwards compatibility.
## Summer 2011
- 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.
- the source for the kernel has been moved from \c kernel to \c modules/kernel. This is unlikely to effect anyone.
- IMP::core::ExcludedVolumeRestraint now supports filters
- IMP::domino::HDF5AssignmentTable now caches internally, which makes it several times faster than before.
- you can now pick which Python to use with the \c python argument to scons.
- the units for BD diffusion coefficients changed to be consistent with other IMP units.
- IMP::domino::get_interaction_graph() now takes an IMP::RestraintsTemp, like other functions
- 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.
- 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.
- IMP::IntsList, IMP::FloatsList and IMP::StringsList have been added to replace the various scattered solutions for passing such types.
- 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.
- 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.
- 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.
- the IMP::core::DiameterRestraint was ignoring the radii of the particles involved and so was giving artificially low scores. It now is on the actual diameter of this molecule.
- the IMP::core::MonteCarlo optimizers now support incremental evaluation. This can be a lot faster when only a few particles are moved each step.
- 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.
- 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.
- Temp and non-temp decorator lists have been merged in C++. This was done to simplify code since no one was using the non-temp variants. Now all decorator lists are temp (non-reference counted) variants.
- 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.
- 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.
- IMP::domino uses the new IMP::Model::evaluate_if_good() support to accelerate computations
- IMP::core::MonteCarlo can use the IMP::Model::evaluate_if_good() support to more quickly reject
very bad conformations. See IMP::core::MonteCarlo::set_maximum_difference().
- IMP::core::ExcludedVolumeRestraint has been rewritten to be faster. It is especially
faster when used with IMP::Model::evaluate_if_good()
- 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.
- 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.
- 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.
- the RMF helper binaries have been moved to their own application so that they get installed.
- 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.
## Spring 2011
- An interactive mode has been added to IMP::domino::DominoSampler. The interactive mode is useful for understanding domino sampling runs and distributing domino computations across a cluster.
- Functions IMP::domino::set_assignments() and IMP::domino::get_assignments() were added which support
writing subset assignments to data fields in hdf5 files. These can be used to helping to distribute
domino on a cluster as well as debugging the sampling process.
- a Python function IMP.show_graphviz() has been added that attempts to render a graph with \c dot and then open the pdf.
- 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.
- IMP.atom.create_cover() was added to facilitate creating a summary particle for part of a hierarchy in order to accelerate restraints.
- 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.
- 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.
- The Python graph interface now has a remove_vertex method.
- 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.
- 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.
- Preliminary symmetry support has been added via the IMP::core::TransformationSymmetry and IMP::core::TransformationAndReflectionSymmetry classes.
## Winter 2011
- 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()
- IMP::core::MonteCarlo::set_temperature() was renamed to IMP::core::MonteCarlo::set_kt() as that is what it is doing.
- 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).
- IMP::algebra::grids::GridD now supports dense grids in arbitrary dimension through use of IMP::algebra::grids::DenseGridStorageD.
- IMP::Optimizer now can use a list of restraint sets to compute the score rather than the complete Model score.
- each IMP::Restraint now has its own weight. This is lightly tested.
- 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.
- IMP::domino::TrivialParticleStates renamed to IMP::domino::IndexParticleStates to be less judgmental
- IMP::domino::CompoundParticleStates and IMP::domino::RecursiveParticleStates added
- IMP::domino::DominoSampler now supports maximum scores on IMP::RestraintSets (untested).
- the name of the clustering methods have been changed to create_ from get_ since they create objects.
- the names of the recently added metric based clustering support has been changed to Metric rather than Distance.
- 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.
- the function IMP::display::create_restraint_geometry() was added to do what its name says.
- 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.
- IMP::atom::DopePairScore has been added to IMP.
- IMP::atom::CHARMMStereochemistryRestraint provides a high-level simplified
interface to the bonded part of the CHARMM forcefield.
- 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.
- Instructions and scripts have been added for building modules and things externally to the IMP build. See the installation guide.
- IMP::atom::CHARMMParameters can now automatically map CHARMM-style atom and
residue naming to PDB-style, so CHARMM topology files can be used unmodified.
- IMP::atom::CHARMMTopology::add_sequence() provides a simple way to generate a topology from a string of amino acid one-letter codes.
- IMP::atom::CHARMMTopology::add_coordinates() will generate atomic Cartesian coordinates from CHARMM internal coordinate information.
- IMP::atom::CHARMMTopology::add_missing_atoms() and
IMP::atom::remove_charmm_untyped_atoms() can now be used to ensure that atoms
read from a PDB file match the CHARMM topology.
- building of deprecated functionality is now false by default
- 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.
- 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).
- 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.
- 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.
- rename IMP::restrainer::Restraint::print_all_restraints() to IMP::restrainer::Restraint::show_all_restraints() to be consistent with the rest of IMP.
- renamed IMP::atom::get_conect_record_string() to IMP::atom::get_pdb_conect_record_string() to make clearer what it is.
- class and method names are now spell checked. Add missing words to spelling_exceptions in the module test call.
- the plural names (eg IMP.Particles()) have been removed from the Python side as they are just Python lists.
- biological systems can now include internal modules. These provide a convenient place to put application specific C++ and Python code. See the example system for more info.
- IMP_VALUES() now includes IMP_OUTPUT_OPERATOR() so you no longer need two namespace macros for each value.
- 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.
- the IMP::atom::PDBSelector and IMP::atom::Mol2Selector became IMP::Object classes. All this
means is that they need to be created with \c new in C++ code. It also means that one is
no longer prohibited from storing them (not that there is much use in doing that).
- 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.
- IMP::core::RigidBody::lazy_set_reference_frame() was renamed to IMP::core::RigidBody::set_reference_frame_lazy() to fit with the standards better.
- the transform based methods on reference frame which have been deprecated for a while were removed
- 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.
- IMP::atom::NonhydrogenMol2Selector was renamed IMP::atom::NonHydrogenMol2Selector to be consistent with the PDB version
## Fall 2010
- IMP::display::PlaneGeometry was added to display planes
- 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
benefit from better checking.
- 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.
- 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()
- IMP::core::WriteModelOptimizerState is going away as it duplicated IMP::WriteParticlesOptimizerState.
- 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.
- the biological systems specification has been improved a little adding ability to run some rudimentary tests to make sure the scripts are ok and to not require that everything be run from the svn directory.
- 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.
- Logging has been improved to better report the name of methods producing the log messages
- a macro IMP_FUNCTION_LOG has been added which should be added to the start of non-member functions which produce significant logging output.
- 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.
- IMP.domino2 was renamed to IMP.domino and the old IMP.domino was moved
- 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.
- applications and biological systems now have their own documentation pages
- IMP::atom::Hierarchy requires radii on its leaves
- IMP::atom::read_pdb add radii to the atoms
- IMP::helper was merged into IMP::restrainer as all the functionality there was primarily to provide support for restrainer
- IMP::domino2::SubsetEvaluatorTable was removed. Pass the model and IMP::domino2::ParticleStatesTable to the IMP::domino2::RestraintScoreSubsetFilterTable instead.
- 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.
- a new example was added in the kernel to show IMP used on a biological system
- IMP::display::PymolWriter now supports adding labels to things
- IMP::display::PairRestraintGeometry and IMP::display::ConnectivityRestraintGeometry were added to aid in visualizing those restraints.
- IMP::bullet was added with an optimizer to use hard body physics to resolve local collisions.
- 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 separate particle so that the molecular hierarchy doesn't have to worry about having its bounding sphere large enough to enclose all the members.
- IMP::core::KClosePairsPairScore was added to have count based cutoffs for close pair scoring.
- IMP::algebra::get_surface_area_and_volume() was added to compute the two numbers for a set of balls
## Summer 2010
- 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 slightly tweaked to work.
- Javi added his 2D EM scoring functionality as IMP::em2D
- 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.
- 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).
- 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.
- 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).
- 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
- a better explanation of how to use reference counted pointers has been added to IMP::Pointer.
- all simple, planar polygons are now supported for display when CGAL is present
## Week of April 1, 2010
- 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
- types are not checked until the lists are passed to C++
- 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)
- swig has issues with some overloads (not always for obvious reasons). These are being sorted out. None are commonly used.
- get_particles() on a plural object doesn't work in Python (and is not needed in C++). Implicit conversions will always work.
- 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 empty lists of particles in the constructors cause check failures. We can figure out a work around if this is too annoying.
## Week of March 13, 2010
- 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.
- 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).
## Week of March 6, 2010
- 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.
## Week of Feb 27, 2010
- IMP::algebra::decompose_rotation_into_axis_angle() was renamed to IMP::algebra::get_angle_and_axis().
- renamed IMP::atom::bond() and IMP::atom::unbond() to IMP::atom::create_bond() and IMP::atom::destroy_bond() to be more consistent with things
- renamed IMP::core::root() to IMP::core::get_root()
## Week of Feb 21, 2010
- IMP::Object::set_was_owned() was changed to IMP::Object::set_was_used() as that better reflects what the flag means.
- various more interpolation and endian methods had their names fixed (by adding \c get_)
- the function get_mean() on vectors was removed as it duplicated IMP::algebra::get_centroid()
- build_Transformation3D_from_transformation3D was replaced by IMP.algebra.get_transformation_3d()
- IMP::algebra::almost_equal() is now IMP::algebra::get_are_almost_equal() to fit the naming conventions.
- the random vector generators have been cleaned up to remove redundant ones and make the names more consistent. They now have the form of either
- IMP::algebra::get_random_vector_in() or IMP::algebra::get_random_vector_on() where there is one argument describing the volume or shape (such as an IMP::algebra::SphereD<4>).
- or IMP::algebra::get_uniform_surface_cover() where the first argument is the primitive whose surface we are covering and the second is the number of points.
Some good sed strings are
- "s\#random_vector_in_unit_sphere()\#get_random_vector_in(IMP.algebra.get_unit_sphere_3d())\#g"
- "s\#random_vector_in_unit_box()\#get_random_vector_in(IMP.algebra.get_unit_bounding_box_3d())\#g"
- "s\#random_vector_on_unit_sphere()\#get_random_vector_on(IMP.algebra.get_unit_sphere_3d())\#g"
- "s\#random_vector_on_unit_box()\#get_random_vector_on(IMP.algebra.get_unit_bounding_box_3d())\#g"
- "s\#random_vector_in_box(\#get_random_vector_in(\#g"
- "s\#random_vector_on_box(\#get_random_vector_on(\#g"
- "s\#random_vector_in_sphere(\#get_random_vector_in(\#g"
- "s\#random_vector_on_sphere(\#get_random_vector_on(\#g"
- "s\#grid_cover\#get_grid_surface_cover\#g"
- "s\#uniform_coverr\#get_uniform_surface_cover\#g"
.
- Spheres in IMP::algebra are now supported in general dimensions. See IMP::algebra::SphereD.
- Many methods in IMP::algebra were renamed to be more consistent with other methods or general conventions. Most of these simply involved adding \c get_ as a prefix and/or add a \c _3d suffix when they did not take any arguments.
- build_Rotation2D_from_Vector2D became IMP::algebra::get_rotation_to_x_axis()
- most of the Rotation3D and Transformation3D functions (in addition, IMP::algebra::get_identity_rotation_3d() and IMP::algebra::get_identity_transformation_3d() added the \c _3d so we can add 2D versions at some point)
- IMP::algebra::Transformation3D::get_transformed() and IMP::algebra::Rotation3D::get_rotated(). Replacing \c ".transform(" worked in the IMP code base.
- IMP::algebra::get_distance(), this also carries over to the IMP::core::get_distance()
The following global replacements are probably safe (in sed expressions)
- "s\#core.distance(\#core.get_distance\#g"
- "s\#algebra.distance(\#algebra.get_distance\#g"
- "s\#\.transform(\#.get_transformed(\#g" Only in C++
- "s\#\.rotate(\#.get_rotated(\#g" Only in C++
- "s\#rotation_from\#get_rotation_from\#g"
- "s\#rotation_in\#get_rotation_in\#g"
- "s\#identity_rotation(\#get_identity_rotation_3d("
- "s\#::distance(\#::get_distance(\#g"
.
- IMP::algebra::Vector3D and IMP::algebra::Vector3Ds were replaced by the expanded (non-typedef) version in functions parsed by SWIG as the current situation was extremely brittle. For the moment, you should not use the typedefs in definitions that swig sees. Sorry.
- IMP::algebra::Sphere3DPatch was renamed to IMP::algebra::SpherePatch3D to be consistent with the other geometry and allow us to support higher dimensions in the future.
- rigid_align_first_to_second was renamed to IMP::algebra::get_transformation_aligning_first_to_second() and build_Transformation2D_from_point_sets was renamed to IMP::algebra::get_transformation_aligning_pair()
## Week of Feb 14, 2010
- The IMP::atom::Bond types were rearranged to reconcile the protein-centric classification with ligand support.
- IMP::atom::Atom no longer has charge since we have IMP::atom::Charged.
- IMP::atom::read_mol2() and IMP::atom::write_mol2() were added
- IMP::atom::Selector and descendants 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.
- 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.
- IMP::example renamed (from examples)
- The IMP_USAGE_CHECK() macro lost the (unused) third argument.
## Week of February 3, 2010
- The model io code as moved into the kernel so it is now IMP::write_model() and IMP::read_model()
- Remove the version_info argument from the implementation macros. Instead, just pick up the module version info automatically.
- Add a function Object::get_type_name() and Object::get_module() to get the respective bits of information about each object.
- 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().
- The containers were moved to IMP.container. See that module page for a full list of what moved. In the process, the backwards compatibility functions were removed from IMP::container::PairsRestraint and kin.
- IMP.atom.create_protein() now returns the created protein
- the simplify functions have been moved from IMP.helper. They are now IMP.atom.create_simplified_along_backbone().
- IMP.helper.clone() has been renamed to IMP.atom.create_clone()
- IMP.misc.ConnectingPairContainer has been moved to IMP.core.ConnectingPairContainer
- The locations for pixels in IMP::em::DensityMap have been moved to the center of the corresponding voxel from the lower left corner.
- IMP::em::get_transformed(), IMP::em::get_resampled() and IMP::em::get_density() have been added.
- 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.
- 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.
- 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.
- Most geometry now has namespace methods IMP::algebra::get_bounding_box(), IMP::algebra::get_surface_area(), IMP::algebra::get_volume().
## Week of January 22, 2010
- A generic geometry layer has been added (see \ref genericgeometry). Using it, IMP::atom::rmsd(),
IMP::algebra::alignment_taking_first_to_second() and the new IMP::atom::native_overlap() all
can work on either collections of either IMP::core::XYZ particles or IMP::algebra::Vector3Ds.
- 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.
- 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.
- Rename IMP::core::MinimumPairScoreRestraint (and kin, Maximum, Singleton, Triplet and Quad) to IMP::core::MinimumPairRestraint.
- Add IMP::core::MinumumPairScore (and kin).
## Week of January 1, 2010
- IMP::em is now using Particles to resample density maps and for fitting restraints. The previous ParticleAccessPoint mechanism is removed.
- IMP::UsageException and IMP::InternalException are now reserved for their respective
checks (and cannot be thrown by IMP_THROW()). This makes the distinction between API
exceptions (which are thrown in any build mode and should be documented and tested)
and helper exceptions which are only thrown when checks are turned on (and hence
should not be documented) clearer.
- IMP::core::RestraintSet moved to IMP::RestraintSet. The restraint sets now simply define a tree
with weights which the model traverses as opposed to being an opaque IMP::Restraint themselves.
This means that incremental evaluation of restraints in restraint sets now works and that
restraints in restraint sets can be individually evaluated. Existing working usage should not
have changed (so \c sed should manage updates just fine), but the internal
implementation is completely new, so pay attention.
- IMP now has a text i/o layer consisting of IMP::TextInput and IMP::TextOutput. These classes are
convertible to C++ streams and implicitly constructable from both streams and file paths. As a result,
functions that take them will work when called with a string for a file path, a Python file or a
C++ stream.
- The IMP.examples module now documents how to use the needed aspects of scons and SWIG.
- 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.
- 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.
- boost program options is now a checked for dependency.
- 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.
- 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.
- 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).
- 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.
- a new base class IMP::Constraint has been added for constraints. Various
other classes have been renamed to be consistent.
## Week of December 11
- 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.
- 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.
- IMP::ParticlePair::first and second went away since no one claimed to be using it and it complicated the implementation.
- The generic restraints/score states/scores infrastructure has been extended to triplets and quads (for angles and torsion angles).
## Week of December 4
- 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.
- 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.
- 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).
## Week of November 19
- imp.xcodeproj was moved into tools and updated accordingly
- the bin directory finally went away
- IMP::display::ChimeraWriter now supports the latest version of Chimera
- IMP::display::CGOWriter was renamed to IMP::display::PymolWriter as it can do more than just CGO.
- IMP::VectorOfRefCounted::operator[] can now be used for assignments just like a normal vector. No more need to use the IMP::VectorOfRefCounted::set() method.
- the IMP::atom::Hierarchy constructor from an IMP::Particle* is now explicit (as were the decorator constructors)
## Week of November 12
- All exception types are now mapped to equivalent classes in Python. The
class hierarchy is similar (e.g. IMP::ModelException derives from IMP::Exception
in both C++ and Python) so all IMP exceptions can be caught in Python using
"except IMP.Exception". For convenience, the IMP::IOException,
IMP::ValueException and IMP::IndexException classes in Python also derive from
the similarly-named standard Python classes (IOError, ValueError and IndexError
respectively).
## week of October 29 Update
- 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).
- 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().
- Added IMP::core::VolumeRestraint.
- Several functions have been added to helper in creating restraints. They are create_simple_connectivity_on_rigid_bodies(), create_simple_connectivity_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.
- 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().
- IMP::em::read_map() will figure out the file type to use automatically from the extension. Other such methods should follow suite.
- A class IMP::core::StructureSet has been added to provide a convenient way to manage solutions of optimization runs.
- IMP::core::RigidBodyMover now takes its angle argument in radians and is documented as such.
- 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.
- IMP::core::AllPairsPairContainer has been renamed to IMP::core::AllPairContainer and a bipartite version has been added.
- All containers now keep track of what they looked like on the previous time step.
- The IMP::core::ListPairContainer and IMP::core::ListSingletonContainer have had their interface reduced a bit in order to make implementing change tracking easier.
- 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.
- 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.
## Week of October 15
- 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.
## Week of October 8
- 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.
- 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.
- IMP_check() and IMP_assert() have been
replaced with IMP_USAGE_CHECK() and IMP_INTERNAL_CHECK()
respectively. Hopefully this makes it clearer when to use
which. IMP::set_check_level() has been revised accordingly (to use
IMP::USAGE and IMP::USAGE_AND_INTERNAL). Also, IMP_failure() and
IMP_not_implemented() have been renamed to IMP_FAILURE() and
IMP_NOT_IMPLEMENTED() to make all macros be all caps. To update
external code,
- replace IMP.EXPENSIVE with IMP.USAGE_AND_INTERNAL
- replace IMP.CHEAP with IMP.USAGE
- replace IMP_assert and IMP_check as above.
## Week of October 1
- 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.
- .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.
- The search module is no longer built by default and is not longer supported. It will get moved out of svn shortly.
- IMP::ScoreState objects now also have IMP::Interacting::get_interacting_particles() methods. Soon IMP::PairScore and IMP::SingletonScore objects will too.
## Week of September 27
- 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.
- A class IMP::core::RigidBodyDistancePairScore has been added which provides accelerated computations for the distance between two rigid bodies.
- The SWIG input files were renamed from swig.i to swig.i-in to aid in dependency tracking.
- 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.
## Week of September 20
- all \c .i files have been renamed to start with \c IMP_ to help make dependency tracking easier.
- static builds (builds with \c static=True) build both the static and dynamic libraries and just static executables
- 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.
- 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.
- \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.
## Week of August 30
- A new score IMP::core::BoundingBox3DSingletonScore has been added to keep particles
in a box.
- str should now work better in Python when applied to IMP::Object objects and a few others. Objects
should use the new IMP_SHOWABLE and IMP_SHOWABLE_INLINE macros instead of declaring show
functions directory to make it so that they work in Python. It is now a bug to \c print or \c str
to not return something useful in Python for any IMP object.
## Week of August 23
- each module now has a version, eg IMP::get_module_version_info() which is also returned by the various restraints of the module. The Python code checks that loaded libraries have the expected version numbers to try to provide better messages when runtime linking problems occur.
- the various bounding_box methods have been renamed to ::get_bounding_box() to be more consistent with the other names.
- Python documentation is now parsed by doxygen
## Week of August 15
- 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.
## Week of August 8
- 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.
- 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).
- IMP::atom::Mass() has been added for decorating particles with mass. IMP::atom::Atom mass has been moved to that.
- The scheme for generating atom types is now fully specified. See the IMP::atom::AtomType documentation.
- 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.
- 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.
- The contents of bin are moving to tools since the two directories both contained assorted development tools
(not all of which were executable). For now, bin/imppy.sh will still work, but that will go away soon.
- IMP::Decorator::show() now just takes the stream (it used to take a prefix also, which was often ignored).
Anyone who implemented a decorator will have to delete the second argument of their show function.
## Week of August 1
- Containers now have methods IMP::SingletonContainer::evaluate(), IMP::PairContainer::evaluate(),
IMP::SingletonContainer::apply() and IMP::PairContainer::apply(). Using these can be significantly
faster than looping over the particles externally. Similarly, there is IMP::SingletonScore::evaluate(),
IMP::PairScore::evaluate(), IMP::SingletonModifier::apply(), IMP::PairModifier::apply().
- The decorator functions have been renamed to IMP::Decorator::setup_particle(), IMP::Decorator::decorate_particle()
and IMP::Decorator::particle_is_instance(). A shell script \c tools/update-decorators is provided which
updates the names in all code in subdirectories of the current directory. Please backup things first.
- a function, IMP::Restraint::safe_evaluate() has been added to be used
when requesting the value of restraints outside of the IMP::Model::evaluate().
## Week of July 18
- The atom::BondPairContainer has been renamed to atom::BondPairFilter
since it wasn't a real container. A real atom::BondPairContainer has
been added.
- Out of source builds mostly works. To do an out of source build, make a link
to \c scons_tools and \c SConstruct from the source directory in the build
directory and then add the line \command{repository="../path_to_src_dir"} in
the \c config.py in the build directory. Then running \c scons in the build
directory will put generated files there. This allows you to make both a
\c release and \c fast build off of the same set of sources. Proper docs
will be added soon.
- The SConscript setup for a module has been greatly simplified so it should
be easy enough for users to maintain their own module and updates to the
build system shouldn't involve changes to user SConscripts any more. This does
mean that any non-svn modules need to be updated. Look at IMP.core or another
module and copy what is there. Again, proper docs will be added soon.
## Week of July 11
- Per Javi's suggestion, the conventions have been split into
"Coding conventions" and "API conventions" and linked from the main page.
- benchmarks got moved to their own module, IMP::benchmark and will
now be tracked over time
## Week of July 4
- FilteredListSingletonContainer and FilteredPairSingletonContainer
went away as there was too much hard to factor code shared with
IMP::core::ListSingletonContainer and IMP::core::PairSingletonContainer. The
IMP::core::ClosePairsScoreState is now handled by a list of filters
on the class itself. That is, do
IMP::core::ClosePairsScoreState::add_close_pair_filter() to add a
filter.
- Hooks have been added to allow actions to be taken on an assertion
or check failure. See IMP::HandleFailure and its descendants for
more details.
- IMP::display::CGOWriter has been much improved and now allows
provides lots of display-time control and easy building of
animations.
- Generic optimizer states have been added
(IMP::core::SingletonsOptimizerState and
IMP::core::PairsOptimizerState).
## Week of June 15
- box distributions (IMP::algebra::random_vector_on_box(),
IMP::algebra::random_vector_in_box()) take bounding boxes
- IMP::em::DensityMap are now IMP::Object objects. Some current
allocations on the stack may need to be changed (since ref counted
objects can't be stack allocated).
- IMP::em::DensityMap::Read() is now deprecated (as is
IMP::em::DensityMap::Write) as they violated a slew of
conventions. Use IMP::em::read_map() and IMP::em::write_map()
instead.
## Week of June 8
- new methods IMP::atom::add_radii() and IMP::atom::add_bonds();
- Hierarchys to IMP::atom::Hierarchies
- IMP::Particles has been changed to a new type. It no longer plays
quite so well with Python lists (you can't create one from an
arbitrary Python list).
- The containers for multiple decorators have been revised to make them
more useful. See IMP::Decorators. You can now implicitly convert,
for %example, a IMP::core::XYZs to an IMP::Particles (as well as use
IMP::Decorators::get_particles()). All methods that take a
collection of particles with a certain type now instead take a
IMP::Decorators.
- A method that has expectations about the particles it takes should
take decorators rather than particles. That is, anything which
expects IMP::core::XYZ particles, should take an IMP::core::XYZs
instead of IMP::Particles.
- IMP_LIST() now takes an extra argument (the name of the plural
container)
- In C++ IMP::Decorator objects are implicitly convertible to
IMP::Particle* objects. Unfortunately, making this work in Python is
problematic.
- More methods take and return decorators rather than
IMP::Particles. This means it is clearer what their expectations are
and what they produce.
## Week of May 15
- The IMP::helper module was added and various functionality moved
there. See its documentation page for a list of what is there.
- IMP::algebra::SphericalCoords was renamed to
IMP::algebra::SphericalVector3D to be consistent with other algebra
classes.
- IMP::algebra::Rotation2D is now IMP::InvalidDefault to be consistent
with the other similar classes.
- We are trying to be a bit more specific about what is expected from
a IMP::atom::Hierarchy. Towards that end, there are two methods for
extracting a representation from a hierarchy,
IMP::atom::get_detailed_representation(), and
IMP::atom::get_simplified_representation()
- A method has been added to produce a simplified copy of an
IMP::atom::Hierarchy. The method is still a bit crude and could
benefit from other people inspecting the output and saying how it
should be improved.
- There is now an IMP::algebra::BoundingBoxD (and
IMP::algebra::BoundingBox3D) to track bounding boxes. There are
methods like IMP::algebra::bound_box(Sphere3D) which gets the
bounding box of a sphere.
- Each IMP::Object has its own log level. If
IMP::Object::set_log_level() is called with a value other than
IMP::DEFAULT, the value is used for code within and called by the
object. To support this in your objects you need to add
IMP_OBJECT_LOG to the start of each major method. It has been added
to some of the core objects.
## Week of May 8
- IMP::atom::MolecularHierarchy has been renamed to
IMP::atom::Hierarchy. Use \command{sed -i.old
"s\#MolecularHierarchy\#Hierarchy\#g" my_files}
- the long-deprecated Name(Decorator) was removed
- The decorator suffix has been removed from decorator names.
- Unit conventions have been established and documented for distance,
energy, force and angle.
- there is a function IMP::atom::create_protein() to create a coarse
grained protein. The function is crude so far, but the idea is that
we should have standard ways of generating such things so that
everyone can benefit from best practices.
- a class IMP::atom::BondGraph has been added so Boost.Graph
algorithms can be used with bond graphs
- the IMP-specific doxygen commands have been documented.
- the doxygen commands unstable{name} and untested{name} have been
added to doxygen to be used for marking methods and functions as
likely to change or not well tested. Pass the name of the class or
method as name.
- bonds can now be added to molecular hierarchies automatically see
IMP::atom::add_bonds()
## Week of May 1
- There is a IMP::Rotation2D
- You can now extract fixed Euler ZYZ angles from a
IMP::Rotation3D. This code can serve as a template for extracting
other Euler angle conventions if they are needed.
- IMP::algebra::rotation_between_two_vectors() changed to
IMP::algebra::rotation_taking_first_to_second() to make it clear
which direction the rotation goes.
## Week of April 27
- IMP::Decorator derived objects are now convertible to bool. So code
like \code if (d) { blah } \endcode works.
- IMP::Decorator::cast now returns a null decorator (\c
DecoratorName()) rather than throwing an exception. This might make
it actually useful.
- New IMP::statistics module for statistical methods
(e.g. clustering).
## Week of April 20
- Support for taking advantage of rigid bodies in collision detection
has been added via the IMP::core::RigidClosePairsFinder.
- All IMP::core::ClosePairsScoreState-related functionality has been
optimized and should be noticeably faster.
- The EMBED project has been merged into the IMP::em module. Thus, it
is no longer necessary to obtain EMBED separately to build IMP::em.
- All C++ methods which work with std::istream or std::ostream
arguments should now be usable from Python: any Python file-like
object can be used.
- The SWIG interface now ties in to the reference counting mechanism
used in the C++ code, for all classes derived from
IMP::RefCounted. So, for %example, deleting a Python object should
not free the underlying C++ object if another C++ object holds a
reference to it, and unrefing a C++ object should not delete it if a
Python object still holds a reference to it. There should be no
further need to manually keep references to Python objects to
prevent things from being prematurely cleaned up. This should be
transparent to the user; please report any problems.
- IMP::atom::AtomDecorator no longer inherits from
IMP::core::XYZDecorator.
## Week of April 13
- The decorators IMP::atom::AtomDecorator, IMP::atom::ChainDecorator,
IMP::atom::ResidueDecorator etc. now inherit from
IMP::atom::MolecularHierarchyDecorator. This means they can set
their IMP::atom::MolecularHierarchyDecorator::Type properly and
saves a lot of typing in the common case. We can always make
hierarchy decorators zero memory overhead if we find that the cost
matters.
- The base classes IMP::Comparable, IMP::NullDefault,
IMP::ValidDefault and IMP::UninitializedDefault were added to
document what the default constructors do for various objects in
IMP.
## Week of April 6
- IMP::Object now defines pure virtual methods
IMP::Object::get_version_info() and IMP::Object::show(). All
non-abstract classes which inherit from IMP::Object must implement
them. Doing this means they are more uniformly implemented and are
documented in one place.
- IMP::Object is now reference counted (the only objects this changes
are IMP::Model and IMP::Optimizer). As a result optimizers and
IMP::Model objects must be created on the heap.
- IMP::RefCounted has had its name changed and no longer inherits from
IMP::Object. This makes it easier to use independently.
- the docs for reference counting (IMP::RefCounted) and and IMP::Decorator
have been improved
- running doxygen produces no warnings. Let's try to keep it that
way. Run \command{scons doc > /dev/null} before you check in large
blocks of new code to make sure that you didn't introduce warnings.
- Helper classes have been added to make SingletonModifier and
PairModifier objects look like functors for C++ and Python. This
makes it so you can use \c map in Python and \c for_each in C++. See
IMP::SingletonFunctor and IMP::PairFunctor for more information.
- The recent changes page has moved to a doxygen page to make it
easier to link changes back to the relevant source code.
## Week of March 20:
- create_rigid_body(), create_rigid_bodies(), create_centroid()
etc. now require you to add the score state to the model
yourself. Whether the rigid body is enforced or not can be
controlled by adding or removing the returned IMP::ScoreState.
- All previously deprecated code has been removed. This includes
indexes in particles, the no-argument constructor for particles and
the functionality that was moved from core to atom.
- The IMP::core::RigidBodyDecorator and
IMP::core::RigidMemberDecorator have been simplified by removing the
traits classes. There is now only one type of rigid body and it
stores the list of member particles internally.
- IMP::core::NameDecorator has been deprecated as IMP::Particles have
built in names (use IMP::Particle::get_name(),
IMP::Particle::set_name()).
- IMP::atom::ChainDecorator has been added
## Week of March 13:
- A new IMP::display::Writer, IMP::display::ChimeraWriter has been
added which exports geometry to native Chimera constructs. It
probably should be used instead of bild and cmm for most purposes as
it combines the best of both types.
- compose() for transformation is now a free function so
compose(rotation, vector) will work via promotions.
- the geometry classes have been cleaned up and are now more
consistent with IMP standards (and more likely to do what their
names/comments suggest). See IMP::algebra::Sphere3D,
IMP::algebra::Cylinder3D, IMP::algebra::Segment3D,
IMP::algebra::Plane3D etc.
- ParticleRefiner has been renamed to IMP::Refiner since the Particle
was long and unnecessary.
eIF1â ¢eIF3 translation initiation complex](http://salilab.org/40S-eIF1-eIF3).
- IMP::domino::DiscreteSampler::set_restraints() now allows the set of
restraints used in DOMINO filtering to be controlled (previously, all
restraints in the IMP::Model were used).
- IMP::modeller::IMPRestraints now transfers an IMP::ScoringFunction into the
MODELLER score, not the implicit (and deprecated) score of the
entire IMP::Model.
- Bugfix #775: coordinates of voxels in EM maps were previously inconsistently
treated (they are supposed to be the centers of the voxels, but in some
cases they were the lower left edge). The fix may result in maps and their
bounding boxes appearing shifted by half the voxel size.
# 2.4.0 - 2015-02-27 # {#changelog_2_4_0}
- Python 3 is now supported. The Windows package now works out of the box
with Python 3.3 or 3.4; a `-python3` subpackage is provided for Ubuntu
and Fedora. (Apple does not yet provide Python 3 so the Mac package is not
built with Python 3 support, but if you install Python 3 you can compile
IMP from source to work with it.)
- A new command line tool, `rrt_sample`, allows for running rapidly exploring
random tree (RRT) based sampling, e.g. to sample conformations of multiple
domains connected by flexible linkers.
- Command line tools are now placed in the `bin` directory of modules (the
old `bin` directory, used for utility programs that are not installed, is
now called `utility`). The `applications` directory is removed.
- Several Python modules that were only used by EMageFit have been moved from
IMP::em2d to IMP::EMageFit.
- A new tutorial that uses the IMP::pmi module is now available (modeling of
the RNA Polymerase II stalk).
# 2.3.1 - 2014-12-01 # {#changelog_2_3_1}
- Minor bug fixes.
- Update to IMP::pmi to support the Nup84 and rnapolii biological systems.
# 2.3.0 - 2014-10-24 # {#changelog_2_3_0}
- 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.
- Binary installers for 64-bit Windows are now available.
- The `.py` extension has been removed from all Python applications, so that they are consistent with the C++ applications.
- 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.
- The integrative docking (idock) application now employs SOAP to improve the scoring.
- 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.
- 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.
# 2.2.1 - 2014-08-11 # {#changelog_2_2_1}
- Bugfix: PoseScore (see the ligand_score application) should now match that used by the Pose&Rank web server (http://salilab.org/poseandrank/)
# 2.2.0 - 2014-04-09 # {#changelog_2_2_0}
- 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.
- The Python support for grids was cleaned up. Hopefully this makes it more robust. If you were using a grid in Python that no longer exists, ping us, we can add it back.
- The generic geometry functions were simplified slightly and renamed to IMP::algebra::get_vector_geometry().
- The IMP::base::Flag class was added to simplify adding flags in C++.
- The `--log_level` and `--check_level` command line argument now take strings (eg VERBOSE) to specify their values, rather than cryptic (and a bit unstable) numbers.
- Command line options are now divided into normal and advanced ones. You do `--help_advanced` to show the advanced ones.
- Support for computing Connolly surfaces was added with IMP::algebra::get_connolly_surface(). In addition, there is now IMP::algebra::get_uniform_surface_cover(const IMP::algebra::Sphere3Ds&,double) to sample the surface of a collection of balls.
- IMP::atom::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.
- IMP::atom::get_rmsd(IMP::atom::Selection, IMP::atom::Selection, const IMP::algebra::Transformation3D&) was deprecated. Use IMP::atom::get_rmsd_transforming_first() instead.
- IMP::algebra::get_rmsd() and IMP::algebra::get_rmsd_transforming_first() were added.
- The family of macros IMP_BASE_[SMALL,LARGE]_[UNORDERED,ORDERED]_[MAP,SET] have been added (eg IMP_BASE_SMALL_ORDERED_SET ()). They provide platform and boost-version independent ways to take advantage of the best set/map for an application. In particular, they use boost::container::flat_set and kin when available.
- IMP::atom::State and IMP::atom::Representation decorators have been added to provide support for multiple states and multiple representation schemes. They are integrated with RMFs and IMP::atom::Selection. See atom/multiresolution.py and atom/multistate.py for examples.
- The container implementations has been cleaned up and simplified a bit. This should not change most usage.
- [RMF](http://salilab.github.io/rmf) has been updated. There are a few minor API changes, in addition to a new, faster format (`.rmf3`).
- [Eigen](#Eigen) is now included with IMP.
- The deprecated function IMP::kernel::Optimizer::set_restraints() was removed. Use IMP::kernel::Optimizer::set_scoring_function() instead.
- The deprecated constructor for IMP::kernel::ModelObject that does not take an IMP::kernel::Model was removed. This propagates to constructors IMP::kernel::Restraint, IMP::kernel::ScoreState and kin. Make sure you pass an IMP::kernel::Model as the first constructor argument. Related to this, deprecated functions like get_is_part_of_model(), set_model() were removed as they don't serve any purpose.
- The deprecated methods in IMP::kernel::Optimizer that pertain to attribute optimization were removed. Inherit from IMP::kernel::AttributeOptimizer instead if you want to use them in your optimizer.
- Some deprecated functionality was removed. If you encounter problems, replace IMP::base::OwnerPointer with IMP::base::PointerMember, find logging stuff in IMP/base/log.h, object in IMP/base/Object.h and random in IMP/base/random.h.
- IMP::atom::Chain now uses strings for the chain ids, to be consistent with changes in the PDB. PDB files are written using the first character of the chain string.
- Added orientation-dependent SOAP scoring (IMP::score_functor::OrientedSoap and IMP::atom::OrientedSoapPairScore). Orientation-dependent SOAP scores include those that score loops (SOAP-Loop), protein-peptide interfaces (SOAP-Peptide) and proteins (SOAP-Protein). The library files themselves are rather large (~1.5GB) and so are not included with IMP. They can be downloaded separately from http://salilab.org/SOAP/.
# 2.1.1 - 2013-11-04 # {#changelog_2_1_1}
- Added support for Mac OS 10.9
# 2.1.0 - 2013-10-24 # {#changelog_2_1_0}
- 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.
- 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.
- Class name OwnerPointer was switched to PointerMember, to denote more clearly a ref-counting pointer that is a class member.
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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`).
- 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.
- 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.
- 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.
- [RMF](https://github.com/salilab/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.
# For IMP 2.0 and earlier # {#changelog_2_0}
## Spring 2013
- Modules and applications now have a _Maintainer_ in their `README.md`, giving the github id of the person to whom issues should be assigned.
- `setup_git.py` supports the `--module` flag which will set up git hooks and things for a git repository that contains a module.
- 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.
- 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.
## Winter 2012-2013
- Scons support was removed. Use cmake to build IMP, it is way better.
- 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.
- 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.
- The IMP_BIG_ENDIAN and IMP_LITTLE_ENDIAN preprocessor symbols are deprecated in favor of the BOOST_BIG_ENDIAN and BOOST_LITTLE_ENDIAN symbols.
- 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.
- 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.
- You can now (probably) build IMP with [CMake on IMP wiki](https://github.com/salilab/imp/wiki/Cmake).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- OpenMP support in IMP is officially released. All tests pass. But there has been little specific testing so far.
- Access to attributes using IMP::ParticleIndex and the IMP::Model now works from Python. See IMP::Model::add_attribute() and kin.
- 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.
- 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.
- 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.
- 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 beginning. You can use `./tools/updaters/update_examples.py modules/mymodule` to update a module that was not already updated.
- IMP::base::FailureHandler has been removed as it wasn't used.
- 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.
- Modules now must be in a folder called `modules`, which must have a `description.py` file.
- The build system should now be a little better about cleaning up after itself.
- How headers/doc files/data/examples
- 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 "_" from the method name.
- Nice version numbers will now be generated if you use git. You need to rerun
tools/git/developer_tools/init_git if you have an existing clone.
## Fall 2012
- 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.
- 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.
- 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.
- 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.
- 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.
- 11/8; Evaluation with containers was greatly simplified, moving many methods on containers. We can add backwards compatibility versions if that is interesting.
- 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.
- 11/7: It is now preferred that IMP::Restraint and IMP::ScoreState descendants 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 deprecated. 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.
- 11/3: IMP::container::InContainerPairFilter and friends now treat pairs as unordered. A flag was added to control this.
- 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.
## Summer 2012
- 7/3: IMP_PERIODIC_OPTIMIZER_STATE() was superseded by the class IMP::core::PeriodicOptimizerState as it is rather cleaner than the macro.
- 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.
- 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.
- 6/24: Benchmarks are now put int \c module/benchmark and build to \c build/benchmark/module to remove a recurring source of errors.
- 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.
- 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.
## Winter 2011/2012
- 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.
- 4/4: the filter types were superseded 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()).
- 29/3: IMP::Particle::get_has_model() has been changed to IMP::ModelObject::get_is_part_of_model() to be consistent with other classes.
- 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.
- 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).
- 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.
- 15/3: The vector used throughout IMP is now exposed at IMP::base::Vector and what it does it documented.
- 10/3: IMP::domino::RestraintCache was introduced to provide a documented centralized place to handle restraint evaluation and caching in DOMINO. In the switch various bugs involving maximum scores and IMP::RestraintSet objects were fixed.
- 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.
- 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.
- 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.
- 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.
- 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).
- 3/2: IMP::domino::WriteAssignmentContainer and IMP::domino::ReadAssignmentContainer were added to do direct binary file writing. This is faster than the HDF5 versions.
- 3/2: The installation instructions have been revamped and the developer instruction, in particular, have been greatly simplified.
- 24/1: \c tools/show-changes has been added that shows the changes in the history log since you last updated.
- 24/1: \c tools/make-source has been added that adds a source/header pair to a module
- 24/1: principal components analysis in IMP::algebra was generalized to work in any dimension. This required renaming the class to IMP::algebra::PrincipalComponentAnalysisD.
- 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
- 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.
- 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.
- 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.
- IMP::algebra::ParabolicFit was renamed to IMP::algebra::ParabolicFit2D (a backwards compatibility typedef is currently provided)
- IMP::algebra::LinearFit was renamed to IMP::algebra::LinearFit2D. It now supports error bars on the y-values.
## Fall 2011
- 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).
- Various IMP::algebra plural typedefs which had been using std::vector (since they never were updated), have now been moved to IMP::vector.
- IMP::statistics::HistogramD now supports display with \c matplotlib.
- IMP::statistics::HistogramD supersedes IMP::statistics::Histogram
- 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.
- the core generic restraint and score state support was moved to the kernel to avoid breaking various scores outside of IMP svn.
- 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.
- Decomposition of restraints now results in restraints that are faster to evaluate, using the generic restraint mechanism in IMP kernel.
- 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()
- 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.
- the way various types of geometry is stored in RMF files was changed, breaking backwards compatibility.
## Summer 2011
- 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.
- the source for the kernel has been moved from \c kernel to \c modules/kernel. This is unlikely to effect anyone.
- IMP::core::ExcludedVolumeRestraint now supports filters
- IMP::domino::HDF5AssignmentTable now caches internally, which makes it several times faster than before.
- you can now pick which Python to use with the \c python argument to scons.
- the units for BD diffusion coefficients changed to be consistent with other IMP units.
- IMP::domino::get_interaction_graph() now takes an IMP::RestraintsTemp, like other functions
- 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.
- 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.
- IMP::IntsList, IMP::FloatsList and IMP::StringsList have been added to replace the various scattered solutions for passing such types.
- 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.
- 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.
- 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.
- the IMP::core::DiameterRestraint was ignoring the radii of the particles involved and so was giving artificially low scores. It now is on the actual diameter of this molecule.
- the IMP::core::MonteCarlo optimizers now support incremental evaluation. This can be a lot faster when only a few particles are moved each step.
- 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.
- 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.
- Temp and non-temp decorator lists have been merged in C++. This was done to simplify code since no one was using the non-temp variants. Now all decorator lists are temp (non-reference counted) variants.
- 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.
- 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.
- IMP::domino uses the new IMP::Model::evaluate_if_good() support to accelerate computations
- IMP::core::MonteCarlo can use the IMP::Model::evaluate_if_good() support to more quickly reject
very bad conformations. See IMP::core::MonteCarlo::set_maximum_difference().
- IMP::core::ExcludedVolumeRestraint has been rewritten to be faster. It is especially
faster when used with IMP::Model::evaluate_if_good()
- 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.
- 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.
- 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.
- the RMF helper binaries have been moved to their own application so that they get installed.
- 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.
## Spring 2011
- An interactive mode has been added to IMP::domino::DominoSampler. The interactive mode is useful for understanding domino sampling runs and distributing domino computations across a cluster.
- Functions IMP::domino::set_assignments() and IMP::domino::get_assignments() were added which support
writing subset assignments to data fields in hdf5 files. These can be used to helping to distribute
domino on a cluster as well as debugging the sampling process.
- a Python function IMP.show_graphviz() has been added that attempts to render a graph with \c dot and then open the pdf.
- 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.
- IMP.atom.create_cover() was added to facilitate creating a summary particle for part of a hierarchy in order to accelerate restraints.
- 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.
- 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.
- The Python graph interface now has a remove_vertex method.
- 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.
- 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.
- Preliminary symmetry support has been added via the IMP::core::TransformationSymmetry and IMP::core::TransformationAndReflectionSymmetry classes.
## Winter 2011
- 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()
- IMP::core::MonteCarlo::set_temperature() was renamed to IMP::core::MonteCarlo::set_kt() as that is what it is doing.
- 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).
- IMP::algebra::grids::GridD now supports dense grids in arbitrary dimension through use of IMP::algebra::grids::DenseGridStorageD.
- IMP::Optimizer now can use a list of restraint sets to compute the score rather than the complete Model score.
- each IMP::Restraint now has its own weight. This is lightly tested.
- 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.
- IMP::domino::TrivialParticleStates renamed to IMP::domino::IndexParticleStates to be less judgmental
- IMP::domino::CompoundParticleStates and IMP::domino::RecursiveParticleStates added
- IMP::domino::DominoSampler now supports maximum scores on IMP::RestraintSets (untested).
- the name of the clustering methods have been changed to create_ from get_ since they create objects.
- the names of the recently added metric based clustering support has been changed to Metric rather than Distance.
- 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.
- the function IMP::display::create_restraint_geometry() was added to do what its name says.
- 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.
- IMP::atom::DopePairScore has been added to IMP.
- IMP::atom::CHARMMStereochemistryRestraint provides a high-level simplified
interface to the bonded part of the CHARMM forcefield.
- 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.
- Instructions and scripts have been added for building modules and things externally to the IMP build. See the installation guide.
- IMP::atom::CHARMMParameters can now automatically map CHARMM-style atom and
residue naming to PDB-style, so CHARMM topology files can be used unmodified.
- IMP::atom::CHARMMTopology::add_sequence() provides a simple way to generate a topology from a string of amino acid one-letter codes.
- IMP::atom::CHARMMTopology::add_coordinates() will generate atomic Cartesian coordinates from CHARMM internal coordinate information.
- IMP::atom::CHARMMTopology::add_missing_atoms() and
IMP::atom::remove_charmm_untyped_atoms() can now be used to ensure that atoms
read from a PDB file match the CHARMM topology.
- building of deprecated functionality is now false by default
- 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.
- 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).
- 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.
- 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.
- rename IMP::restrainer::Restraint::print_all_restraints() to IMP::restrainer::Restraint::show_all_restraints() to be consistent with the rest of IMP.
- renamed IMP::atom::get_conect_record_string() to IMP::atom::get_pdb_conect_record_string() to make clearer what it is.
- class and method names are now spell checked. Add missing words to spelling_exceptions in the module test call.
- the plural names (eg IMP.Particles()) have been removed from the Python side as they are just Python lists.
- biological systems can now include internal modules. These provide a convenient place to put application specific C++ and Python code. See the example system for more info.
- IMP_VALUES() now includes IMP_OUTPUT_OPERATOR() so you no longer need two namespace macros for each value.
- 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.
- the IMP::atom::PDBSelector and IMP::atom::Mol2Selector became IMP::Object classes. All this
means is that they need to be created with \c new in C++ code. It also means that one is
no longer prohibited from storing them (not that there is much use in doing that).
- 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.
- IMP::core::RigidBody::lazy_set_reference_frame() was renamed to IMP::core::RigidBody::set_reference_frame_lazy() to fit with the standards better.
- the transform based methods on reference frame which have been deprecated for a while were removed
- 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.
- IMP::atom::NonhydrogenMol2Selector was renamed IMP::atom::NonHydrogenMol2Selector to be consistent with the PDB version
## Fall 2010
- IMP::display::PlaneGeometry was added to display planes
- 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
benefit from better checking.
- 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.
- 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()
- IMP::core::WriteModelOptimizerState is going away as it duplicated IMP::WriteParticlesOptimizerState.
- 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.
- the biological systems specification has been improved a little adding ability to run some rudimentary tests to make sure the scripts are ok and to not require that everything be run from the svn directory.
- 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.
- Logging has been improved to better report the name of methods producing the log messages
- a macro IMP_FUNCTION_LOG has been added which should be added to the start of non-member functions which produce significant logging output.
- 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.
- IMP.domino2 was renamed to IMP.domino and the old IMP.domino was moved
- 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.
- applications and biological systems now have their own documentation pages
- IMP::atom::Hierarchy requires radii on its leaves
- IMP::atom::read_pdb add radii to the atoms
- IMP::helper was merged into IMP::restrainer as all the functionality there was primarily to provide support for restrainer
- IMP::domino2::SubsetEvaluatorTable was removed. Pass the model and IMP::domino2::ParticleStatesTable to the IMP::domino2::RestraintScoreSubsetFilterTable instead.
- 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.
- a new example was added in the kernel to show IMP used on a biological system
- IMP::display::PymolWriter now supports adding labels to things
- IMP::display::PairRestraintGeometry and IMP::display::ConnectivityRestraintGeometry were added to aid in visualizing those restraints.
- IMP::bullet was added with an optimizer to use hard body physics to resolve local collisions.
- 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 separate particle so that the molecular hierarchy doesn't have to worry about having its bounding sphere large enough to enclose all the members.
- IMP::core::KClosePairsPairScore was added to have count based cutoffs for close pair scoring.
- IMP::algebra::get_surface_area_and_volume() was added to compute the two numbers for a set of balls
## Summer 2010
- 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 slightly tweaked to work.
- Javi added his 2D EM scoring functionality as IMP::em2D
- 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.
- 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).
- 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.
- 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).
- 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
- a better explanation of how to use reference counted pointers has been added to IMP::Pointer.
- all simple, planar polygons are now supported for display when CGAL is present
## Week of April 1, 2010
- 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
- types are not checked until the lists are passed to C++
- 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)
- swig has issues with some overloads (not always for obvious reasons). These are being sorted out. None are commonly used.
- get_particles() on a plural object doesn't work in Python (and is not needed in C++). Implicit conversions will always work.
- 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 empty lists of particles in the constructors cause check failures. We can figure out a work around if this is too annoying.
## Week of March 13, 2010
- 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.
- 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).
## Week of March 6, 2010
- 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.
## Week of Feb 27, 2010
- IMP::algebra::decompose_rotation_into_axis_angle() was renamed to IMP::algebra::get_angle_and_axis().
- renamed IMP::atom::bond() and IMP::atom::unbond() to IMP::atom::create_bond() and IMP::atom::destroy_bond() to be more consistent with things
- renamed IMP::core::root() to IMP::core::get_root()
## Week of Feb 21, 2010
- IMP::Object::set_was_owned() was changed to IMP::Object::set_was_used() as that better reflects what the flag means.
- various more interpolation and endian methods had their names fixed (by adding \c get_)
- the function get_mean() on vectors was removed as it duplicated IMP::algebra::get_centroid()
- build_Transformation3D_from_transformation3D was replaced by IMP.algebra.get_transformation_3d()
- IMP::algebra::almost_equal() is now IMP::algebra::get_are_almost_equal() to fit the naming conventions.
- the random vector generators have been cleaned up to remove redundant ones and make the names more consistent. They now have the form of either
- IMP::algebra::get_random_vector_in() or IMP::algebra::get_random_vector_on() where there is one argument describing the volume or shape (such as an IMP::algebra::SphereD<4>).
- or IMP::algebra::get_uniform_surface_cover() where the first argument is the primitive whose surface we are covering and the second is the number of points.
Some good sed strings are
- "s\#random_vector_in_unit_sphere()\#get_random_vector_in(IMP.algebra.get_unit_sphere_3d())\#g"
- "s\#random_vector_in_unit_box()\#get_random_vector_in(IMP.algebra.get_unit_bounding_box_3d())\#g"
- "s\#random_vector_on_unit_sphere()\#get_random_vector_on(IMP.algebra.get_unit_sphere_3d())\#g"
- "s\#random_vector_on_unit_box()\#get_random_vector_on(IMP.algebra.get_unit_bounding_box_3d())\#g"
- "s\#random_vector_in_box(\#get_random_vector_in(\#g"
- "s\#random_vector_on_box(\#get_random_vector_on(\#g"
- "s\#random_vector_in_sphere(\#get_random_vector_in(\#g"
- "s\#random_vector_on_sphere(\#get_random_vector_on(\#g"
- "s\#grid_cover\#get_grid_surface_cover\#g"
- "s\#uniform_coverr\#get_uniform_surface_cover\#g"
.
- Spheres in IMP::algebra are now supported in general dimensions. See IMP::algebra::SphereD.
- Many methods in IMP::algebra were renamed to be more consistent with other methods or general conventions. Most of these simply involved adding \c get_ as a prefix and/or add a \c _3d suffix when they did not take any arguments.
- build_Rotation2D_from_Vector2D became IMP::algebra::get_rotation_to_x_axis()
- most of the Rotation3D and Transformation3D functions (in addition, IMP::algebra::get_identity_rotation_3d() and IMP::algebra::get_identity_transformation_3d() added the \c _3d so we can add 2D versions at some point)
- IMP::algebra::Transformation3D::get_transformed() and IMP::algebra::Rotation3D::get_rotated(). Replacing \c ".transform(" worked in the IMP code base.
- IMP::algebra::get_distance(), this also carries over to the IMP::core::get_distance()
The following global replacements are probably safe (in sed expressions)
- "s\#core.distance(\#core.get_distance\#g"
- "s\#algebra.distance(\#algebra.get_distance\#g"
- "s\#\.transform(\#.get_transformed(\#g" Only in C++
- "s\#\.rotate(\#.get_rotated(\#g" Only in C++
- "s\#rotation_from\#get_rotation_from\#g"
- "s\#rotation_in\#get_rotation_in\#g"
- "s\#identity_rotation(\#get_identity_rotation_3d("
- "s\#::distance(\#::get_distance(\#g"
.
- IMP::algebra::Vector3D and IMP::algebra::Vector3Ds were replaced by the expanded (non-typedef) version in functions parsed by SWIG as the current situation was extremely brittle. For the moment, you should not use the typedefs in definitions that swig sees. Sorry.
- IMP::algebra::Sphere3DPatch was renamed to IMP::algebra::SpherePatch3D to be consistent with the other geometry and allow us to support higher dimensions in the future.
- rigid_align_first_to_second was renamed to IMP::algebra::get_transformation_aligning_first_to_second() and build_Transformation2D_from_point_sets was renamed to IMP::algebra::get_transformation_aligning_pair()
## Week of Feb 14, 2010
- The IMP::atom::Bond types were rearranged to reconcile the protein-centric classification with ligand support.
- IMP::atom::Atom no longer has charge since we have IMP::atom::Charged.
- IMP::atom::read_mol2() and IMP::atom::write_mol2() were added
- IMP::atom::Selector and descendants 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.
- 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.
- IMP::example renamed (from examples)
- The IMP_USAGE_CHECK() macro lost the (unused) third argument.
## Week of February 3, 2010
- The model io code as moved into the kernel so it is now IMP::write_model() and IMP::read_model()
- Remove the version_info argument from the implementation macros. Instead, just pick up the module version info automatically.
- Add a function Object::get_type_name() and Object::get_module() to get the respective bits of information about each object.
- 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().
- The containers were moved to IMP.container. See that module page for a full list of what moved. In the process, the backwards compatibility functions were removed from IMP::container::PairsRestraint and kin.
- IMP.atom.create_protein() now returns the created protein
- the simplify functions have been moved from IMP.helper. They are now IMP.atom.create_simplified_along_backbone().
- IMP.helper.clone() has been renamed to IMP.atom.create_clone()
- IMP.misc.ConnectingPairContainer has been moved to IMP.core.ConnectingPairContainer
- The locations for pixels in IMP::em::DensityMap have been moved to the center of the corresponding voxel from the lower left corner.
- IMP::em::get_transformed(), IMP::em::get_resampled() and IMP::em::get_density() have been added.
- 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.
- 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.
- 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.
- Most geometry now has namespace methods IMP::algebra::get_bounding_box(), IMP::algebra::get_surface_area(), IMP::algebra::get_volume().
## Week of January 22, 2010
- A generic geometry layer has been added (see \ref genericgeometry). Using it, IMP::atom::rmsd(),
IMP::algebra::alignment_taking_first_to_second() and the new IMP::atom::native_overlap() all
can work on either collections of either IMP::core::XYZ particles or IMP::algebra::Vector3Ds.
- 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.
- 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.
- Rename IMP::core::MinimumPairScoreRestraint (and kin, Maximum, Singleton, Triplet and Quad) to IMP::core::MinimumPairRestraint.
- Add IMP::core::MinumumPairScore (and kin).
## Week of January 1, 2010
- IMP::em is now using Particles to resample density maps and for fitting restraints. The previous ParticleAccessPoint mechanism is removed.
- IMP::UsageException and IMP::InternalException are now reserved for their respective
checks (and cannot be thrown by IMP_THROW()). This makes the distinction between API
exceptions (which are thrown in any build mode and should be documented and tested)
and helper exceptions which are only thrown when checks are turned on (and hence
should not be documented) clearer.
- IMP::core::RestraintSet moved to IMP::RestraintSet. The restraint sets now simply define a tree
with weights which the model traverses as opposed to being an opaque IMP::Restraint themselves.
This means that incremental evaluation of restraints in restraint sets now works and that
restraints in restraint sets can be individually evaluated. Existing working usage should not
have changed (so \c sed should manage updates just fine), but the internal
implementation is completely new, so pay attention.
- IMP now has a text i/o layer consisting of IMP::TextInput and IMP::TextOutput. These classes are
convertible to C++ streams and implicitly constructable from both streams and file paths. As a result,
functions that take them will work when called with a string for a file path, a Python file or a
C++ stream.
- The IMP.examples module now documents how to use the needed aspects of scons and SWIG.
- 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.
- 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.
- boost program options is now a checked for dependency.
- 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.
- 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.
- 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).
- 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.
- a new base class IMP::Constraint has been added for constraints. Various
other classes have been renamed to be consistent.
## Week of December 11
- 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.
- 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.
- IMP::ParticlePair::first and second went away since no one claimed to be using it and it complicated the implementation.
- The generic restraints/score states/scores infrastructure has been extended to triplets and quads (for angles and torsion angles).
## Week of December 4
- 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.
- 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.
- 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).
## Week of November 19
- imp.xcodeproj was moved into tools and updated accordingly
- the bin directory finally went away
- IMP::display::ChimeraWriter now supports the latest version of Chimera
- IMP::display::CGOWriter was renamed to IMP::display::PymolWriter as it can do more than just CGO.
- IMP::VectorOfRefCounted::operator[] can now be used for assignments just like a normal vector. No more need to use the IMP::VectorOfRefCounted::set() method.
- the IMP::atom::Hierarchy constructor from an IMP::Particle* is now explicit (as were the decorator constructors)
## Week of November 12
- All exception types are now mapped to equivalent classes in Python. The
class hierarchy is similar (e.g. IMP::ModelException derives from IMP::Exception
in both C++ and Python) so all IMP exceptions can be caught in Python using
"except IMP.Exception". For convenience, the IMP::IOException,
IMP::ValueException and IMP::IndexException classes in Python also derive from
the similarly-named standard Python classes (IOError, ValueError and IndexError
respectively).
## week of October 29 Update
- 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).
- 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().
- Added IMP::core::VolumeRestraint.
- Several functions have been added to helper in creating restraints. They are create_simple_connectivity_on_rigid_bodies(), create_simple_connectivity_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.
- 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().
- IMP::em::read_map() will figure out the file type to use automatically from the extension. Other such methods should follow suite.
- A class IMP::core::StructureSet has been added to provide a convenient way to manage solutions of optimization runs.
- IMP::core::RigidBodyMover now takes its angle argument in radians and is documented as such.
- 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.
- IMP::core::AllPairsPairContainer has been renamed to IMP::core::AllPairContainer and a bipartite version has been added.
- All containers now keep track of what they looked like on the previous time step.
- The IMP::core::ListPairContainer and IMP::core::ListSingletonContainer have had their interface reduced a bit in order to make implementing change tracking easier.
- 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.
- 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.
## Week of October 15
- 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.
## Week of October 8
- 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.
- 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.
- IMP_check() and IMP_assert() have been
replaced with IMP_USAGE_CHECK() and IMP_INTERNAL_CHECK()
respectively. Hopefully this makes it clearer when to use
which. IMP::set_check_level() has been revised accordingly (to use
IMP::USAGE and IMP::USAGE_AND_INTERNAL). Also, IMP_failure() and
IMP_not_implemented() have been renamed to IMP_FAILURE() and
IMP_NOT_IMPLEMENTED() to make all macros be all caps. To update
external code,
- replace IMP.EXPENSIVE with IMP.USAGE_AND_INTERNAL
- replace IMP.CHEAP with IMP.USAGE
- replace IMP_assert and IMP_check as above.
## Week of October 1
- 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.
- .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.
- The search module is no longer built by default and is not longer supported. It will get moved out of svn shortly.
- IMP::ScoreState objects now also have IMP::Interacting::get_interacting_particles() methods. Soon IMP::PairScore and IMP::SingletonScore objects will too.
## Week of September 27
- 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.
- A class IMP::core::RigidBodyDistancePairScore has been added which provides accelerated computations for the distance between two rigid bodies.
- The SWIG input files were renamed from swig.i to swig.i-in to aid in dependency tracking.
- 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.
## Week of September 20
- all \c .i files have been renamed to start with \c IMP_ to help make dependency tracking easier.
- static builds (builds with \c static=True) build both the static and dynamic libraries and just static executables
- 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.
- 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.
- \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.
## Week of August 30
- A new score IMP::core::BoundingBox3DSingletonScore has been added to keep particles
in a box.
- str should now work better in Python when applied to IMP::Object objects and a few others. Objects
should use the new IMP_SHOWABLE and IMP_SHOWABLE_INLINE macros instead of declaring show
functions directory to make it so that they work in Python. It is now a bug to \c print or \c str
to not return something useful in Python for any IMP object.
## Week of August 23
- each module now has a version, eg IMP::get_module_version_info() which is also returned by the various restraints of the module. The Python code checks that loaded libraries have the expected version numbers to try to provide better messages when runtime linking problems occur.
- the various bounding_box methods have been renamed to ::get_bounding_box() to be more consistent with the other names.
- Python documentation is now parsed by doxygen
## Week of August 15
- 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.
## Week of August 8
- 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.
- 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).
- IMP::atom::Mass() has been added for decorating particles with mass. IMP::atom::Atom mass has been moved to that.
- The scheme for generating atom types is now fully specified. See the IMP::atom::AtomType documentation.
- 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.
- 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.
- The contents of bin are moving to tools since the two directories both contained assorted development tools
(not all of which were executable). For now, bin/imppy.sh will still work, but that will go away soon.
- IMP::Decorator::show() now just takes the stream (it used to take a prefix also, which was often ignored).
Anyone who implemented a decorator will have to delete the second argument of their show function.
## Week of August 1
- Containers now have methods IMP::SingletonContainer::evaluate(), IMP::PairContainer::evaluate(),
IMP::SingletonContainer::apply() and IMP::PairContainer::apply(). Using these can be significantly
faster than looping over the particles externally. Similarly, there is IMP::SingletonScore::evaluate(),
IMP::PairScore::evaluate(), IMP::SingletonModifier::apply(), IMP::PairModifier::apply().
- The decorator functions have been renamed to IMP::Decorator::setup_particle(), IMP::Decorator::decorate_particle()
and IMP::Decorator::particle_is_instance(). A shell script \c tools/update-decorators is provided which
updates the names in all code in subdirectories of the current directory. Please backup things first.
- a function, IMP::Restraint::safe_evaluate() has been added to be used
when requesting the value of restraints outside of the IMP::Model::evaluate().
## Week of July 18
- The atom::BondPairContainer has been renamed to atom::BondPairFilter
since it wasn't a real container. A real atom::BondPairContainer has
been added.
- Out of source builds mostly works. To do an out of source build, make a link
to \c scons_tools and \c SConstruct from the source directory in the build
directory and then add the line \command{repository="../path_to_src_dir"} in
the \c config.py in the build directory. Then running \c scons in the build
directory will put generated files there. This allows you to make both a
\c release and \c fast build off of the same set of sources. Proper docs
will be added soon.
- The SConscript setup for a module has been greatly simplified so it should
be easy enough for users to maintain their own module and updates to the
build system shouldn't involve changes to user SConscripts any more. This does
mean that any non-svn modules need to be updated. Look at IMP.core or another
module and copy what is there. Again, proper docs will be added soon.
## Week of July 11
- Per Javi's suggestion, the conventions have been split into
"Coding conventions" and "API conventions" and linked from the main page.
- benchmarks got moved to their own module, IMP::benchmark and will
now be tracked over time
## Week of July 4
- FilteredListSingletonContainer and FilteredPairSingletonContainer
went away as there was too much hard to factor code shared with
IMP::core::ListSingletonContainer and IMP::core::PairSingletonContainer. The
IMP::core::ClosePairsScoreState is now handled by a list of filters
on the class itself. That is, do
IMP::core::ClosePairsScoreState::add_close_pair_filter() to add a
filter.
- Hooks have been added to allow actions to be taken on an assertion
or check failure. See IMP::HandleFailure and its descendants for
more details.
- IMP::display::CGOWriter has been much improved and now allows
provides lots of display-time control and easy building of
animations.
- Generic optimizer states have been added
(IMP::core::SingletonsOptimizerState and
IMP::core::PairsOptimizerState).
## Week of June 15
- box distributions (IMP::algebra::random_vector_on_box(),
IMP::algebra::random_vector_in_box()) take bounding boxes
- IMP::em::DensityMap are now IMP::Object objects. Some current
allocations on the stack may need to be changed (since ref counted
objects can't be stack allocated).
- IMP::em::DensityMap::Read() is now deprecated (as is
IMP::em::DensityMap::Write) as they violated a slew of
conventions. Use IMP::em::read_map() and IMP::em::write_map()
instead.
## Week of June 8
- new methods IMP::atom::add_radii() and IMP::atom::add_bonds();
- Hierarchys to IMP::atom::Hierarchies
- IMP::Particles has been changed to a new type. It no longer plays
quite so well with Python lists (you can't create one from an
arbitrary Python list).
- The containers for multiple decorators have been revised to make them
more useful. See IMP::Decorators. You can now implicitly convert,
for %example, a IMP::core::XYZs to an IMP::Particles (as well as use
IMP::Decorators::get_particles()). All methods that take a
collection of particles with a certain type now instead take a
IMP::Decorators.
- A method that has expectations about the particles it takes should
take decorators rather than particles. That is, anything which
expects IMP::core::XYZ particles, should take an IMP::core::XYZs
instead of IMP::Particles.
- IMP_LIST() now takes an extra argument (the name of the plural
container)
- In C++ IMP::Decorator objects are implicitly convertible to
IMP::Particle* objects. Unfortunately, making this work in Python is
problematic.
- More methods take and return decorators rather than
IMP::Particles. This means it is clearer what their expectations are
and what they produce.
## Week of May 15
- The IMP::helper module was added and various functionality moved
there. See its documentation page for a list of what is there.
- IMP::algebra::SphericalCoords was renamed to
IMP::algebra::SphericalVector3D to be consistent with other algebra
classes.
- IMP::algebra::Rotation2D is now IMP::InvalidDefault to be consistent
with the other similar classes.
- We are trying to be a bit more specific about what is expected from
a IMP::atom::Hierarchy. Towards that end, there are two methods for
extracting a representation from a hierarchy,
IMP::atom::get_detailed_representation(), and
IMP::atom::get_simplified_representation()
- A method has been added to produce a simplified copy of an
IMP::atom::Hierarchy. The method is still a bit crude and could
benefit from other people inspecting the output and saying how it
should be improved.
- There is now an IMP::algebra::BoundingBoxD (and
IMP::algebra::BoundingBox3D) to track bounding boxes. There are
methods like IMP::algebra::bound_box(Sphere3D) which gets the
bounding box of a sphere.
- Each IMP::Object has its own log level. If
IMP::Object::set_log_level() is called with a value other than
IMP::DEFAULT, the value is used for code within and called by the
object. To support this in your objects you need to add
IMP_OBJECT_LOG to the start of each major method. It has been added
to some of the core objects.
## Week of May 8
- IMP::atom::MolecularHierarchy has been renamed to
IMP::atom::Hierarchy. Use \command{sed -i.old
"s\#MolecularHierarchy\#Hierarchy\#g" my_files}
- the long-deprecated Name(Decorator) was removed
- The decorator suffix has been removed from decorator names.
- Unit conventions have been established and documented for distance,
energy, force and angle.
- there is a function IMP::atom::create_protein() to create a coarse
grained protein. The function is crude so far, but the idea is that
we should have standard ways of generating such things so that
everyone can benefit from best practices.
- a class IMP::atom::BondGraph has been added so Boost.Graph
algorithms can be used with bond graphs
- the IMP-specific doxygen commands have been documented.
- the doxygen commands unstable{name} and untested{name} have been
added to doxygen to be used for marking methods and functions as
likely to change or not well tested. Pass the name of the class or
method as name.
- bonds can now be added to molecular hierarchies automatically see
IMP::atom::add_bonds()
## Week of May 1
- There is a IMP::Rotation2D
- You can now extract fixed Euler ZYZ angles from a
IMP::Rotation3D. This code can serve as a template for extracting
other Euler angle conventions if they are needed.
- IMP::algebra::rotation_between_two_vectors() changed to
IMP::algebra::rotation_taking_first_to_second() to make it clear
which direction the rotation goes.
## Week of April 27
- IMP::Decorator derived objects are now convertible to bool. So code
like \code if (d) { blah } \endcode works.
- IMP::Decorator::cast now returns a null decorator (\c
DecoratorName()) rather than throwing an exception. This might make
it actually useful.
- New IMP::statistics module for statistical methods
(e.g. clustering).
## Week of April 20
- Support for taking advantage of rigid bodies in collision detection
has been added via the IMP::core::RigidClosePairsFinder.
- All IMP::core::ClosePairsScoreState-related functionality has been
optimized and should be noticeably faster.
- The EMBED project has been merged into the IMP::em module. Thus, it
is no longer necessary to obtain EMBED separately to build IMP::em.
- All C++ methods which work with std::istream or std::ostream
arguments should now be usable from Python: any Python file-like
object can be used.
- The SWIG interface now ties in to the reference counting mechanism
used in the C++ code, for all classes derived from
IMP::RefCounted. So, for %example, deleting a Python object should
not free the underlying C++ object if another C++ object holds a
reference to it, and unrefing a C++ object should not delete it if a
Python object still holds a reference to it. There should be no
further need to manually keep references to Python objects to
prevent things from being prematurely cleaned up. This should be
transparent to the user; please report any problems.
- IMP::atom::AtomDecorator no longer inherits from
IMP::core::XYZDecorator.
## Week of April 13
- The decorators IMP::atom::AtomDecorator, IMP::atom::ChainDecorator,
IMP::atom::ResidueDecorator etc. now inherit from
IMP::atom::MolecularHierarchyDecorator. This means they can set
their IMP::atom::MolecularHierarchyDecorator::Type properly and
saves a lot of typing in the common case. We can always make
hierarchy decorators zero memory overhead if we find that the cost
matters.
- The base classes IMP::Comparable, IMP::NullDefault,
IMP::ValidDefault and IMP::UninitializedDefault were added to
document what the default constructors do for various objects in
IMP.
## Week of April 6
- IMP::Object now defines pure virtual methods
IMP::Object::get_version_info() and IMP::Object::show(). All
non-abstract classes which inherit from IMP::Object must implement
them. Doing this means they are more uniformly implemented and are
documented in one place.
- IMP::Object is now reference counted (the only objects this changes
are IMP::Model and IMP::Optimizer). As a result optimizers and
IMP::Model objects must be created on the heap.
- IMP::RefCounted has had its name changed and no longer inherits from
IMP::Object. This makes it easier to use independently.
- the docs for reference counting (IMP::RefCounted) and and IMP::Decorator
have been improved
- running doxygen produces no warnings. Let's try to keep it that
way. Run \command{scons doc > /dev/null} before you check in large
blocks of new code to make sure that you didn't introduce warnings.
- Helper classes have been added to make SingletonModifier and
PairModifier objects look like functors for C++ and Python. This
makes it so you can use \c map in Python and \c for_each in C++. See
IMP::SingletonFunctor and IMP::PairFunctor for more information.
- The recent changes page has moved to a doxygen page to make it
easier to link changes back to the relevant source code.
## Week of March 20:
- create_rigid_body(), create_rigid_bodies(), create_centroid()
etc. now require you to add the score state to the model
yourself. Whether the rigid body is enforced or not can be
controlled by adding or removing the returned IMP::ScoreState.
- All previously deprecated code has been removed. This includes
indexes in particles, the no-argument constructor for particles and
the functionality that was moved from core to atom.
- The IMP::core::RigidBodyDecorator and
IMP::core::RigidMemberDecorator have been simplified by removing the
traits classes. There is now only one type of rigid body and it
stores the list of member particles internally.
- IMP::core::NameDecorator has been deprecated as IMP::Particles have
built in names (use IMP::Particle::get_name(),
IMP::Particle::set_name()).
- IMP::atom::ChainDecorator has been added
## Week of March 13:
- A new IMP::display::Writer, IMP::display::ChimeraWriter has been
added which exports geometry to native Chimera constructs. It
probably should be used instead of bild and cmm for most purposes as
it combines the best of both types.
- compose() for transformation is now a free function so
compose(rotation, vector) will work via promotions.
- the geometry classes have been cleaned up and are now more
consistent with IMP standards (and more likely to do what their
names/comments suggest). See IMP::algebra::Sphere3D,
IMP::algebra::Cylinder3D, IMP::algebra::Segment3D,
IMP::algebra::Plane3D etc.
- ParticleRefiner has been renamed to IMP::Refiner since the Particle
was long and unnecessary.
€ eIF3 translation initiation complex](http://salilab.org/40S-eIF1-eIF3).
- IMP::domino::DiscreteSampler::set_restraints() now allows the set of
restraints used in DOMINO filtering to be controlled (previously, all
restraints in the IMP::Model were used).
- IMP::modeller::IMPRestraints now transfers an IMP::ScoringFunction into the
MODELLER score, not the implicit (and deprecated) score of the
entire IMP::Model.
- Bugfix #775: coordinates of voxels in EM maps were previously inconsistently
treated (they are supposed to be the centers of the voxels, but in some
cases they were the lower left edge). The fix may result in maps and their
bounding boxes appearing shifted by half the voxel size.
# 2.4.0 - 2015-02-27 # {#changelog_2_4_0}
- Python 3 is now supported. The Windows package now works out of the box
with Python 3.3 or 3.4; a `-python3` subpackage is provided for Ubuntu
and Fedora. (Apple does not yet provide Python 3 so the Mac package is not
built with Python 3 support, but if you install Python 3 you can compile
IMP from source to work with it.)
- A new command line tool, `rrt_sample`, allows for running rapidly exploring
random tree (RRT) based sampling, e.g. to sample conformations of multiple
domains connected by flexible linkers.
- Command line tools are now placed in the `bin` directory of modules (the
old `bin` directory, used for utility programs that are not installed, is
now called `utility`). The `applications` directory is removed.
- Several Python modules that were only used by EMageFit have been moved from
IMP::em2d to IMP::EMageFit.
- A new tutorial that uses the IMP::pmi module is now available (modeling of
the RNA Polymerase II stalk).
# 2.3.1 - 2014-12-01 # {#changelog_2_3_1}
- Minor bug fixes.
- Update to IMP::pmi to support the Nup84 and rnapolii biological systems.
# 2.3.0 - 2014-10-24 # {#changelog_2_3_0}
- 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.
- Binary installers for 64-bit Windows are now available.
- The `.py` extension has been removed from all Python applications, so that they are consistent with the C++ applications.
- 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.
- The integrative docking (idock) application now employs SOAP to improve the scoring.
- 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.
- 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.
# 2.2.1 - 2014-08-11 # {#changelog_2_2_1}
- Bugfix: PoseScore (see the ligand_score application) should now match that used by the Pose&Rank web server (http://salilab.org/poseandrank/)
# 2.2.0 - 2014-04-09 # {#changelog_2_2_0}
- 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.
- The Python support for grids was cleaned up. Hopefully this makes it more robust. If you were using a grid in Python that no longer exists, ping us, we can add it back.
- The generic geometry functions were simplified slightly and renamed to IMP::algebra::get_vector_geometry().
- The IMP::base::Flag class was added to simplify adding flags in C++.
- The `--log_level` and `--check_level` command line argument now take strings (eg VERBOSE) to specify their values, rather than cryptic (and a bit unstable) numbers.
- Command line options are now divided into normal and advanced ones. You do `--help_advanced` to show the advanced ones.
- Support for computing Connolly surfaces was added with IMP::algebra::get_connolly_surface(). In addition, there is now IMP::algebra::get_uniform_surface_cover(const IMP::algebra::Sphere3Ds&,double) to sample the surface of a collection of balls.
- IMP::atom::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.
- IMP::atom::get_rmsd(IMP::atom::Selection, IMP::atom::Selection, const IMP::algebra::Transformation3D&) was deprecated. Use IMP::atom::get_rmsd_transforming_first() instead.
- IMP::algebra::get_rmsd() and IMP::algebra::get_rmsd_transforming_first() were added.
- The family of macros IMP_BASE_[SMALL,LARGE]_[UNORDERED,ORDERED]_[MAP,SET] have been added (eg IMP_BASE_SMALL_ORDERED_SET ()). They provide platform and boost-version independent ways to take advantage of the best set/map for an application. In particular, they use boost::container::flat_set and kin when available.
- IMP::atom::State and IMP::atom::Representation decorators have been added to provide support for multiple states and multiple representation schemes. They are integrated with RMFs and IMP::atom::Selection. See atom/multiresolution.py and atom/multistate.py for examples.
- The container implementations has been cleaned up and simplified a bit. This should not change most usage.
- [RMF](http://salilab.github.io/rmf) has been updated. There are a few minor API changes, in addition to a new, faster format (`.rmf3`).
- [Eigen](#Eigen) is now included with IMP.
- The deprecated function IMP::kernel::Optimizer::set_restraints() was removed. Use IMP::kernel::Optimizer::set_scoring_function() instead.
- The deprecated constructor for IMP::kernel::ModelObject that does not take an IMP::kernel::Model was removed. This propagates to constructors IMP::kernel::Restraint, IMP::kernel::ScoreState and kin. Make sure you pass an IMP::kernel::Model as the first constructor argument. Related to this, deprecated functions like get_is_part_of_model(), set_model() were removed as they don't serve any purpose.
- The deprecated methods in IMP::kernel::Optimizer that pertain to attribute optimization were removed. Inherit from IMP::kernel::AttributeOptimizer instead if you want to use them in your optimizer.
- Some deprecated functionality was removed. If you encounter problems, replace IMP::base::OwnerPointer with IMP::base::PointerMember, find logging stuff in IMP/base/log.h, object in IMP/base/Object.h and random in IMP/base/random.h.
- IMP::atom::Chain now uses strings for the chain ids, to be consistent with changes in the PDB. PDB files are written using the first character of the chain string.
- Added orientation-dependent SOAP scoring (IMP::score_functor::OrientedSoap and IMP::atom::OrientedSoapPairScore). Orientation-dependent SOAP scores include those that score loops (SOAP-Loop), protein-peptide interfaces (SOAP-Peptide) and proteins (SOAP-Protein). The library files themselves are rather large (~1.5GB) and so are not included with IMP. They can be downloaded separately from http://salilab.org/SOAP/.
# 2.1.1 - 2013-11-04 # {#changelog_2_1_1}
- Added support for Mac OS 10.9
# 2.1.0 - 2013-10-24 # {#changelog_2_1_0}
- 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.
- 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.
- Class name OwnerPointer was switched to PointerMember, to denote more clearly a ref-counting pointer that is a class member.
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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`).
- 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.
- 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.
- 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.
- [RMF](https://github.com/salilab/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.
# For IMP 2.0 and earlier # {#changelog_2_0}
## Spring 2013
- Modules and applications now have a _Maintainer_ in their `README.md`, giving the github id of the person to whom issues should be assigned.
- `setup_git.py` supports the `--module` flag which will set up git hooks and things for a git repository that contains a module.
- 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.
- 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.
## Winter 2012-2013
- Scons support was removed. Use cmake to build IMP, it is way better.
- 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.
- 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.
- The IMP_BIG_ENDIAN and IMP_LITTLE_ENDIAN preprocessor symbols are deprecated in favor of the BOOST_BIG_ENDIAN and BOOST_LITTLE_ENDIAN symbols.
- 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.
- 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.
- You can now (probably) build IMP with [CMake on IMP wiki](https://github.com/salilab/imp/wiki/Cmake).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- OpenMP support in IMP is officially released. All tests pass. But there has been little specific testing so far.
- Access to attributes using IMP::ParticleIndex and the IMP::Model now works from Python. See IMP::Model::add_attribute() and kin.
- 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.
- 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.
- 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.
- 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 beginning. You can use `./tools/updaters/update_examples.py modules/mymodule` to update a module that was not already updated.
- IMP::base::FailureHandler has been removed as it wasn't used.
- 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.
- Modules now must be in a folder called `modules`, which must have a `description.py` file.
- The build system should now be a little better about cleaning up after itself.
- How headers/doc files/data/examples
- 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 "_" from the method name.
- Nice version numbers will now be generated if you use git. You need to rerun
tools/git/developer_tools/init_git if you have an existing clone.
## Fall 2012
- 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.
- 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.
- 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.
- 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.
- 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.
- 11/8; Evaluation with containers was greatly simplified, moving many methods on containers. We can add backwards compatibility versions if that is interesting.
- 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.
- 11/7: It is now preferred that IMP::Restraint and IMP::ScoreState descendants 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 deprecated. 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.
- 11/3: IMP::container::InContainerPairFilter and friends now treat pairs as unordered. A flag was added to control this.
- 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.
## Summer 2012
- 7/3: IMP_PERIODIC_OPTIMIZER_STATE() was superseded by the class IMP::core::PeriodicOptimizerState as it is rather cleaner than the macro.
- 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.
- 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.
- 6/24: Benchmarks are now put int \c module/benchmark and build to \c build/benchmark/module to remove a recurring source of errors.
- 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.
- 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.
## Winter 2011/2012
- 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.
- 4/4: the filter types were superseded 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()).
- 29/3: IMP::Particle::get_has_model() has been changed to IMP::ModelObject::get_is_part_of_model() to be consistent with other classes.
- 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.
- 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).
- 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.
- 15/3: The vector used throughout IMP is now exposed at IMP::base::Vector and what it does it documented.
- 10/3: IMP::domino::RestraintCache was introduced to provide a documented centralized place to handle restraint evaluation and caching in DOMINO. In the switch various bugs involving maximum scores and IMP::RestraintSet objects were fixed.
- 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.
- 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.
- 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.
- 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.
- 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).
- 3/2: IMP::domino::WriteAssignmentContainer and IMP::domino::ReadAssignmentContainer were added to do direct binary file writing. This is faster than the HDF5 versions.
- 3/2: The installation instructions have been revamped and the developer instruction, in particular, have been greatly simplified.
- 24/1: \c tools/show-changes has been added that shows the changes in the history log since you last updated.
- 24/1: \c tools/make-source has been added that adds a source/header pair to a module
- 24/1: principal components analysis in IMP::algebra was generalized to work in any dimension. This required renaming the class to IMP::algebra::PrincipalComponentAnalysisD.
- 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
- 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.
- 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.
- 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.
- IMP::algebra::ParabolicFit was renamed to IMP::algebra::ParabolicFit2D (a backwards compatibility typedef is currently provided)
- IMP::algebra::LinearFit was renamed to IMP::algebra::LinearFit2D. It now supports error bars on the y-values.
## Fall 2011
- 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).
- Various IMP::algebra plural typedefs which had been using std::vector (since they never were updated), have now been moved to IMP::vector.
- IMP::statistics::HistogramD now supports display with \c matplotlib.
- IMP::statistics::HistogramD supersedes IMP::statistics::Histogram
- 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.
- the core generic restraint and score state support was moved to the kernel to avoid breaking various scores outside of IMP svn.
- 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.
- Decomposition of restraints now results in restraints that are faster to evaluate, using the generic restraint mechanism in IMP kernel.
- 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()
- 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.
- the way various types of geometry is stored in RMF files was changed, breaking backwards compatibility.
## Summer 2011
- 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.
- the source for the kernel has been moved from \c kernel to \c modules/kernel. This is unlikely to effect anyone.
- IMP::core::ExcludedVolumeRestraint now supports filters
- IMP::domino::HDF5AssignmentTable now caches internally, which makes it several times faster than before.
- you can now pick which Python to use with the \c python argument to scons.
- the units for BD diffusion coefficients changed to be consistent with other IMP units.
- IMP::domino::get_interaction_graph() now takes an IMP::RestraintsTemp, like other functions
- 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.
- 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.
- IMP::IntsList, IMP::FloatsList and IMP::StringsList have been added to replace the various scattered solutions for passing such types.
- 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.
- 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.
- 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.
- the IMP::core::DiameterRestraint was ignoring the radii of the particles involved and so was giving artificially low scores. It now is on the actual diameter of this molecule.
- the IMP::core::MonteCarlo optimizers now support incremental evaluation. This can be a lot faster when only a few particles are moved each step.
- 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.
- 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.
- Temp and non-temp decorator lists have been merged in C++. This was done to simplify code since no one was using the non-temp variants. Now all decorator lists are temp (non-reference counted) variants.
- 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.
- 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.
- IMP::domino uses the new IMP::Model::evaluate_if_good() support to accelerate computations
- IMP::core::MonteCarlo can use the IMP::Model::evaluate_if_good() support to more quickly reject
very bad conformations. See IMP::core::MonteCarlo::set_maximum_difference().
- IMP::core::ExcludedVolumeRestraint has been rewritten to be faster. It is especially
faster when used with IMP::Model::evaluate_if_good()
- 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.
- 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.
- 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.
- the RMF helper binaries have been moved to their own application so that they get installed.
- 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.
## Spring 2011
- An interactive mode has been added to IMP::domino::DominoSampler. The interactive mode is useful for understanding domino sampling runs and distributing domino computations across a cluster.
- Functions IMP::domino::set_assignments() and IMP::domino::get_assignments() were added which support
writing subset assignments to data fields in hdf5 files. These can be used to helping to distribute
domino on a cluster as well as debugging the sampling process.
- a Python function IMP.show_graphviz() has been added that attempts to render a graph with \c dot and then open the pdf.
- 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.
- IMP.atom.create_cover() was added to facilitate creating a summary particle for part of a hierarchy in order to accelerate restraints.
- 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.
- 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.
- The Python graph interface now has a remove_vertex method.
- 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.
- 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.
- Preliminary symmetry support has been added via the IMP::core::TransformationSymmetry and IMP::core::TransformationAndReflectionSymmetry classes.
## Winter 2011
- 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()
- IMP::core::MonteCarlo::set_temperature() was renamed to IMP::core::MonteCarlo::set_kt() as that is what it is doing.
- 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).
- IMP::algebra::grids::GridD now supports dense grids in arbitrary dimension through use of IMP::algebra::grids::DenseGridStorageD.
- IMP::Optimizer now can use a list of restraint sets to compute the score rather than the complete Model score.
- each IMP::Restraint now has its own weight. This is lightly tested.
- 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.
- IMP::domino::TrivialParticleStates renamed to IMP::domino::IndexParticleStates to be less judgmental
- IMP::domino::CompoundParticleStates and IMP::domino::RecursiveParticleStates added
- IMP::domino::DominoSampler now supports maximum scores on IMP::RestraintSets (untested).
- the name of the clustering methods have been changed to create_ from get_ since they create objects.
- the names of the recently added metric based clustering support has been changed to Metric rather than Distance.
- 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.
- the function IMP::display::create_restraint_geometry() was added to do what its name says.
- 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.
- IMP::atom::DopePairScore has been added to IMP.
- IMP::atom::CHARMMStereochemistryRestraint provides a high-level simplified
interface to the bonded part of the CHARMM forcefield.
- 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.
- Instructions and scripts have been added for building modules and things externally to the IMP build. See the installation guide.
- IMP::atom::CHARMMParameters can now automatically map CHARMM-style atom and
residue naming to PDB-style, so CHARMM topology files can be used unmodified.
- IMP::atom::CHARMMTopology::add_sequence() provides a simple way to generate a topology from a string of amino acid one-letter codes.
- IMP::atom::CHARMMTopology::add_coordinates() will generate atomic Cartesian coordinates from CHARMM internal coordinate information.
- IMP::atom::CHARMMTopology::add_missing_atoms() and
IMP::atom::remove_charmm_untyped_atoms() can now be used to ensure that atoms
read from a PDB file match the CHARMM topology.
- building of deprecated functionality is now false by default
- 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.
- 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).
- 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.
- 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.
- rename IMP::restrainer::Restraint::print_all_restraints() to IMP::restrainer::Restraint::show_all_restraints() to be consistent with the rest of IMP.
- renamed IMP::atom::get_conect_record_string() to IMP::atom::get_pdb_conect_record_string() to make clearer what it is.
- class and method names are now spell checked. Add missing words to spelling_exceptions in the module test call.
- the plural names (eg IMP.Particles()) have been removed from the Python side as they are just Python lists.
- biological systems can now include internal modules. These provide a convenient place to put application specific C++ and Python code. See the example system for more info.
- IMP_VALUES() now includes IMP_OUTPUT_OPERATOR() so you no longer need two namespace macros for each value.
- 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.
- the IMP::atom::PDBSelector and IMP::atom::Mol2Selector became IMP::Object classes. All this
means is that they need to be created with \c new in C++ code. It also means that one is
no longer prohibited from storing them (not that there is much use in doing that).
- 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.
- IMP::core::RigidBody::lazy_set_reference_frame() was renamed to IMP::core::RigidBody::set_reference_frame_lazy() to fit with the standards better.
- the transform based methods on reference frame which have been deprecated for a while were removed
- 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.
- IMP::atom::NonhydrogenMol2Selector was renamed IMP::atom::NonHydrogenMol2Selector to be consistent with the PDB version
## Fall 2010
- IMP::display::PlaneGeometry was added to display planes
- 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
benefit from better checking.
- 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.
- 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()
- IMP::core::WriteModelOptimizerState is going away as it duplicated IMP::WriteParticlesOptimizerState.
- 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.
- the biological systems specification has been improved a little adding ability to run some rudimentary tests to make sure the scripts are ok and to not require that everything be run from the svn directory.
- 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.
- Logging has been improved to better report the name of methods producing the log messages
- a macro IMP_FUNCTION_LOG has been added which should be added to the start of non-member functions which produce significant logging output.
- 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.
- IMP.domino2 was renamed to IMP.domino and the old IMP.domino was moved
- 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.
- applications and biological systems now have their own documentation pages
- IMP::atom::Hierarchy requires radii on its leaves
- IMP::atom::read_pdb add radii to the atoms
- IMP::helper was merged into IMP::restrainer as all the functionality there was primarily to provide support for restrainer
- IMP::domino2::SubsetEvaluatorTable was removed. Pass the model and IMP::domino2::ParticleStatesTable to the IMP::domino2::RestraintScoreSubsetFilterTable instead.
- 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.
- a new example was added in the kernel to show IMP used on a biological system
- IMP::display::PymolWriter now supports adding labels to things
- IMP::display::PairRestraintGeometry and IMP::display::ConnectivityRestraintGeometry were added to aid in visualizing those restraints.
- IMP::bullet was added with an optimizer to use hard body physics to resolve local collisions.
- 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 separate particle so that the molecular hierarchy doesn't have to worry about having its bounding sphere large enough to enclose all the members.
- IMP::core::KClosePairsPairScore was added to have count based cutoffs for close pair scoring.
- IMP::algebra::get_surface_area_and_volume() was added to compute the two numbers for a set of balls
## Summer 2010
- 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 slightly tweaked to work.
- Javi added his 2D EM scoring functionality as IMP::em2D
- 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.
- 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).
- 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.
- 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).
- 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
- a better explanation of how to use reference counted pointers has been added to IMP::Pointer.
- all simple, planar polygons are now supported for display when CGAL is present
## Week of April 1, 2010
- 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
- types are not checked until the lists are passed to C++
- 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)
- swig has issues with some overloads (not always for obvious reasons). These are being sorted out. None are commonly used.
- get_particles() on a plural object doesn't work in Python (and is not needed in C++). Implicit conversions will always work.
- 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 empty lists of particles in the constructors cause check failures. We can figure out a work around if this is too annoying.
## Week of March 13, 2010
- 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.
- 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).
## Week of March 6, 2010
- 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.
## Week of Feb 27, 2010
- IMP::algebra::decompose_rotation_into_axis_angle() was renamed to IMP::algebra::get_angle_and_axis().
- renamed IMP::atom::bond() and IMP::atom::unbond() to IMP::atom::create_bond() and IMP::atom::destroy_bond() to be more consistent with things
- renamed IMP::core::root() to IMP::core::get_root()
## Week of Feb 21, 2010
- IMP::Object::set_was_owned() was changed to IMP::Object::set_was_used() as that better reflects what the flag means.
- various more interpolation and endian methods had their names fixed (by adding \c get_)
- the function get_mean() on vectors was removed as it duplicated IMP::algebra::get_centroid()
- build_Transformation3D_from_transformation3D was replaced by IMP.algebra.get_transformation_3d()
- IMP::algebra::almost_equal() is now IMP::algebra::get_are_almost_equal() to fit the naming conventions.
- the random vector generators have been cleaned up to remove redundant ones and make the names more consistent. They now have the form of either
- IMP::algebra::get_random_vector_in() or IMP::algebra::get_random_vector_on() where there is one argument describing the volume or shape (such as an IMP::algebra::SphereD<4>).
- or IMP::algebra::get_uniform_surface_cover() where the first argument is the primitive whose surface we are covering and the second is the number of points.
Some good sed strings are
- "s\#random_vector_in_unit_sphere()\#get_random_vector_in(IMP.algebra.get_unit_sphere_3d())\#g"
- "s\#random_vector_in_unit_box()\#get_random_vector_in(IMP.algebra.get_unit_bounding_box_3d())\#g"
- "s\#random_vector_on_unit_sphere()\#get_random_vector_on(IMP.algebra.get_unit_sphere_3d())\#g"
- "s\#random_vector_on_unit_box()\#get_random_vector_on(IMP.algebra.get_unit_bounding_box_3d())\#g"
- "s\#random_vector_in_box(\#get_random_vector_in(\#g"
- "s\#random_vector_on_box(\#get_random_vector_on(\#g"
- "s\#random_vector_in_sphere(\#get_random_vector_in(\#g"
- "s\#random_vector_on_sphere(\#get_random_vector_on(\#g"
- "s\#grid_cover\#get_grid_surface_cover\#g"
- "s\#uniform_coverr\#get_uniform_surface_cover\#g"
.
- Spheres in IMP::algebra are now supported in general dimensions. See IMP::algebra::SphereD.
- Many methods in IMP::algebra were renamed to be more consistent with other methods or general conventions. Most of these simply involved adding \c get_ as a prefix and/or add a \c _3d suffix when they did not take any arguments.
- build_Rotation2D_from_Vector2D became IMP::algebra::get_rotation_to_x_axis()
- most of the Rotation3D and Transformation3D functions (in addition, IMP::algebra::get_identity_rotation_3d() and IMP::algebra::get_identity_transformation_3d() added the \c _3d so we can add 2D versions at some point)
- IMP::algebra::Transformation3D::get_transformed() and IMP::algebra::Rotation3D::get_rotated(). Replacing \c ".transform(" worked in the IMP code base.
- IMP::algebra::get_distance(), this also carries over to the IMP::core::get_distance()
The following global replacements are probably safe (in sed expressions)
- "s\#core.distance(\#core.get_distance\#g"
- "s\#algebra.distance(\#algebra.get_distance\#g"
- "s\#\.transform(\#.get_transformed(\#g" Only in C++
- "s\#\.rotate(\#.get_rotated(\#g" Only in C++
- "s\#rotation_from\#get_rotation_from\#g"
- "s\#rotation_in\#get_rotation_in\#g"
- "s\#identity_rotation(\#get_identity_rotation_3d("
- "s\#::distance(\#::get_distance(\#g"
.
- IMP::algebra::Vector3D and IMP::algebra::Vector3Ds were replaced by the expanded (non-typedef) version in functions parsed by SWIG as the current situation was extremely brittle. For the moment, you should not use the typedefs in definitions that swig sees. Sorry.
- IMP::algebra::Sphere3DPatch was renamed to IMP::algebra::SpherePatch3D to be consistent with the other geometry and allow us to support higher dimensions in the future.
- rigid_align_first_to_second was renamed to IMP::algebra::get_transformation_aligning_first_to_second() and build_Transformation2D_from_point_sets was renamed to IMP::algebra::get_transformation_aligning_pair()
## Week of Feb 14, 2010
- The IMP::atom::Bond types were rearranged to reconcile the protein-centric classification with ligand support.
- IMP::atom::Atom no longer has charge since we have IMP::atom::Charged.
- IMP::atom::read_mol2() and IMP::atom::write_mol2() were added
- IMP::atom::Selector and descendants 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.
- 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.
- IMP::example renamed (from examples)
- The IMP_USAGE_CHECK() macro lost the (unused) third argument.
## Week of February 3, 2010
- The model io code as moved into the kernel so it is now IMP::write_model() and IMP::read_model()
- Remove the version_info argument from the implementation macros. Instead, just pick up the module version info automatically.
- Add a function Object::get_type_name() and Object::get_module() to get the respective bits of information about each object.
- 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().
- The containers were moved to IMP.container. See that module page for a full list of what moved. In the process, the backwards compatibility functions were removed from IMP::container::PairsRestraint and kin.
- IMP.atom.create_protein() now returns the created protein
- the simplify functions have been moved from IMP.helper. They are now IMP.atom.create_simplified_along_backbone().
- IMP.helper.clone() has been renamed to IMP.atom.create_clone()
- IMP.misc.ConnectingPairContainer has been moved to IMP.core.ConnectingPairContainer
- The locations for pixels in IMP::em::DensityMap have been moved to the center of the corresponding voxel from the lower left corner.
- IMP::em::get_transformed(), IMP::em::get_resampled() and IMP::em::get_density() have been added.
- 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.
- 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.
- 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.
- Most geometry now has namespace methods IMP::algebra::get_bounding_box(), IMP::algebra::get_surface_area(), IMP::algebra::get_volume().
## Week of January 22, 2010
- A generic geometry layer has been added (see \ref genericgeometry). Using it, IMP::atom::rmsd(),
IMP::algebra::alignment_taking_first_to_second() and the new IMP::atom::native_overlap() all
can work on either collections of either IMP::core::XYZ particles or IMP::algebra::Vector3Ds.
- 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.
- 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.
- Rename IMP::core::MinimumPairScoreRestraint (and kin, Maximum, Singleton, Triplet and Quad) to IMP::core::MinimumPairRestraint.
- Add IMP::core::MinumumPairScore (and kin).
## Week of January 1, 2010
- IMP::em is now using Particles to resample density maps and for fitting restraints. The previous ParticleAccessPoint mechanism is removed.
- IMP::UsageException and IMP::InternalException are now reserved for their respective
checks (and cannot be thrown by IMP_THROW()). This makes the distinction between API
exceptions (which are thrown in any build mode and should be documented and tested)
and helper exceptions which are only thrown when checks are turned on (and hence
should not be documented) clearer.
- IMP::core::RestraintSet moved to IMP::RestraintSet. The restraint sets now simply define a tree
with weights which the model traverses as opposed to being an opaque IMP::Restraint themselves.
This means that incremental evaluation of restraints in restraint sets now works and that
restraints in restraint sets can be individually evaluated. Existing working usage should not
have changed (so \c sed should manage updates just fine), but the internal
implementation is completely new, so pay attention.
- IMP now has a text i/o layer consisting of IMP::TextInput and IMP::TextOutput. These classes are
convertible to C++ streams and implicitly constructable from both streams and file paths. As a result,
functions that take them will work when called with a string for a file path, a Python file or a
C++ stream.
- The IMP.examples module now documents how to use the needed aspects of scons and SWIG.
- 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.
- 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.
- boost program options is now a checked for dependency.
- 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.
- 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.
- 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).
- 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.
- a new base class IMP::Constraint has been added for constraints. Various
other classes have been renamed to be consistent.
## Week of December 11
- 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.
- 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.
- IMP::ParticlePair::first and second went away since no one claimed to be using it and it complicated the implementation.
- The generic restraints/score states/scores infrastructure has been extended to triplets and quads (for angles and torsion angles).
## Week of December 4
- 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.
- 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.
- 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).
## Week of November 19
- imp.xcodeproj was moved into tools and updated accordingly
- the bin directory finally went away
- IMP::display::ChimeraWriter now supports the latest version of Chimera
- IMP::display::CGOWriter was renamed to IMP::display::PymolWriter as it can do more than just CGO.
- IMP::VectorOfRefCounted::operator[] can now be used for assignments just like a normal vector. No more need to use the IMP::VectorOfRefCounted::set() method.
- the IMP::atom::Hierarchy constructor from an IMP::Particle* is now explicit (as were the decorator constructors)
## Week of November 12
- All exception types are now mapped to equivalent classes in Python. The
class hierarchy is similar (e.g. IMP::ModelException derives from IMP::Exception
in both C++ and Python) so all IMP exceptions can be caught in Python using
"except IMP.Exception". For convenience, the IMP::IOException,
IMP::ValueException and IMP::IndexException classes in Python also derive from
the similarly-named standard Python classes (IOError, ValueError and IndexError
respectively).
## week of October 29 Update
- 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).
- 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().
- Added IMP::core::VolumeRestraint.
- Several functions have been added to helper in creating restraints. They are create_simple_connectivity_on_rigid_bodies(), create_simple_connectivity_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.
- 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().
- IMP::em::read_map() will figure out the file type to use automatically from the extension. Other such methods should follow suite.
- A class IMP::core::StructureSet has been added to provide a convenient way to manage solutions of optimization runs.
- IMP::core::RigidBodyMover now takes its angle argument in radians and is documented as such.
- 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.
- IMP::core::AllPairsPairContainer has been renamed to IMP::core::AllPairContainer and a bipartite version has been added.
- All containers now keep track of what they looked like on the previous time step.
- The IMP::core::ListPairContainer and IMP::core::ListSingletonContainer have had their interface reduced a bit in order to make implementing change tracking easier.
- 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.
- 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.
## Week of October 15
- 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.
## Week of October 8
- 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.
- 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.
- IMP_check() and IMP_assert() have been
replaced with IMP_USAGE_CHECK() and IMP_INTERNAL_CHECK()
respectively. Hopefully this makes it clearer when to use
which. IMP::set_check_level() has been revised accordingly (to use
IMP::USAGE and IMP::USAGE_AND_INTERNAL). Also, IMP_failure() and
IMP_not_implemented() have been renamed to IMP_FAILURE() and
IMP_NOT_IMPLEMENTED() to make all macros be all caps. To update
external code,
- replace IMP.EXPENSIVE with IMP.USAGE_AND_INTERNAL
- replace IMP.CHEAP with IMP.USAGE
- replace IMP_assert and IMP_check as above.
## Week of October 1
- 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.
- .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.
- The search module is no longer built by default and is not longer supported. It will get moved out of svn shortly.
- IMP::ScoreState objects now also have IMP::Interacting::get_interacting_particles() methods. Soon IMP::PairScore and IMP::SingletonScore objects will too.
## Week of September 27
- 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.
- A class IMP::core::RigidBodyDistancePairScore has been added which provides accelerated computations for the distance between two rigid bodies.
- The SWIG input files were renamed from swig.i to swig.i-in to aid in dependency tracking.
- 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.
## Week of September 20
- all \c .i files have been renamed to start with \c IMP_ to help make dependency tracking easier.
- static builds (builds with \c static=True) build both the static and dynamic libraries and just static executables
- 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.
- 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.
- \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.
## Week of August 30
- A new score IMP::core::BoundingBox3DSingletonScore has been added to keep particles
in a box.
- str should now work better in Python when applied to IMP::Object objects and a few others. Objects
should use the new IMP_SHOWABLE and IMP_SHOWABLE_INLINE macros instead of declaring show
functions directory to make it so that they work in Python. It is now a bug to \c print or \c str
to not return something useful in Python for any IMP object.
## Week of August 23
- each module now has a version, eg IMP::get_module_version_info() which is also returned by the various restraints of the module. The Python code checks that loaded libraries have the expected version numbers to try to provide better messages when runtime linking problems occur.
- the various bounding_box methods have been renamed to ::get_bounding_box() to be more consistent with the other names.
- Python documentation is now parsed by doxygen
## Week of August 15
- 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.
## Week of August 8
- 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.
- 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).
- IMP::atom::Mass() has been added for decorating particles with mass. IMP::atom::Atom mass has been moved to that.
- The scheme for generating atom types is now fully specified. See the IMP::atom::AtomType documentation.
- 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.
- 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.
- The contents of bin are moving to tools since the two directories both contained assorted development tools
(not all of which were executable). For now, bin/imppy.sh will still work, but that will go away soon.
- IMP::Decorator::show() now just takes the stream (it used to take a prefix also, which was often ignored).
Anyone who implemented a decorator will have to delete the second argument of their show function.
## Week of August 1
- Containers now have methods IMP::SingletonContainer::evaluate(), IMP::PairContainer::evaluate(),
IMP::SingletonContainer::apply() and IMP::PairContainer::apply(). Using these can be significantly
faster than looping over the particles externally. Similarly, there is IMP::SingletonScore::evaluate(),
IMP::PairScore::evaluate(), IMP::SingletonModifier::apply(), IMP::PairModifier::apply().
- The decorator functions have been renamed to IMP::Decorator::setup_particle(), IMP::Decorator::decorate_particle()
and IMP::Decorator::particle_is_instance(). A shell script \c tools/update-decorators is provided which
updates the names in all code in subdirectories of the current directory. Please backup things first.
- a function, IMP::Restraint::safe_evaluate() has been added to be used
when requesting the value of restraints outside of the IMP::Model::evaluate().
## Week of July 18
- The atom::BondPairContainer has been renamed to atom::BondPairFilter
since it wasn't a real container. A real atom::BondPairContainer has
been added.
- Out of source builds mostly works. To do an out of source build, make a link
to \c scons_tools and \c SConstruct from the source directory in the build
directory and then add the line \command{repository="../path_to_src_dir"} in
the \c config.py in the build directory. Then running \c scons in the build
directory will put generated files there. This allows you to make both a
\c release and \c fast build off of the same set of sources. Proper docs
will be added soon.
- The SConscript setup for a module has been greatly simplified so it should
be easy enough for users to maintain their own module and updates to the
build system shouldn't involve changes to user SConscripts any more. This does
mean that any non-svn modules need to be updated. Look at IMP.core or another
module and copy what is there. Again, proper docs will be added soon.
## Week of July 11
- Per Javi's suggestion, the conventions have been split into
"Coding conventions" and "API conventions" and linked from the main page.
- benchmarks got moved to their own module, IMP::benchmark and will
now be tracked over time
## Week of July 4
- FilteredListSingletonContainer and FilteredPairSingletonContainer
went away as there was too much hard to factor code shared with
IMP::core::ListSingletonContainer and IMP::core::PairSingletonContainer. The
IMP::core::ClosePairsScoreState is now handled by a list of filters
on the class itself. That is, do
IMP::core::ClosePairsScoreState::add_close_pair_filter() to add a
filter.
- Hooks have been added to allow actions to be taken on an assertion
or check failure. See IMP::HandleFailure and its descendants for
more details.
- IMP::display::CGOWriter has been much improved and now allows
provides lots of display-time control and easy building of
animations.
- Generic optimizer states have been added
(IMP::core::SingletonsOptimizerState and
IMP::core::PairsOptimizerState).
## Week of June 15
- box distributions (IMP::algebra::random_vector_on_box(),
IMP::algebra::random_vector_in_box()) take bounding boxes
- IMP::em::DensityMap are now IMP::Object objects. Some current
allocations on the stack may need to be changed (since ref counted
objects can't be stack allocated).
- IMP::em::DensityMap::Read() is now deprecated (as is
IMP::em::DensityMap::Write) as they violated a slew of
conventions. Use IMP::em::read_map() and IMP::em::write_map()
instead.
## Week of June 8
- new methods IMP::atom::add_radii() and IMP::atom::add_bonds();
- Hierarchys to IMP::atom::Hierarchies
- IMP::Particles has been changed to a new type. It no longer plays
quite so well with Python lists (you can't create one from an
arbitrary Python list).
- The containers for multiple decorators have been revised to make them
more useful. See IMP::Decorators. You can now implicitly convert,
for %example, a IMP::core::XYZs to an IMP::Particles (as well as use
IMP::Decorators::get_particles()). All methods that take a
collection of particles with a certain type now instead take a
IMP::Decorators.
- A method that has expectations about the particles it takes should
take decorators rather than particles. That is, anything which
expects IMP::core::XYZ particles, should take an IMP::core::XYZs
instead of IMP::Particles.
- IMP_LIST() now takes an extra argument (the name of the plural
container)
- In C++ IMP::Decorator objects are implicitly convertible to
IMP::Particle* objects. Unfortunately, making this work in Python is
problematic.
- More methods take and return decorators rather than
IMP::Particles. This means it is clearer what their expectations are
and what they produce.
## Week of May 15
- The IMP::helper module was added and various functionality moved
there. See its documentation page for a list of what is there.
- IMP::algebra::SphericalCoords was renamed to
IMP::algebra::SphericalVector3D to be consistent with other algebra
classes.
- IMP::algebra::Rotation2D is now IMP::InvalidDefault to be consistent
with the other similar classes.
- We are trying to be a bit more specific about what is expected from
a IMP::atom::Hierarchy. Towards that end, there are two methods for
extracting a representation from a hierarchy,
IMP::atom::get_detailed_representation(), and
IMP::atom::get_simplified_representation()
- A method has been added to produce a simplified copy of an
IMP::atom::Hierarchy. The method is still a bit crude and could
benefit from other people inspecting the output and saying how it
should be improved.
- There is now an IMP::algebra::BoundingBoxD (and
IMP::algebra::BoundingBox3D) to track bounding boxes. There are
methods like IMP::algebra::bound_box(Sphere3D) which gets the
bounding box of a sphere.
- Each IMP::Object has its own log level. If
IMP::Object::set_log_level() is called with a value other than
IMP::DEFAULT, the value is used for code within and called by the
object. To support this in your objects you need to add
IMP_OBJECT_LOG to the start of each major method. It has been added
to some of the core objects.
## Week of May 8
- IMP::atom::MolecularHierarchy has been renamed to
IMP::atom::Hierarchy. Use \command{sed -i.old
"s\#MolecularHierarchy\#Hierarchy\#g" my_files}
- the long-deprecated Name(Decorator) was removed
- The decorator suffix has been removed from decorator names.
- Unit conventions have been established and documented for distance,
energy, force and angle.
- there is a function IMP::atom::create_protein() to create a coarse
grained protein. The function is crude so far, but the idea is that
we should have standard ways of generating such things so that
everyone can benefit from best practices.
- a class IMP::atom::BondGraph has been added so Boost.Graph
algorithms can be used with bond graphs
- the IMP-specific doxygen commands have been documented.
- the doxygen commands unstable{name} and untested{name} have been
added to doxygen to be used for marking methods and functions as
likely to change or not well tested. Pass the name of the class or
method as name.
- bonds can now be added to molecular hierarchies automatically see
IMP::atom::add_bonds()
## Week of May 1
- There is a IMP::Rotation2D
- You can now extract fixed Euler ZYZ angles from a
IMP::Rotation3D. This code can serve as a template for extracting
other Euler angle conventions if they are needed.
- IMP::algebra::rotation_between_two_vectors() changed to
IMP::algebra::rotation_taking_first_to_second() to make it clear
which direction the rotation goes.
## Week of April 27
- IMP::Decorator derived objects are now convertible to bool. So code
like \code if (d) { blah } \endcode works.
- IMP::Decorator::cast now returns a null decorator (\c
DecoratorName()) rather than throwing an exception. This might make
it actually useful.
- New IMP::statistics module for statistical methods
(e.g. clustering).
## Week of April 20
- Support for taking advantage of rigid bodies in collision detection
has been added via the IMP::core::RigidClosePairsFinder.
- All IMP::core::ClosePairsScoreState-related functionality has been
optimized and should be noticeably faster.
- The EMBED project has been merged into the IMP::em module. Thus, it
is no longer necessary to obtain EMBED separately to build IMP::em.
- All C++ methods which work with std::istream or std::ostream
arguments should now be usable from Python: any Python file-like
object can be used.
- The SWIG interface now ties in to the reference counting mechanism
used in the C++ code, for all classes derived from
IMP::RefCounted. So, for %example, deleting a Python object should
not free the underlying C++ object if another C++ object holds a
reference to it, and unrefing a C++ object should not delete it if a
Python object still holds a reference to it. There should be no
further need to manually keep references to Python objects to
prevent things from being prematurely cleaned up. This should be
transparent to the user; please report any problems.
- IMP::atom::AtomDecorator no longer inherits from
IMP::core::XYZDecorator.
## Week of April 13
- The decorators IMP::atom::AtomDecorator, IMP::atom::ChainDecorator,
IMP::atom::ResidueDecorator etc. now inherit from
IMP::atom::MolecularHierarchyDecorator. This means they can set
their IMP::atom::MolecularHierarchyDecorator::Type properly and
saves a lot of typing in the common case. We can always make
hierarchy decorators zero memory overhead if we find that the cost
matters.
- The base classes IMP::Comparable, IMP::NullDefault,
IMP::ValidDefault and IMP::UninitializedDefault were added to
document what the default constructors do for various objects in
IMP.
## Week of April 6
- IMP::Object now defines pure virtual methods
IMP::Object::get_version_info() and IMP::Object::show(). All
non-abstract classes which inherit from IMP::Object must implement
them. Doing this means they are more uniformly implemented and are
documented in one place.
- IMP::Object is now reference counted (the only objects this changes
are IMP::Model and IMP::Optimizer). As a result optimizers and
IMP::Model objects must be created on the heap.
- IMP::RefCounted has had its name changed and no longer inherits from
IMP::Object. This makes it easier to use independently.
- the docs for reference counting (IMP::RefCounted) and and IMP::Decorator
have been improved
- running doxygen produces no warnings. Let's try to keep it that
way. Run \command{scons doc > /dev/null} before you check in large
blocks of new code to make sure that you didn't introduce warnings.
- Helper classes have been added to make SingletonModifier and
PairModifier objects look like functors for C++ and Python. This
makes it so you can use \c map in Python and \c for_each in C++. See
IMP::SingletonFunctor and IMP::PairFunctor for more information.
- The recent changes page has moved to a doxygen page to make it
easier to link changes back to the relevant source code.
## Week of March 20:
- create_rigid_body(), create_rigid_bodies(), create_centroid()
etc. now require you to add the score state to the model
yourself. Whether the rigid body is enforced or not can be
controlled by adding or removing the returned IMP::ScoreState.
- All previously deprecated code has been removed. This includes
indexes in particles, the no-argument constructor for particles and
the functionality that was moved from core to atom.
- The IMP::core::RigidBodyDecorator and
IMP::core::RigidMemberDecorator have been simplified by removing the
traits classes. There is now only one type of rigid body and it
stores the list of member particles internally.
- IMP::core::NameDecorator has been deprecated as IMP::Particles have
built in names (use IMP::Particle::get_name(),
IMP::Particle::set_name()).
- IMP::atom::ChainDecorator has been added
## Week of March 13:
- A new IMP::display::Writer, IMP::display::ChimeraWriter has been
added which exports geometry to native Chimera constructs. It
probably should be used instead of bild and cmm for most purposes as
it combines the best of both types.
- compose() for transformation is now a free function so
compose(rotation, vector) will work via promotions.
- the geometry classes have been cleaned up and are now more
consistent with IMP standards (and more likely to do what their
names/comments suggest). See IMP::algebra::Sphere3D,
IMP::algebra::Cylinder3D, IMP::algebra::Segment3D,
IMP::algebra::Plane3D etc.
- ParticleRefiner has been renamed to IMP::Refiner since the Particle
was long and unnecessary.
¢ IF3 translation initiation complex](http://salilab.org/40S-eIF1-eIF3).
- IMP::domino::DiscreteSampler::set_restraints() now allows the set of
restraints used in DOMINO filtering to be controlled (previously, all
restraints in the IMP::Model were used).
- IMP::modeller::IMPRestraints now transfers an IMP::ScoringFunction into the
MODELLER score, not the implicit (and deprecated) score of the
entire IMP::Model.
- Bugfix #775: coordinates of voxels in EM maps were previously inconsistently
treated (they are supposed to be the centers of the voxels, but in some
cases they were the lower left edge). The fix may result in maps and their
bounding boxes appearing shifted by half the voxel size.
# 2.4.0 - 2015-02-27 # {#changelog_2_4_0}
- Python 3 is now supported. The Windows package now works out of the box
with Python 3.3 or 3.4; a `-python3` subpackage is provided for Ubuntu
and Fedora. (Apple does not yet provide Python 3 so the Mac package is not
built with Python 3 support, but if you install Python 3 you can compile
IMP from source to work with it.)
- A new command line tool, `rrt_sample`, allows for running rapidly exploring
random tree (RRT) based sampling, e.g. to sample conformations of multiple
domains connected by flexible linkers.
- Command line tools are now placed in the `bin` directory of modules (the
old `bin` directory, used for utility programs that are not installed, is
now called `utility`). The `applications` directory is removed.
- Several Python modules that were only used by EMageFit have been moved from
IMP::em2d to IMP::EMageFit.
- A new tutorial that uses the IMP::pmi module is now available (modeling of
the RNA Polymerase II stalk).
# 2.3.1 - 2014-12-01 # {#changelog_2_3_1}
- Minor bug fixes.
- Update to IMP::pmi to support the Nup84 and rnapolii biological systems.
# 2.3.0 - 2014-10-24 # {#changelog_2_3_0}
- 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.
- Binary installers for 64-bit Windows are now available.
- The `.py` extension has been removed from all Python applications, so that they are consistent with the C++ applications.
- 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.
- The integrative docking (idock) application now employs SOAP to improve the scoring.
- 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.
- 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.
# 2.2.1 - 2014-08-11 # {#changelog_2_2_1}
- Bugfix: PoseScore (see the ligand_score application) should now match that used by the Pose&Rank web server (http://salilab.org/poseandrank/)
# 2.2.0 - 2014-04-09 # {#changelog_2_2_0}
- 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.
- The Python support for grids was cleaned up. Hopefully this makes it more robust. If you were using a grid in Python that no longer exists, ping us, we can add it back.
- The generic geometry functions were simplified slightly and renamed to IMP::algebra::get_vector_geometry().
- The IMP::base::Flag class was added to simplify adding flags in C++.
- The `--log_level` and `--check_level` command line argument now take strings (eg VERBOSE) to specify their values, rather than cryptic (and a bit unstable) numbers.
- Command line options are now divided into normal and advanced ones. You do `--help_advanced` to show the advanced ones.
- Support for computing Connolly surfaces was added with IMP::algebra::get_connolly_surface(). In addition, there is now IMP::algebra::get_uniform_surface_cover(const IMP::algebra::Sphere3Ds&,double) to sample the surface of a collection of balls.
- IMP::atom::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.
- IMP::atom::get_rmsd(IMP::atom::Selection, IMP::atom::Selection, const IMP::algebra::Transformation3D&) was deprecated. Use IMP::atom::get_rmsd_transforming_first() instead.
- IMP::algebra::get_rmsd() and IMP::algebra::get_rmsd_transforming_first() were added.
- The family of macros IMP_BASE_[SMALL,LARGE]_[UNORDERED,ORDERED]_[MAP,SET] have been added (eg IMP_BASE_SMALL_ORDERED_SET ()). They provide platform and boost-version independent ways to take advantage of the best set/map for an application. In particular, they use boost::container::flat_set and kin when available.
- IMP::atom::State and IMP::atom::Representation decorators have been added to provide support for multiple states and multiple representation schemes. They are integrated with RMFs and IMP::atom::Selection. See atom/multiresolution.py and atom/multistate.py for examples.
- The container implementations has been cleaned up and simplified a bit. This should not change most usage.
- [RMF](http://salilab.github.io/rmf) has been updated. There are a few minor API changes, in addition to a new, faster format (`.rmf3`).
- [Eigen](#Eigen) is now included with IMP.
- The deprecated function IMP::kernel::Optimizer::set_restraints() was removed. Use IMP::kernel::Optimizer::set_scoring_function() instead.
- The deprecated constructor for IMP::kernel::ModelObject that does not take an IMP::kernel::Model was removed. This propagates to constructors IMP::kernel::Restraint, IMP::kernel::ScoreState and kin. Make sure you pass an IMP::kernel::Model as the first constructor argument. Related to this, deprecated functions like get_is_part_of_model(), set_model() were removed as they don't serve any purpose.
- The deprecated methods in IMP::kernel::Optimizer that pertain to attribute optimization were removed. Inherit from IMP::kernel::AttributeOptimizer instead if you want to use them in your optimizer.
- Some deprecated functionality was removed. If you encounter problems, replace IMP::base::OwnerPointer with IMP::base::PointerMember, find logging stuff in IMP/base/log.h, object in IMP/base/Object.h and random in IMP/base/random.h.
- IMP::atom::Chain now uses strings for the chain ids, to be consistent with changes in the PDB. PDB files are written using the first character of the chain string.
- Added orientation-dependent SOAP scoring (IMP::score_functor::OrientedSoap and IMP::atom::OrientedSoapPairScore). Orientation-dependent SOAP scores include those that score loops (SOAP-Loop), protein-peptide interfaces (SOAP-Peptide) and proteins (SOAP-Protein). The library files themselves are rather large (~1.5GB) and so are not included with IMP. They can be downloaded separately from http://salilab.org/SOAP/.
# 2.1.1 - 2013-11-04 # {#changelog_2_1_1}
- Added support for Mac OS 10.9
# 2.1.0 - 2013-10-24 # {#changelog_2_1_0}
- 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.
- 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.
- Class name OwnerPointer was switched to PointerMember, to denote more clearly a ref-counting pointer that is a class member.
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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`).
- 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.
- 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.
- 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.
- [RMF](https://github.com/salilab/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.
# For IMP 2.0 and earlier # {#changelog_2_0}
## Spring 2013
- Modules and applications now have a _Maintainer_ in their `README.md`, giving the github id of the person to whom issues should be assigned.
- `setup_git.py` supports the `--module` flag which will set up git hooks and things for a git repository that contains a module.
- 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.
- 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.
## Winter 2012-2013
- Scons support was removed. Use cmake to build IMP, it is way better.
- 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.
- 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.
- The IMP_BIG_ENDIAN and IMP_LITTLE_ENDIAN preprocessor symbols are deprecated in favor of the BOOST_BIG_ENDIAN and BOOST_LITTLE_ENDIAN symbols.
- 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.
- 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.
- You can now (probably) build IMP with [CMake on IMP wiki](https://github.com/salilab/imp/wiki/Cmake).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- OpenMP support in IMP is officially released. All tests pass. But there has been little specific testing so far.
- Access to attributes using IMP::ParticleIndex and the IMP::Model now works from Python. See IMP::Model::add_attribute() and kin.
- 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.
- 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.
- 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.
- 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 beginning. You can use `./tools/updaters/update_examples.py modules/mymodule` to update a module that was not already updated.
- IMP::base::FailureHandler has been removed as it wasn't used.
- 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.
- Modules now must be in a folder called `modules`, which must have a `description.py` file.
- The build system should now be a little better about cleaning up after itself.
- How headers/doc files/data/examples
- 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 "_" from the method name.
- Nice version numbers will now be generated if you use git. You need to rerun
tools/git/developer_tools/init_git if you have an existing clone.
## Fall 2012
- 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.
- 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.
- 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.
- 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.
- 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.
- 11/8; Evaluation with containers was greatly simplified, moving many methods on containers. We can add backwards compatibility versions if that is interesting.
- 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.
- 11/7: It is now preferred that IMP::Restraint and IMP::ScoreState descendants 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 deprecated. 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.
- 11/3: IMP::container::InContainerPairFilter and friends now treat pairs as unordered. A flag was added to control this.
- 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.
## Summer 2012
- 7/3: IMP_PERIODIC_OPTIMIZER_STATE() was superseded by the class IMP::core::PeriodicOptimizerState as it is rather cleaner than the macro.
- 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.
- 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.
- 6/24: Benchmarks are now put int \c module/benchmark and build to \c build/benchmark/module to remove a recurring source of errors.
- 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.
- 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.
## Winter 2011/2012
- 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.
- 4/4: the filter types were superseded 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()).
- 29/3: IMP::Particle::get_has_model() has been changed to IMP::ModelObject::get_is_part_of_model() to be consistent with other classes.
- 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.
- 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).
- 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.
- 15/3: The vector used throughout IMP is now exposed at IMP::base::Vector and what it does it documented.
- 10/3: IMP::domino::RestraintCache was introduced to provide a documented centralized place to handle restraint evaluation and caching in DOMINO. In the switch various bugs involving maximum scores and IMP::RestraintSet objects were fixed.
- 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.
- 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.
- 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.
- 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.
- 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).
- 3/2: IMP::domino::WriteAssignmentContainer and IMP::domino::ReadAssignmentContainer were added to do direct binary file writing. This is faster than the HDF5 versions.
- 3/2: The installation instructions have been revamped and the developer instruction, in particular, have been greatly simplified.
- 24/1: \c tools/show-changes has been added that shows the changes in the history log since you last updated.
- 24/1: \c tools/make-source has been added that adds a source/header pair to a module
- 24/1: principal components analysis in IMP::algebra was generalized to work in any dimension. This required renaming the class to IMP::algebra::PrincipalComponentAnalysisD.
- 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
- 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.
- 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.
- 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.
- IMP::algebra::ParabolicFit was renamed to IMP::algebra::ParabolicFit2D (a backwards compatibility typedef is currently provided)
- IMP::algebra::LinearFit was renamed to IMP::algebra::LinearFit2D. It now supports error bars on the y-values.
## Fall 2011
- 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).
- Various IMP::algebra plural typedefs which had been using std::vector (since they never were updated), have now been moved to IMP::vector.
- IMP::statistics::HistogramD now supports display with \c matplotlib.
- IMP::statistics::HistogramD supersedes IMP::statistics::Histogram
- 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.
- the core generic restraint and score state support was moved to the kernel to avoid breaking various scores outside of IMP svn.
- 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.
- Decomposition of restraints now results in restraints that are faster to evaluate, using the generic restraint mechanism in IMP kernel.
- 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()
- 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.
- the way various types of geometry is stored in RMF files was changed, breaking backwards compatibility.
## Summer 2011
- 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.
- the source for the kernel has been moved from \c kernel to \c modules/kernel. This is unlikely to effect anyone.
- IMP::core::ExcludedVolumeRestraint now supports filters
- IMP::domino::HDF5AssignmentTable now caches internally, which makes it several times faster than before.
- you can now pick which Python to use with the \c python argument to scons.
- the units for BD diffusion coefficients changed to be consistent with other IMP units.
- IMP::domino::get_interaction_graph() now takes an IMP::RestraintsTemp, like other functions
- 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.
- 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.
- IMP::IntsList, IMP::FloatsList and IMP::StringsList have been added to replace the various scattered solutions for passing such types.
- 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.
- 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.
- 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.
- the IMP::core::DiameterRestraint was ignoring the radii of the particles involved and so was giving artificially low scores. It now is on the actual diameter of this molecule.
- the IMP::core::MonteCarlo optimizers now support incremental evaluation. This can be a lot faster when only a few particles are moved each step.
- 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.
- 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.
- Temp and non-temp decorator lists have been merged in C++. This was done to simplify code since no one was using the non-temp variants. Now all decorator lists are temp (non-reference counted) variants.
- 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.
- 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.
- IMP::domino uses the new IMP::Model::evaluate_if_good() support to accelerate computations
- IMP::core::MonteCarlo can use the IMP::Model::evaluate_if_good() support to more quickly reject
very bad conformations. See IMP::core::MonteCarlo::set_maximum_difference().
- IMP::core::ExcludedVolumeRestraint has been rewritten to be faster. It is especially
faster when used with IMP::Model::evaluate_if_good()
- 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.
- 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.
- 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.
- the RMF helper binaries have been moved to their own application so that they get installed.
- 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.
## Spring 2011
- An interactive mode has been added to IMP::domino::DominoSampler. The interactive mode is useful for understanding domino sampling runs and distributing domino computations across a cluster.
- Functions IMP::domino::set_assignments() and IMP::domino::get_assignments() were added which support
writing subset assignments to data fields in hdf5 files. These can be used to helping to distribute
domino on a cluster as well as debugging the sampling process.
- a Python function IMP.show_graphviz() has been added that attempts to render a graph with \c dot and then open the pdf.
- 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.
- IMP.atom.create_cover() was added to facilitate creating a summary particle for part of a hierarchy in order to accelerate restraints.
- 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.
- 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.
- The Python graph interface now has a remove_vertex method.
- 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.
- 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.
- Preliminary symmetry support has been added via the IMP::core::TransformationSymmetry and IMP::core::TransformationAndReflectionSymmetry classes.
## Winter 2011
- 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()
- IMP::core::MonteCarlo::set_temperature() was renamed to IMP::core::MonteCarlo::set_kt() as that is what it is doing.
- 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).
- IMP::algebra::grids::GridD now supports dense grids in arbitrary dimension through use of IMP::algebra::grids::DenseGridStorageD.
- IMP::Optimizer now can use a list of restraint sets to compute the score rather than the complete Model score.
- each IMP::Restraint now has its own weight. This is lightly tested.
- 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.
- IMP::domino::TrivialParticleStates renamed to IMP::domino::IndexParticleStates to be less judgmental
- IMP::domino::CompoundParticleStates and IMP::domino::RecursiveParticleStates added
- IMP::domino::DominoSampler now supports maximum scores on IMP::RestraintSets (untested).
- the name of the clustering methods have been changed to create_ from get_ since they create objects.
- the names of the recently added metric based clustering support has been changed to Metric rather than Distance.
- 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.
- the function IMP::display::create_restraint_geometry() was added to do what its name says.
- 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.
- IMP::atom::DopePairScore has been added to IMP.
- IMP::atom::CHARMMStereochemistryRestraint provides a high-level simplified
interface to the bonded part of the CHARMM forcefield.
- 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.
- Instructions and scripts have been added for building modules and things externally to the IMP build. See the installation guide.
- IMP::atom::CHARMMParameters can now automatically map CHARMM-style atom and
residue naming to PDB-style, so CHARMM topology files can be used unmodified.
- IMP::atom::CHARMMTopology::add_sequence() provides a simple way to generate a topology from a string of amino acid one-letter codes.
- IMP::atom::CHARMMTopology::add_coordinates() will generate atomic Cartesian coordinates from CHARMM internal coordinate information.
- IMP::atom::CHARMMTopology::add_missing_atoms() and
IMP::atom::remove_charmm_untyped_atoms() can now be used to ensure that atoms
read from a PDB file match the CHARMM topology.
- building of deprecated functionality is now false by default
- 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.
- 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).
- 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.
- 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.
- rename IMP::restrainer::Restraint::print_all_restraints() to IMP::restrainer::Restraint::show_all_restraints() to be consistent with the rest of IMP.
- renamed IMP::atom::get_conect_record_string() to IMP::atom::get_pdb_conect_record_string() to make clearer what it is.
- class and method names are now spell checked. Add missing words to spelling_exceptions in the module test call.
- the plural names (eg IMP.Particles()) have been removed from the Python side as they are just Python lists.
- biological systems can now include internal modules. These provide a convenient place to put application specific C++ and Python code. See the example system for more info.
- IMP_VALUES() now includes IMP_OUTPUT_OPERATOR() so you no longer need two namespace macros for each value.
- 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.
- the IMP::atom::PDBSelector and IMP::atom::Mol2Selector became IMP::Object classes. All this
means is that they need to be created with \c new in C++ code. It also means that one is
no longer prohibited from storing them (not that there is much use in doing that).
- 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.
- IMP::core::RigidBody::lazy_set_reference_frame() was renamed to IMP::core::RigidBody::set_reference_frame_lazy() to fit with the standards better.
- the transform based methods on reference frame which have been deprecated for a while were removed
- 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.
- IMP::atom::NonhydrogenMol2Selector was renamed IMP::atom::NonHydrogenMol2Selector to be consistent with the PDB version
## Fall 2010
- IMP::display::PlaneGeometry was added to display planes
- 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
benefit from better checking.
- 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.
- 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()
- IMP::core::WriteModelOptimizerState is going away as it duplicated IMP::WriteParticlesOptimizerState.
- 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.
- the biological systems specification has been improved a little adding ability to run some rudimentary tests to make sure the scripts are ok and to not require that everything be run from the svn directory.
- 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.
- Logging has been improved to better report the name of methods producing the log messages
- a macro IMP_FUNCTION_LOG has been added which should be added to the start of non-member functions which produce significant logging output.
- 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.
- IMP.domino2 was renamed to IMP.domino and the old IMP.domino was moved
- 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.
- applications and biological systems now have their own documentation pages
- IMP::atom::Hierarchy requires radii on its leaves
- IMP::atom::read_pdb add radii to the atoms
- IMP::helper was merged into IMP::restrainer as all the functionality there was primarily to provide support for restrainer
- IMP::domino2::SubsetEvaluatorTable was removed. Pass the model and IMP::domino2::ParticleStatesTable to the IMP::domino2::RestraintScoreSubsetFilterTable instead.
- 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.
- a new example was added in the kernel to show IMP used on a biological system
- IMP::display::PymolWriter now supports adding labels to things
- IMP::display::PairRestraintGeometry and IMP::display::ConnectivityRestraintGeometry were added to aid in visualizing those restraints.
- IMP::bullet was added with an optimizer to use hard body physics to resolve local collisions.
- 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 separate particle so that the molecular hierarchy doesn't have to worry about having its bounding sphere large enough to enclose all the members.
- IMP::core::KClosePairsPairScore was added to have count based cutoffs for close pair scoring.
- IMP::algebra::get_surface_area_and_volume() was added to compute the two numbers for a set of balls
## Summer 2010
- 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 slightly tweaked to work.
- Javi added his 2D EM scoring functionality as IMP::em2D
- 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.
- 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).
- 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.
- 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).
- 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
- a better explanation of how to use reference counted pointers has been added to IMP::Pointer.
- all simple, planar polygons are now supported for display when CGAL is present
## Week of April 1, 2010
- 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
- types are not checked until the lists are passed to C++
- 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)
- swig has issues with some overloads (not always for obvious reasons). These are being sorted out. None are commonly used.
- get_particles() on a plural object doesn't work in Python (and is not needed in C++). Implicit conversions will always work.
- 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 empty lists of particles in the constructors cause check failures. We can figure out a work around if this is too annoying.
## Week of March 13, 2010
- 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.
- 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).
## Week of March 6, 2010
- 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.
## Week of Feb 27, 2010
- IMP::algebra::decompose_rotation_into_axis_angle() was renamed to IMP::algebra::get_angle_and_axis().
- renamed IMP::atom::bond() and IMP::atom::unbond() to IMP::atom::create_bond() and IMP::atom::destroy_bond() to be more consistent with things
- renamed IMP::core::root() to IMP::core::get_root()
## Week of Feb 21, 2010
- IMP::Object::set_was_owned() was changed to IMP::Object::set_was_used() as that better reflects what the flag means.
- various more interpolation and endian methods had their names fixed (by adding \c get_)
- the function get_mean() on vectors was removed as it duplicated IMP::algebra::get_centroid()
- build_Transformation3D_from_transformation3D was replaced by IMP.algebra.get_transformation_3d()
- IMP::algebra::almost_equal() is now IMP::algebra::get_are_almost_equal() to fit the naming conventions.
- the random vector generators have been cleaned up to remove redundant ones and make the names more consistent. They now have the form of either
- IMP::algebra::get_random_vector_in() or IMP::algebra::get_random_vector_on() where there is one argument describing the volume or shape (such as an IMP::algebra::SphereD<4>).
- or IMP::algebra::get_uniform_surface_cover() where the first argument is the primitive whose surface we are covering and the second is the number of points.
Some good sed strings are
- "s\#random_vector_in_unit_sphere()\#get_random_vector_in(IMP.algebra.get_unit_sphere_3d())\#g"
- "s\#random_vector_in_unit_box()\#get_random_vector_in(IMP.algebra.get_unit_bounding_box_3d())\#g"
- "s\#random_vector_on_unit_sphere()\#get_random_vector_on(IMP.algebra.get_unit_sphere_3d())\#g"
- "s\#random_vector_on_unit_box()\#get_random_vector_on(IMP.algebra.get_unit_bounding_box_3d())\#g"
- "s\#random_vector_in_box(\#get_random_vector_in(\#g"
- "s\#random_vector_on_box(\#get_random_vector_on(\#g"
- "s\#random_vector_in_sphere(\#get_random_vector_in(\#g"
- "s\#random_vector_on_sphere(\#get_random_vector_on(\#g"
- "s\#grid_cover\#get_grid_surface_cover\#g"
- "s\#uniform_coverr\#get_uniform_surface_cover\#g"
.
- Spheres in IMP::algebra are now supported in general dimensions. See IMP::algebra::SphereD.
- Many methods in IMP::algebra were renamed to be more consistent with other methods or general conventions. Most of these simply involved adding \c get_ as a prefix and/or add a \c _3d suffix when they did not take any arguments.
- build_Rotation2D_from_Vector2D became IMP::algebra::get_rotation_to_x_axis()
- most of the Rotation3D and Transformation3D functions (in addition, IMP::algebra::get_identity_rotation_3d() and IMP::algebra::get_identity_transformation_3d() added the \c _3d so we can add 2D versions at some point)
- IMP::algebra::Transformation3D::get_transformed() and IMP::algebra::Rotation3D::get_rotated(). Replacing \c ".transform(" worked in the IMP code base.
- IMP::algebra::get_distance(), this also carries over to the IMP::core::get_distance()
The following global replacements are probably safe (in sed expressions)
- "s\#core.distance(\#core.get_distance\#g"
- "s\#algebra.distance(\#algebra.get_distance\#g"
- "s\#\.transform(\#.get_transformed(\#g" Only in C++
- "s\#\.rotate(\#.get_rotated(\#g" Only in C++
- "s\#rotation_from\#get_rotation_from\#g"
- "s\#rotation_in\#get_rotation_in\#g"
- "s\#identity_rotation(\#get_identity_rotation_3d("
- "s\#::distance(\#::get_distance(\#g"
.
- IMP::algebra::Vector3D and IMP::algebra::Vector3Ds were replaced by the expanded (non-typedef) version in functions parsed by SWIG as the current situation was extremely brittle. For the moment, you should not use the typedefs in definitions that swig sees. Sorry.
- IMP::algebra::Sphere3DPatch was renamed to IMP::algebra::SpherePatch3D to be consistent with the other geometry and allow us to support higher dimensions in the future.
- rigid_align_first_to_second was renamed to IMP::algebra::get_transformation_aligning_first_to_second() and build_Transformation2D_from_point_sets was renamed to IMP::algebra::get_transformation_aligning_pair()
## Week of Feb 14, 2010
- The IMP::atom::Bond types were rearranged to reconcile the protein-centric classification with ligand support.
- IMP::atom::Atom no longer has charge since we have IMP::atom::Charged.
- IMP::atom::read_mol2() and IMP::atom::write_mol2() were added
- IMP::atom::Selector and descendants 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.
- 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.
- IMP::example renamed (from examples)
- The IMP_USAGE_CHECK() macro lost the (unused) third argument.
## Week of February 3, 2010
- The model io code as moved into the kernel so it is now IMP::write_model() and IMP::read_model()
- Remove the version_info argument from the implementation macros. Instead, just pick up the module version info automatically.
- Add a function Object::get_type_name() and Object::get_module() to get the respective bits of information about each object.
- 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().
- The containers were moved to IMP.container. See that module page for a full list of what moved. In the process, the backwards compatibility functions were removed from IMP::container::PairsRestraint and kin.
- IMP.atom.create_protein() now returns the created protein
- the simplify functions have been moved from IMP.helper. They are now IMP.atom.create_simplified_along_backbone().
- IMP.helper.clone() has been renamed to IMP.atom.create_clone()
- IMP.misc.ConnectingPairContainer has been moved to IMP.core.ConnectingPairContainer
- The locations for pixels in IMP::em::DensityMap have been moved to the center of the corresponding voxel from the lower left corner.
- IMP::em::get_transformed(), IMP::em::get_resampled() and IMP::em::get_density() have been added.
- 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.
- 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.
- 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.
- Most geometry now has namespace methods IMP::algebra::get_bounding_box(), IMP::algebra::get_surface_area(), IMP::algebra::get_volume().
## Week of January 22, 2010
- A generic geometry layer has been added (see \ref genericgeometry). Using it, IMP::atom::rmsd(),
IMP::algebra::alignment_taking_first_to_second() and the new IMP::atom::native_overlap() all
can work on either collections of either IMP::core::XYZ particles or IMP::algebra::Vector3Ds.
- 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.
- 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.
- Rename IMP::core::MinimumPairScoreRestraint (and kin, Maximum, Singleton, Triplet and Quad) to IMP::core::MinimumPairRestraint.
- Add IMP::core::MinumumPairScore (and kin).
## Week of January 1, 2010
- IMP::em is now using Particles to resample density maps and for fitting restraints. The previous ParticleAccessPoint mechanism is removed.
- IMP::UsageException and IMP::InternalException are now reserved for their respective
checks (and cannot be thrown by IMP_THROW()). This makes the distinction between API
exceptions (which are thrown in any build mode and should be documented and tested)
and helper exceptions which are only thrown when checks are turned on (and hence
should not be documented) clearer.
- IMP::core::RestraintSet moved to IMP::RestraintSet. The restraint sets now simply define a tree
with weights which the model traverses as opposed to being an opaque IMP::Restraint themselves.
This means that incremental evaluation of restraints in restraint sets now works and that
restraints in restraint sets can be individually evaluated. Existing working usage should not
have changed (so \c sed should manage updates just fine), but the internal
implementation is completely new, so pay attention.
- IMP now has a text i/o layer consisting of IMP::TextInput and IMP::TextOutput. These classes are
convertible to C++ streams and implicitly constructable from both streams and file paths. As a result,
functions that take them will work when called with a string for a file path, a Python file or a
C++ stream.
- The IMP.examples module now documents how to use the needed aspects of scons and SWIG.
- 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.
- 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.
- boost program options is now a checked for dependency.
- 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.
- 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.
- 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).
- 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.
- a new base class IMP::Constraint has been added for constraints. Various
other classes have been renamed to be consistent.
## Week of December 11
- 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.
- 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.
- IMP::ParticlePair::first and second went away since no one claimed to be using it and it complicated the implementation.
- The generic restraints/score states/scores infrastructure has been extended to triplets and quads (for angles and torsion angles).
## Week of December 4
- 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.
- 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.
- 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).
## Week of November 19
- imp.xcodeproj was moved into tools and updated accordingly
- the bin directory finally went away
- IMP::display::ChimeraWriter now supports the latest version of Chimera
- IMP::display::CGOWriter was renamed to IMP::display::PymolWriter as it can do more than just CGO.
- IMP::VectorOfRefCounted::operator[] can now be used for assignments just like a normal vector. No more need to use the IMP::VectorOfRefCounted::set() method.
- the IMP::atom::Hierarchy constructor from an IMP::Particle* is now explicit (as were the decorator constructors)
## Week of November 12
- All exception types are now mapped to equivalent classes in Python. The
class hierarchy is similar (e.g. IMP::ModelException derives from IMP::Exception
in both C++ and Python) so all IMP exceptions can be caught in Python using
"except IMP.Exception". For convenience, the IMP::IOException,
IMP::ValueException and IMP::IndexException classes in Python also derive from
the similarly-named standard Python classes (IOError, ValueError and IndexError
respectively).
## week of October 29 Update
- 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).
- 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().
- Added IMP::core::VolumeRestraint.
- Several functions have been added to helper in creating restraints. They are create_simple_connectivity_on_rigid_bodies(), create_simple_connectivity_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.
- 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().
- IMP::em::read_map() will figure out the file type to use automatically from the extension. Other such methods should follow suite.
- A class IMP::core::StructureSet has been added to provide a convenient way to manage solutions of optimization runs.
- IMP::core::RigidBodyMover now takes its angle argument in radians and is documented as such.
- 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.
- IMP::core::AllPairsPairContainer has been renamed to IMP::core::AllPairContainer and a bipartite version has been added.
- All containers now keep track of what they looked like on the previous time step.
- The IMP::core::ListPairContainer and IMP::core::ListSingletonContainer have had their interface reduced a bit in order to make implementing change tracking easier.
- 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.
- 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.
## Week of October 15
- 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.
## Week of October 8
- 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.
- 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.
- IMP_check() and IMP_assert() have been
replaced with IMP_USAGE_CHECK() and IMP_INTERNAL_CHECK()
respectively. Hopefully this makes it clearer when to use
which. IMP::set_check_level() has been revised accordingly (to use
IMP::USAGE and IMP::USAGE_AND_INTERNAL). Also, IMP_failure() and
IMP_not_implemented() have been renamed to IMP_FAILURE() and
IMP_NOT_IMPLEMENTED() to make all macros be all caps. To update
external code,
- replace IMP.EXPENSIVE with IMP.USAGE_AND_INTERNAL
- replace IMP.CHEAP with IMP.USAGE
- replace IMP_assert and IMP_check as above.
## Week of October 1
- 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.
- .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.
- The search module is no longer built by default and is not longer supported. It will get moved out of svn shortly.
- IMP::ScoreState objects now also have IMP::Interacting::get_interacting_particles() methods. Soon IMP::PairScore and IMP::SingletonScore objects will too.
## Week of September 27
- 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.
- A class IMP::core::RigidBodyDistancePairScore has been added which provides accelerated computations for the distance between two rigid bodies.
- The SWIG input files were renamed from swig.i to swig.i-in to aid in dependency tracking.
- 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.
## Week of September 20
- all \c .i files have been renamed to start with \c IMP_ to help make dependency tracking easier.
- static builds (builds with \c static=True) build both the static and dynamic libraries and just static executables
- 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.
- 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.
- \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.
## Week of August 30
- A new score IMP::core::BoundingBox3DSingletonScore has been added to keep particles
in a box.
- str should now work better in Python when applied to IMP::Object objects and a few others. Objects
should use the new IMP_SHOWABLE and IMP_SHOWABLE_INLINE macros instead of declaring show
functions directory to make it so that they work in Python. It is now a bug to \c print or \c str
to not return something useful in Python for any IMP object.
## Week of August 23
- each module now has a version, eg IMP::get_module_version_info() which is also returned by the various restraints of the module. The Python code checks that loaded libraries have the expected version numbers to try to provide better messages when runtime linking problems occur.
- the various bounding_box methods have been renamed to ::get_bounding_box() to be more consistent with the other names.
- Python documentation is now parsed by doxygen
## Week of August 15
- 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.
## Week of August 8
- 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.
- 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).
- IMP::atom::Mass() has been added for decorating particles with mass. IMP::atom::Atom mass has been moved to that.
- The scheme for generating atom types is now fully specified. See the IMP::atom::AtomType documentation.
- 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.
- 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.
- The contents of bin are moving to tools since the two directories both contained assorted development tools
(not all of which were executable). For now, bin/imppy.sh will still work, but that will go away soon.
- IMP::Decorator::show() now just takes the stream (it used to take a prefix also, which was often ignored).
Anyone who implemented a decorator will have to delete the second argument of their show function.
## Week of August 1
- Containers now have methods IMP::SingletonContainer::evaluate(), IMP::PairContainer::evaluate(),
IMP::SingletonContainer::apply() and IMP::PairContainer::apply(). Using these can be significantly
faster than looping over the particles externally. Similarly, there is IMP::SingletonScore::evaluate(),
IMP::PairScore::evaluate(), IMP::SingletonModifier::apply(), IMP::PairModifier::apply().
- The decorator functions have been renamed to IMP::Decorator::setup_particle(), IMP::Decorator::decorate_particle()
and IMP::Decorator::particle_is_instance(). A shell script \c tools/update-decorators is provided which
updates the names in all code in subdirectories of the current directory. Please backup things first.
- a function, IMP::Restraint::safe_evaluate() has been added to be used
when requesting the value of restraints outside of the IMP::Model::evaluate().
## Week of July 18
- The atom::BondPairContainer has been renamed to atom::BondPairFilter
since it wasn't a real container. A real atom::BondPairContainer has
been added.
- Out of source builds mostly works. To do an out of source build, make a link
to \c scons_tools and \c SConstruct from the source directory in the build
directory and then add the line \command{repository="../path_to_src_dir"} in
the \c config.py in the build directory. Then running \c scons in the build
directory will put generated files there. This allows you to make both a
\c release and \c fast build off of the same set of sources. Proper docs
will be added soon.
- The SConscript setup for a module has been greatly simplified so it should
be easy enough for users to maintain their own module and updates to the
build system shouldn't involve changes to user SConscripts any more. This does
mean that any non-svn modules need to be updated. Look at IMP.core or another
module and copy what is there. Again, proper docs will be added soon.
## Week of July 11
- Per Javi's suggestion, the conventions have been split into
"Coding conventions" and "API conventions" and linked from the main page.
- benchmarks got moved to their own module, IMP::benchmark and will
now be tracked over time
## Week of July 4
- FilteredListSingletonContainer and FilteredPairSingletonContainer
went away as there was too much hard to factor code shared with
IMP::core::ListSingletonContainer and IMP::core::PairSingletonContainer. The
IMP::core::ClosePairsScoreState is now handled by a list of filters
on the class itself. That is, do
IMP::core::ClosePairsScoreState::add_close_pair_filter() to add a
filter.
- Hooks have been added to allow actions to be taken on an assertion
or check failure. See IMP::HandleFailure and its descendants for
more details.
- IMP::display::CGOWriter has been much improved and now allows
provides lots of display-time control and easy building of
animations.
- Generic optimizer states have been added
(IMP::core::SingletonsOptimizerState and
IMP::core::PairsOptimizerState).
## Week of June 15
- box distributions (IMP::algebra::random_vector_on_box(),
IMP::algebra::random_vector_in_box()) take bounding boxes
- IMP::em::DensityMap are now IMP::Object objects. Some current
allocations on the stack may need to be changed (since ref counted
objects can't be stack allocated).
- IMP::em::DensityMap::Read() is now deprecated (as is
IMP::em::DensityMap::Write) as they violated a slew of
conventions. Use IMP::em::read_map() and IMP::em::write_map()
instead.
## Week of June 8
- new methods IMP::atom::add_radii() and IMP::atom::add_bonds();
- Hierarchys to IMP::atom::Hierarchies
- IMP::Particles has been changed to a new type. It no longer plays
quite so well with Python lists (you can't create one from an
arbitrary Python list).
- The containers for multiple decorators have been revised to make them
more useful. See IMP::Decorators. You can now implicitly convert,
for %example, a IMP::core::XYZs to an IMP::Particles (as well as use
IMP::Decorators::get_particles()). All methods that take a
collection of particles with a certain type now instead take a
IMP::Decorators.
- A method that has expectations about the particles it takes should
take decorators rather than particles. That is, anything which
expects IMP::core::XYZ particles, should take an IMP::core::XYZs
instead of IMP::Particles.
- IMP_LIST() now takes an extra argument (the name of the plural
container)
- In C++ IMP::Decorator objects are implicitly convertible to
IMP::Particle* objects. Unfortunately, making this work in Python is
problematic.
- More methods take and return decorators rather than
IMP::Particles. This means it is clearer what their expectations are
and what they produce.
## Week of May 15
- The IMP::helper module was added and various functionality moved
there. See its documentation page for a list of what is there.
- IMP::algebra::SphericalCoords was renamed to
IMP::algebra::SphericalVector3D to be consistent with other algebra
classes.
- IMP::algebra::Rotation2D is now IMP::InvalidDefault to be consistent
with the other similar classes.
- We are trying to be a bit more specific about what is expected from
a IMP::atom::Hierarchy. Towards that end, there are two methods for
extracting a representation from a hierarchy,
IMP::atom::get_detailed_representation(), and
IMP::atom::get_simplified_representation()
- A method has been added to produce a simplified copy of an
IMP::atom::Hierarchy. The method is still a bit crude and could
benefit from other people inspecting the output and saying how it
should be improved.
- There is now an IMP::algebra::BoundingBoxD (and
IMP::algebra::BoundingBox3D) to track bounding boxes. There are
methods like IMP::algebra::bound_box(Sphere3D) which gets the
bounding box of a sphere.
- Each IMP::Object has its own log level. If
IMP::Object::set_log_level() is called with a value other than
IMP::DEFAULT, the value is used for code within and called by the
object. To support this in your objects you need to add
IMP_OBJECT_LOG to the start of each major method. It has been added
to some of the core objects.
## Week of May 8
- IMP::atom::MolecularHierarchy has been renamed to
IMP::atom::Hierarchy. Use \command{sed -i.old
"s\#MolecularHierarchy\#Hierarchy\#g" my_files}
- the long-deprecated Name(Decorator) was removed
- The decorator suffix has been removed from decorator names.
- Unit conventions have been established and documented for distance,
energy, force and angle.
- there is a function IMP::atom::create_protein() to create a coarse
grained protein. The function is crude so far, but the idea is that
we should have standard ways of generating such things so that
everyone can benefit from best practices.
- a class IMP::atom::BondGraph has been added so Boost.Graph
algorithms can be used with bond graphs
- the IMP-specific doxygen commands have been documented.
- the doxygen commands unstable{name} and untested{name} have been
added to doxygen to be used for marking methods and functions as
likely to change or not well tested. Pass the name of the class or
method as name.
- bonds can now be added to molecular hierarchies automatically see
IMP::atom::add_bonds()
## Week of May 1
- There is a IMP::Rotation2D
- You can now extract fixed Euler ZYZ angles from a
IMP::Rotation3D. This code can serve as a template for extracting
other Euler angle conventions if they are needed.
- IMP::algebra::rotation_between_two_vectors() changed to
IMP::algebra::rotation_taking_first_to_second() to make it clear
which direction the rotation goes.
## Week of April 27
- IMP::Decorator derived objects are now convertible to bool. So code
like \code if (d) { blah } \endcode works.
- IMP::Decorator::cast now returns a null decorator (\c
DecoratorName()) rather than throwing an exception. This might make
it actually useful.
- New IMP::statistics module for statistical methods
(e.g. clustering).
## Week of April 20
- Support for taking advantage of rigid bodies in collision detection
has been added via the IMP::core::RigidClosePairsFinder.
- All IMP::core::ClosePairsScoreState-related functionality has been
optimized and should be noticeably faster.
- The EMBED project has been merged into the IMP::em module. Thus, it
is no longer necessary to obtain EMBED separately to build IMP::em.
- All C++ methods which work with std::istream or std::ostream
arguments should now be usable from Python: any Python file-like
object can be used.
- The SWIG interface now ties in to the reference counting mechanism
used in the C++ code, for all classes derived from
IMP::RefCounted. So, for %example, deleting a Python object should
not free the underlying C++ object if another C++ object holds a
reference to it, and unrefing a C++ object should not delete it if a
Python object still holds a reference to it. There should be no
further need to manually keep references to Python objects to
prevent things from being prematurely cleaned up. This should be
transparent to the user; please report any problems.
- IMP::atom::AtomDecorator no longer inherits from
IMP::core::XYZDecorator.
## Week of April 13
- The decorators IMP::atom::AtomDecorator, IMP::atom::ChainDecorator,
IMP::atom::ResidueDecorator etc. now inherit from
IMP::atom::MolecularHierarchyDecorator. This means they can set
their IMP::atom::MolecularHierarchyDecorator::Type properly and
saves a lot of typing in the common case. We can always make
hierarchy decorators zero memory overhead if we find that the cost
matters.
- The base classes IMP::Comparable, IMP::NullDefault,
IMP::ValidDefault and IMP::UninitializedDefault were added to
document what the default constructors do for various objects in
IMP.
## Week of April 6
- IMP::Object now defines pure virtual methods
IMP::Object::get_version_info() and IMP::Object::show(). All
non-abstract classes which inherit from IMP::Object must implement
them. Doing this means they are more uniformly implemented and are
documented in one place.
- IMP::Object is now reference counted (the only objects this changes
are IMP::Model and IMP::Optimizer). As a result optimizers and
IMP::Model objects must be created on the heap.
- IMP::RefCounted has had its name changed and no longer inherits from
IMP::Object. This makes it easier to use independently.
- the docs for reference counting (IMP::RefCounted) and and IMP::Decorator
have been improved
- running doxygen produces no warnings. Let's try to keep it that
way. Run \command{scons doc > /dev/null} before you check in large
blocks of new code to make sure that you didn't introduce warnings.
- Helper classes have been added to make SingletonModifier and
PairModifier objects look like functors for C++ and Python. This
makes it so you can use \c map in Python and \c for_each in C++. See
IMP::SingletonFunctor and IMP::PairFunctor for more information.
- The recent changes page has moved to a doxygen page to make it
easier to link changes back to the relevant source code.
## Week of March 20:
- create_rigid_body(), create_rigid_bodies(), create_centroid()
etc. now require you to add the score state to the model
yourself. Whether the rigid body is enforced or not can be
controlled by adding or removing the returned IMP::ScoreState.
- All previously deprecated code has been removed. This includes
indexes in particles, the no-argument constructor for particles and
the functionality that was moved from core to atom.
- The IMP::core::RigidBodyDecorator and
IMP::core::RigidMemberDecorator have been simplified by removing the
traits classes. There is now only one type of rigid body and it
stores the list of member particles internally.
- IMP::core::NameDecorator has been deprecated as IMP::Particles have
built in names (use IMP::Particle::get_name(),
IMP::Particle::set_name()).
- IMP::atom::ChainDecorator has been added
## Week of March 13:
- A new IMP::display::Writer, IMP::display::ChimeraWriter has been
added which exports geometry to native Chimera constructs. It
probably should be used instead of bild and cmm for most purposes as
it combines the best of both types.
- compose() for transformation is now a free function so
compose(rotation, vector) will work via promotions.
- the geometry classes have been cleaned up and are now more
consistent with IMP standards (and more likely to do what their
names/comments suggest). See IMP::algebra::Sphere3D,
IMP::algebra::Cylinder3D, IMP::algebra::Segment3D,
IMP::algebra::Plane3D etc.
- ParticleRefiner has been renamed to IMP::Refiner since the Particle
was long and unnecessary.
eIF3 translation initiation complex](http:
645 - IMP::domino::DiscreteSampler::set_restraints() now allows the set of
646 restraints used in DOMINO filtering to be controlled (previously, all
647 restraints in the IMP::Model were used).
648 - IMP::modeller::IMPRestraints now transfers an IMP::ScoringFunction into the
649 MODELLER score, not the implicit (and deprecated) score of the
651 - Bugfix #775: coordinates of voxels in EM maps were previously inconsistently
652 treated (they are supposed to be the centers of the voxels, but in some
653 cases they were the lower left edge). The fix may result in maps and their
654 bounding boxes appearing shifted by half the voxel size.
656 # 2.4.0 - 2015-02-27 # {#changelog_2_4_0}
657 - Python 3 is now supported. The Windows package now works out of the box
658 with Python 3.3 or 3.4; a `-python3` subpackage is provided for Ubuntu
659 and Fedora. (Apple does not yet provide Python 3 so the Mac package is not
660 built with Python 3 support, but if you install Python 3 you can compile
661 IMP from source to work with it.)
662 - A new command line tool, `rrt_sample`, allows for running rapidly exploring
663 random tree (RRT) based sampling, e.g. to sample conformations of multiple
664 domains connected by flexible linkers.
665 - Command line tools are now placed in the `bin` directory of modules (the
666 old `bin` directory, used for utility programs that are not installed, is
667 now called `utility`). The `applications` directory is removed.
668 - Several Python modules that were only used by EMageFit have been moved from
669 IMP::em2d to IMP::EMageFit.
670 - A new tutorial that uses the IMP::pmi module is now available (modeling of
671 the RNA Polymerase II stalk).
673 # 2.3.1 - 2014-12-01 # {#changelog_2_3_1}
675 - Update to IMP::pmi to support the Nup84 and rnapolii biological systems.
677 # 2.3.0 - 2014-10-24 # {#changelog_2_3_0}
678 - 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.
679 - Binary installers for 64-bit Windows are now available.
680 - The `.py` extension has been removed from all Python applications, so that they are consistent with the C++ applications.
681 - 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.
682 - The integrative docking (idock) application now employs SOAP to improve the scoring.
683 - 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.
684 - 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.
686 # 2.2.1 - 2014-08-11 # {#changelog_2_2_1}
687 - Bugfix: PoseScore (see the ligand_score application) should now match that used by the Pose&Rank web server (http:
689 # 2.2.0 - 2014-04-09 # {#changelog_2_2_0}
690 - 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.
691 - 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.
692 - The generic geometry functions were simplified slightly and renamed to IMP::algebra::get_vector_geometry().
693 - The IMP::base::Flag class was added to simplify adding flags in C++.
694 - 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.
695 - Command line options are now divided into normal and advanced ones. You do `--help_advanced` to show the advanced ones.
696 - 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.
697 - 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.
698 - IMP::atom::get_rmsd(IMP::atom::Selection, IMP::atom::Selection, const IMP::algebra::Transformation3D&) was deprecated. Use IMP::atom::get_rmsd_transforming_first() instead.
699 - IMP::algebra::get_rmsd() and IMP::algebra::get_rmsd_transforming_first() were added.
700 - 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.
701 - 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.
702 - The container implementations has been cleaned up and simplified a bit. This should not change most usage.
704 - [Eigen](#Eigen) is now included with IMP.
705 - The deprecated function IMP::kernel::Optimizer::set_restraints() was removed. Use IMP::kernel::Optimizer::set_scoring_function() instead.
706 - 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.
707 - 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.
708 - 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.
709 - 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.
710 - 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:
712 # 2.1.1 - 2013-11-04 # {#changelog_2_1_1}
713 - Added support for Mac OS 10.9
715 # 2.1.0 - 2013-10-24 # {#changelog_2_1_0}
716 - 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.
717 - 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.
718 - Class name OwnerPointer was switched to PointerMember, to denote more clearly a ref-counting pointer that is a class member.
719 - 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).
720 - 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.
721 - 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.
722 - 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.
723 - IMP is now much more selective about when it invalidates the dependency graph. See [Dependencies](http:
724 - 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.
725 - 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.
726 - 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`).
727 - 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.
728 - 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.
729 - 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.
733 # For IMP 2.0 and earlier # {#changelog_2_0}
735 - Modules and applications now have a _Maintainer_ in their `README.md`, giving the github id of the person to whom issues should be assigned.
736 - `setup_git.py` supports the `--module` flag which will set up git hooks and things for a git repository that contains a module.
737 - 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.
738 - 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.
741 - Scons support was removed. Use cmake to build IMP, it is way better.
742 - 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.
743 - 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.
744 - The IMP_BIG_ENDIAN and IMP_LITTLE_ENDIAN preprocessor symbols are deprecated in favor of the BOOST_BIG_ENDIAN and BOOST_LITTLE_ENDIAN symbols.
745 - 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.
746 - 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.
747 - You can now (probably) build IMP with [CMake on IMP wiki](https:
748 - 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.
749 - 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.
750 - 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.
751 - 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.
752 - 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.
753 - 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.
754 - 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.
755 - OpenMP support in IMP is officially released. All tests pass. But there has been little specific testing so far.
756 - Access to attributes using IMP::ParticleIndex and the IMP::Model now works from Python. See IMP::Model::add_attribute() and kin.
757 - 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.
758 - 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.
759 - 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.
760 - 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 beginning. You can use `./tools/updaters/update_examples.py modules/mymodule` to update a module that was not already updated.
761 - IMP::base::FailureHandler has been removed as it wasn't used.
762 - 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.
763 - Modules now must be in a folder called `modules`, which must have a `description.py` file.
764 - The build system should now be a little better about cleaning up after itself.
765 - How headers/doc files/data/examples
766 - 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 "_" from the method name.
767 - Nice version numbers will now be generated if you use git. You need to rerun
768 tools/git/developer_tools/init_git if you have an existing clone.
771 - 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.
772 - 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.
773 - 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.
774 - 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.
775 - 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.
776 - 11/8; Evaluation with containers was greatly simplified, moving many methods on containers. We can add backwards compatibility versions if that is interesting.
777 - 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.
778 - 11/7: It is now preferred that IMP::Restraint and IMP::ScoreState descendants 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 deprecated. 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.
779 - 11/3: IMP::container::InContainerPairFilter and friends now treat pairs as unordered. A flag was added to control this.
780 - 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.
782 - 7/3: IMP_PERIODIC_OPTIMIZER_STATE() was superseded by the class IMP::core::PeriodicOptimizerState as it is rather cleaner than the macro.
783 - 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.
784 - 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.
785 - 6/24: Benchmarks are now put int \c module/benchmark and build to \c build/benchmark/module to remove a recurring source of errors.
786 - 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.
787 - 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.
789 - 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.
790 - 4/4: the filter types were superseded 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()).
791 - 29/3: IMP::Particle::get_has_model() has been changed to IMP::ModelObject::get_is_part_of_model() to be consistent with other classes.
792 - 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.
793 - 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).
794 - 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.
795 - 15/3: The vector used throughout IMP is now exposed at IMP::base::Vector and what it does it documented.
796 - 10/3: IMP::domino::RestraintCache was introduced to provide a documented centralized place to handle restraint evaluation and caching in DOMINO. In the switch various bugs involving maximum scores and IMP::RestraintSet objects were fixed.
797 - 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.
798 - 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.
799 - 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.
800 - 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.
801 - 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).
802 - 3/2: IMP::domino::WriteAssignmentContainer and IMP::domino::ReadAssignmentContainer were added to do direct binary file writing. This is faster than the HDF5 versions.
803 - 3/2: The installation instructions have been revamped and the developer instruction, in particular, have been greatly simplified.
804 - 24/1: \c tools/show-changes has been added that shows the changes in the history log since you last updated.
805 - 24/1: \c tools/make-source has been added that adds a source/header pair to a module
806 - 24/1: principal components analysis in IMP::algebra was generalized to work in any dimension. This required renaming the class to IMP::algebra::PrincipalComponentAnalysisD.
807 - 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
808 - 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.
809 - 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.
810 - 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.
811 - IMP::algebra::ParabolicFit was renamed to IMP::algebra::ParabolicFit2D (a backwards compatibility typedef is currently provided)
812 - IMP::algebra::LinearFit was renamed to IMP::algebra::LinearFit2D. It now supports error bars on the y-values.
814 - 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).
815 - Various IMP::algebra plural typedefs which had been using std::vector (since they never were updated), have now been moved to IMP::vector.
816 - IMP::statistics::HistogramD now supports display with \c matplotlib.
817 - IMP::statistics::HistogramD supersedes IMP::statistics::Histogram
818 - 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.
819 - the core generic restraint and score state support was moved to the kernel to avoid breaking various scores outside of IMP svn.
820 - 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.
821 - Decomposition of restraints now results in restraints that are faster to evaluate, using the generic restraint mechanism in IMP kernel.
822 - 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()
823 - 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.
824 - the way various types of geometry is stored in RMF files was changed, breaking backwards compatibility.
826 - 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.
827 - the source for the kernel has been moved from \c kernel to \c modules/kernel. This is unlikely to effect anyone.
828 - IMP::core::ExcludedVolumeRestraint now supports filters
829 - IMP::domino::HDF5AssignmentTable now caches internally, which makes it several times faster than before.
830 - you can now pick which Python to use with the \c python argument to scons.
831 - the units for BD diffusion coefficients changed to be consistent with other IMP units.
832 - IMP::domino::get_interaction_graph() now takes an IMP::RestraintsTemp, like other functions
833 - 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.
834 - 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.
835 - IMP::IntsList, IMP::FloatsList and IMP::StringsList have been added to replace the various scattered solutions for passing such types.
836 - 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.
837 - 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.
838 - 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.
839 - the IMP::core::DiameterRestraint was ignoring the radii of the particles involved and so was giving artificially low scores. It now is on the actual diameter of this molecule.
840 - the IMP::core::MonteCarlo optimizers now support incremental evaluation. This can be a lot faster when only a few particles are moved each step.
841 - 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.
842 - 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.
843 - Temp and non-temp decorator lists have been merged in C++. This was done to simplify code since no one was using the non-temp variants. Now all decorator lists are temp (non-reference counted) variants.
844 - 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.
845 - 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.
846 - IMP::domino uses the new IMP::Model::evaluate_if_good() support to accelerate computations
847 - IMP::core::MonteCarlo can use the IMP::Model::evaluate_if_good() support to more quickly reject
848 very bad conformations. See IMP::core::MonteCarlo::set_maximum_difference().
849 - IMP::core::ExcludedVolumeRestraint has been rewritten to be faster. It is especially
850 faster when used with IMP::Model::evaluate_if_good()
851 - 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.
852 - 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.
853 - 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.
854 - the RMF helper binaries have been moved to their own application so that they get installed.
855 - 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.
858 - An interactive mode has been added to IMP::domino::DominoSampler. The interactive mode is useful for understanding domino sampling runs and distributing domino computations across a cluster.
859 - Functions IMP::domino::set_assignments() and IMP::domino::get_assignments() were added which support
860 writing subset assignments to data fields in hdf5 files. These can be used to helping to distribute
861 domino on a cluster as well as debugging the sampling process.
862 - a Python function IMP.show_graphviz() has been added that attempts to render a graph with \c dot and then open the pdf.
863 - 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.
864 - IMP.atom.create_cover() was added to facilitate creating a summary particle for part of a hierarchy in order to accelerate restraints.
865 - 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.
866 - 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.
867 - The Python graph interface now has a remove_vertex method.
868 - 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.
869 - 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.
870 - Preliminary symmetry support has been added via the IMP::core::TransformationSymmetry and IMP::core::TransformationAndReflectionSymmetry classes.
873 - 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()
874 - IMP::core::MonteCarlo::set_temperature() was renamed to IMP::core::MonteCarlo::set_kt() as that is what it is doing.
875 - 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).
876 - IMP::algebra::grids::GridD now supports dense grids in arbitrary dimension through use of IMP::algebra::grids::DenseGridStorageD.
877 - IMP::Optimizer now can use a list of restraint sets to compute the score rather than the complete Model score.
878 - each IMP::Restraint now has its own weight. This is lightly tested.
879 - 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.
880 - IMP::domino::TrivialParticleStates renamed to IMP::domino::IndexParticleStates to be less judgmental
881 - IMP::domino::CompoundParticleStates and IMP::domino::RecursiveParticleStates added
882 - IMP::domino::DominoSampler now supports maximum scores on IMP::RestraintSets (untested).
883 - the name of the clustering methods have been changed to create_ from get_ since they create objects.
884 - the names of the recently added metric based clustering support has been changed to Metric rather than Distance.
885 - 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.
886 - the function IMP::display::create_restraint_geometry() was added to do what its name says.
887 - 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.
888 - IMP::atom::DopePairScore has been added to IMP.
889 - IMP::atom::CHARMMStereochemistryRestraint provides a high-level simplified
890 interface to the bonded part of the CHARMM forcefield.
891 - 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.
892 - Instructions and scripts have been added for building modules and things externally to the IMP build. See the installation guide.
893 - IMP::atom::CHARMMParameters can now automatically map CHARMM-style atom and
894 residue naming to PDB-style, so CHARMM topology files can be used unmodified.
895 - IMP::atom::CHARMMTopology::add_sequence() provides a simple way to generate a topology from a string of amino acid one-letter codes.
896 - IMP::atom::CHARMMTopology::add_coordinates() will generate atomic Cartesian coordinates from CHARMM internal coordinate information.
897 - IMP::atom::CHARMMTopology::add_missing_atoms() and
898 IMP::atom::remove_charmm_untyped_atoms() can now be used to ensure that atoms
899 read from a PDB file match the CHARMM topology.
900 - building of deprecated functionality is now false by default
901 - 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.
902 - 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).
903 - 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.
904 - 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.
905 - rename IMP::restrainer::Restraint::print_all_restraints() to IMP::restrainer::Restraint::show_all_restraints() to be consistent with the rest of IMP.
906 - renamed IMP::atom::get_conect_record_string() to IMP::atom::get_pdb_conect_record_string() to make clearer what it is.
907 - class and method names are now spell checked. Add missing words to spelling_exceptions in the module test call.
908 - the plural names (eg IMP.Particles()) have been removed from the Python side as they are just Python lists.
909 - biological systems can now include internal modules. These provide a convenient place to put application specific C++ and Python code. See the example system for more info.
910 - IMP_VALUES() now includes IMP_OUTPUT_OPERATOR() so you no longer need two namespace macros for each value.
911 - 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.
912 - the IMP::atom::PDBSelector and IMP::atom::Mol2Selector became IMP::Object classes. All this
913 means is that they need to be created with \c new in C++ code. It also means that one is
914 no longer prohibited from storing them (not that there is much use in doing that).
915 - 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.
916 - IMP::core::RigidBody::lazy_set_reference_frame() was renamed to IMP::core::RigidBody::set_reference_frame_lazy() to fit with the standards better.
917 - the transform based methods on reference frame which have been deprecated for a while were removed
918 - 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.
919 - IMP::atom::NonhydrogenMol2Selector was renamed IMP::atom::NonHydrogenMol2Selector to be consistent with the PDB version
922 - IMP::display::PlaneGeometry was added to display planes
923 - 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
924 benefit from better checking.
925 - 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.
926 - 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()
927 - IMP::core::WriteModelOptimizerState is going away as it duplicated IMP::WriteParticlesOptimizerState.
928 - 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.
929 - the biological systems specification has been improved a little adding ability to run some rudimentary tests to make sure the scripts are ok and to not require that everything be run from the svn directory.
930 - 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.
931 - Logging has been improved to better report the name of methods producing the log messages
932 - a macro IMP_FUNCTION_LOG has been added which should be added to the start of non-member functions which produce significant logging output.
933 - 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.
934 - IMP.domino2 was renamed to IMP.domino and the old IMP.domino was moved
935 - 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.
936 - applications and biological systems now have their own documentation pages
937 - IMP::atom::Hierarchy requires radii on its leaves
938 - IMP::atom::read_pdb add radii to the atoms
939 - IMP::helper was merged into IMP::restrainer as all the functionality there was primarily to provide support for restrainer
940 - IMP::domino2::SubsetEvaluatorTable was removed. Pass the model and IMP::domino2::ParticleStatesTable to the IMP::domino2::RestraintScoreSubsetFilterTable instead.
941 - 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.
942 - a new example was added in the kernel to show IMP used on a biological system
943 - IMP::display::PymolWriter now supports adding labels to things
944 - IMP::display::PairRestraintGeometry and IMP::display::ConnectivityRestraintGeometry were added to aid in visualizing those restraints.
945 - IMP::bullet was added with an optimizer to use hard body physics to resolve local collisions.
946 - 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 separate particle so that the molecular hierarchy doesn't have to worry about having its bounding sphere large enough to enclose all the members.
947 - IMP::core::KClosePairsPairScore was added to have count based cutoffs for close pair scoring.
948 - IMP::algebra::get_surface_area_and_volume() was added to compute the two numbers for a set of balls
951 - 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 slightly tweaked to work.
952 - Javi added his 2D EM scoring functionality as IMP::em2D
953 - 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.
954 - 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).
955 - 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.
956 - 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).
957 - 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
958 - a better explanation of how to use reference counted pointers has been added to IMP::Pointer.
959 - all simple, planar polygons are now supported for display when CGAL is present
961 ## Week of April 1, 2010
963 - 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
964 - types are not checked until the lists are passed to C++
965 - 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)
966 - swig has issues with some overloads (not always for obvious reasons). These are being sorted out. None are commonly used.
967 - get_particles() on a plural object doesn't work in Python (and is not needed in C++). Implicit conversions will always work.
969 - 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 empty lists of particles in the constructors cause check failures. We can figure out a work around if this is too annoying.
971 ## Week of March 13, 2010
972 - 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.
974 - 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).
976 ## Week of March 6, 2010
977 - 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.
980 ## Week of Feb 27, 2010
981 - IMP::algebra::decompose_rotation_into_axis_angle() was renamed to IMP::algebra::get_angle_and_axis().
983 - renamed IMP::atom::bond() and IMP::atom::unbond() to IMP::atom::create_bond() and IMP::atom::destroy_bond() to be more consistent with things
985 - renamed IMP::core::root() to IMP::core::get_root()
988 ## Week of Feb 21, 2010
990 - IMP::Object::set_was_owned() was changed to IMP::Object::set_was_used() as that better reflects what the flag means.
991 - various more interpolation and endian methods had their names fixed (by adding \c get_)
992 - the function get_mean() on vectors was removed as it duplicated IMP::algebra::get_centroid()
993 - build_Transformation3D_from_transformation3D was replaced by IMP.algebra.get_transformation_3d()
994 - IMP::algebra::almost_equal() is now IMP::algebra::get_are_almost_equal() to fit the naming conventions.
995 - 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
996 - 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>).
997 - 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.
998 Some good sed strings are
999 - "s\#random_vector_in_unit_sphere()\#get_random_vector_in(IMP.algebra.get_unit_sphere_3d())\#g"
1000 - "s\#random_vector_in_unit_box()\#get_random_vector_in(IMP.algebra.get_unit_bounding_box_3d())\#g"
1001 - "s\#random_vector_on_unit_sphere()\#get_random_vector_on(IMP.algebra.get_unit_sphere_3d())\#g"
1002 - "s\#random_vector_on_unit_box()\#get_random_vector_on(IMP.algebra.get_unit_bounding_box_3d())\#g"
1003 - "s\#random_vector_in_box(\#get_random_vector_in(\#g"
1004 - "s\#random_vector_on_box(\#get_random_vector_on(\#g"
1005 - "s\#random_vector_in_sphere(\#get_random_vector_in(\#g"
1006 - "s\#random_vector_on_sphere(\#get_random_vector_on(\#g"
1007 - "s\#grid_cover\#get_grid_surface_cover\#g"
1008 - "s\#uniform_coverr\#get_uniform_surface_cover\#g"
1010 - Spheres in IMP::algebra are now supported in general dimensions. See IMP::algebra::SphereD.
1011 - 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.
1012 - build_Rotation2D_from_Vector2D became IMP::algebra::get_rotation_to_x_axis()
1013 - 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)
1014 - IMP::algebra::Transformation3D::get_transformed() and IMP::algebra::Rotation3D::get_rotated(). Replacing \c ".transform(" worked in the IMP code base.
1015 - IMP::algebra::get_distance(), this also carries over to the IMP::core::get_distance()
1016 The following global replacements are probably safe (in sed expressions)
1017 - "s\#core.distance(\#core.get_distance\#g"
1018 - "s\#algebra.distance(\#algebra.get_distance\#g"
1019 - "s\#\.transform(\#.get_transformed(\#g" Only in C++
1020 - "s\#\.rotate(\#.get_rotated(\#g" Only in C++
1021 - "s\#rotation_from\#get_rotation_from\#g"
1022 - "s\#rotation_in\#get_rotation_in\#g"
1023 - "s\#identity_rotation(\#get_identity_rotation_3d("
1024 - "s\#::distance(\#::get_distance(\#g"
1026 - 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.
1027 - 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.
1028 - 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()
1030 ## Week of Feb 14, 2010
1032 - The IMP::atom::Bond types were rearranged to reconcile the protein-centric classification with ligand support.
1034 - IMP::atom::Atom no longer has charge since we have IMP::atom::Charged.
1036 - IMP::atom::read_mol2() and IMP::atom::write_mol2() were added
1038 - IMP::atom::Selector and descendants 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.
1040 - 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.
1042 - IMP::example renamed (from examples)
1044 - The IMP_USAGE_CHECK() macro lost the (unused) third argument.
1046 ## Week of February 3, 2010
1048 - The model io code as moved into the kernel so it is now IMP::write_model() and IMP::read_model()
1050 - Remove the version_info argument from the implementation macros. Instead, just pick up the module version info automatically.
1052 - Add a function Object::get_type_name() and Object::get_module() to get the respective bits of information about each object.
1054 - 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().
1056 - The containers were moved to IMP.container. See that module page for a full list of what moved. In the process, the backwards compatibility functions were removed from IMP::container::PairsRestraint and kin.
1058 - IMP.atom.create_protein() now returns the created protein
1060 - the simplify functions have been moved from IMP.helper. They are now IMP.atom.create_simplified_along_backbone().
1062 - IMP.helper.clone() has been renamed to IMP.atom.create_clone()
1064 - IMP.misc.ConnectingPairContainer has been moved to IMP.core.ConnectingPairContainer
1066 - The locations for pixels in IMP::em::DensityMap have been moved to the center of the corresponding voxel from the lower left corner.
1068 - IMP::em::get_transformed(), IMP::em::get_resampled() and IMP::em::get_density() have been added.
1070 - 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.
1072 - 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.
1074 - 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.
1076 - Most geometry now has namespace methods IMP::algebra::get_bounding_box(), IMP::algebra::get_surface_area(), IMP::algebra::get_volume().
1078 ## Week of January 22, 2010
1080 - A generic geometry layer has been added (see \ref genericgeometry). Using it, IMP::atom::rmsd(),
1081 IMP::algebra::alignment_taking_first_to_second() and the new IMP::atom::native_overlap() all
1082 can work on either collections of either IMP::core::XYZ particles or IMP::algebra::Vector3Ds.
1084 - 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.
1086 - 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.
1088 - Rename IMP::core::MinimumPairScoreRestraint (and kin, Maximum, Singleton, Triplet and Quad) to IMP::core::MinimumPairRestraint.
1090 - Add IMP::core::MinumumPairScore (and kin).
1092 ## Week of January 1, 2010
1094 - IMP::em is now using Particles to resample density maps and for fitting restraints. The previous ParticleAccessPoint mechanism is removed.
1096 - IMP::UsageException and IMP::InternalException are now reserved for their respective
1097 checks (and cannot be thrown by IMP_THROW()). This makes the distinction between API
1098 exceptions (which are thrown in any build mode and should be documented and tested)
1099 and helper exceptions which are only thrown when checks are turned on (and hence
1100 should not be documented) clearer.
1102 - IMP::core::RestraintSet moved to IMP::RestraintSet. The restraint sets now simply define a tree
1103 with weights which the model traverses as opposed to being an opaque IMP::Restraint themselves.
1104 This means that incremental evaluation of restraints in restraint sets now works and that
1105 restraints in restraint sets can be individually evaluated. Existing working usage should not
1106 have changed (so \c sed should manage updates just fine), but the internal
1107 implementation is completely new, so pay attention.
1109 - IMP now has a text i/o layer consisting of IMP::TextInput and IMP::TextOutput. These classes are
1110 convertible to C++ streams and implicitly constructable from both streams and file paths. As a result,
1111 functions that take them will work when called with a string for a file path, a Python file or a
1114 - The IMP.examples module now documents how to use the needed aspects of scons and SWIG.
1116 - 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.
1118 - 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.
1120 - boost program options is now a checked for dependency.
1122 - 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.
1124 - 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.
1126 - 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).
1128 - 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.
1130 - a new base class IMP::Constraint has been added for constraints. Various
1131 other classes have been renamed to be consistent.
1133 ## Week of December 11
1135 - 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.
1137 - 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.
1139 - IMP::ParticlePair::first and second went away since no one claimed to be using it and it complicated the implementation.
1141 - The generic restraints/score states/scores infrastructure has been extended to triplets and quads (for angles and torsion angles).
1143 ## Week of December 4
1145 - 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.
1147 - 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.
1149 - 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).
1151 ## Week of November 19
1153 - imp.xcodeproj was moved into tools and updated accordingly
1155 - the bin directory finally went away
1157 - IMP::display::ChimeraWriter now supports the latest version of Chimera
1159 - IMP::display::CGOWriter was renamed to IMP::display::PymolWriter as it can do more than just CGO.
1161 - IMP::VectorOfRefCounted::operator[] can now be used for assignments just like a normal vector. No more need to use the IMP::VectorOfRefCounted::set() method.
1163 - the IMP::atom::Hierarchy constructor from an IMP::Particle* is now explicit (as were the decorator constructors)
1166 ## Week of November 12
1168 - All exception types are now mapped to equivalent classes in Python. The
1169 class hierarchy is similar (e.g. IMP::ModelException derives from IMP::Exception
1170 in both C++ and Python) so all IMP exceptions can be caught in Python using
1171 "except IMP.Exception". For convenience, the IMP::IOException,
1172 IMP::ValueException and IMP::IndexException classes in Python also derive from
1173 the similarly-named standard Python classes (IOError, ValueError and IndexError
1176 ## week of October 29 Update
1178 - 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).
1180 - 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().
1182 - Added IMP::core::VolumeRestraint.
1184 - Several functions have been added to helper in creating restraints. They are create_simple_connectivity_on_rigid_bodies(), create_simple_connectivity_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.
1187 - 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().
1189 - IMP::em::read_map() will figure out the file type to use automatically from the extension. Other such methods should follow suite.
1191 - A class IMP::core::StructureSet has been added to provide a convenient way to manage solutions of optimization runs.
1193 - IMP::core::RigidBodyMover now takes its angle argument in radians and is documented as such.
1195 - 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.
1197 - IMP::core::AllPairsPairContainer has been renamed to IMP::core::AllPairContainer and a bipartite version has been added.
1199 - All containers now keep track of what they looked like on the previous time step.
1201 - The IMP::core::ListPairContainer and IMP::core::ListSingletonContainer have had their interface reduced a bit in order to make implementing change tracking easier.
1203 - 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.
1205 - 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.
1207 ## Week of October 15
1209 - 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.
1211 ## Week of October 8
1213 - 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.
1215 - 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.
1217 - IMP_check() and IMP_assert() have been
1218 replaced with IMP_USAGE_CHECK() and IMP_INTERNAL_CHECK()
1219 respectively. Hopefully this makes it clearer when to use
1220 which. IMP::set_check_level() has been revised accordingly (to use
1221 IMP::USAGE and IMP::USAGE_AND_INTERNAL). Also, IMP_failure() and
1222 IMP_not_implemented() have been renamed to IMP_FAILURE() and
1223 IMP_NOT_IMPLEMENTED() to make all macros be all caps. To update
1225 - replace IMP.EXPENSIVE with IMP.USAGE_AND_INTERNAL
1226 - replace IMP.CHEAP with IMP.USAGE
1227 - replace IMP_assert and IMP_check as above.
1229 ## Week of October 1
1230 - 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.
1232 - .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.
1234 - The search module is no longer built by default and is not longer supported. It will get moved out of svn shortly.
1236 - IMP::ScoreState objects now also have IMP::Interacting::get_interacting_particles() methods. Soon IMP::PairScore and IMP::SingletonScore objects will too.
1238 ## Week of September 27
1240 - 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.
1242 - A class IMP::core::RigidBodyDistancePairScore has been added which provides accelerated computations for the distance between two rigid bodies.
1244 - The SWIG input files were renamed from swig.i to swig.i-in to aid in dependency tracking.
1246 - 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.
1248 ## Week of September 20
1250 - all \c .i files have been renamed to start with \c IMP_ to help make dependency tracking easier.
1252 - static builds (builds with \c static=True) build both the static and dynamic libraries and just static executables
1254 - 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.
1256 - 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.
1258 - \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.
1260 ## Week of August 30
1262 - A new score IMP::core::BoundingBox3DSingletonScore has been added to keep particles
1265 - str should now work better in Python when applied to IMP::Object objects and a few others. Objects
1266 should use the new IMP_SHOWABLE and IMP_SHOWABLE_INLINE macros instead of declaring show
1267 functions directory to make it so that they work in Python. It is now a bug to \c print or \c str
1268 to not return something useful in Python for any IMP object.
1270 ## Week of August 23
1272 - each module now has a version, eg IMP::get_module_version_info() which is also returned by the various restraints of the module. The Python code checks that loaded libraries have the expected version numbers to try to provide better messages when runtime linking problems occur.
1274 - the various bounding_box methods have been renamed to ::get_bounding_box() to be more consistent with the other names.
1276 - Python documentation is now parsed by doxygen
1278 ## Week of August 15
1280 - 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.
1284 - 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.
1286 - 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).
1288 - IMP::atom::Mass() has been added for decorating particles with mass. IMP::atom::Atom mass has been moved to that.
1290 - The scheme for generating atom types is now fully specified. See the IMP::atom::AtomType documentation.
1292 - 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.
1294 - 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.
1296 - The contents of bin are moving to tools since the two directories both contained assorted development tools
1297 (not all of which were executable). For now, bin/imppy.sh will still work, but that will go away soon.
1299 - IMP::Decorator::show() now just takes the stream (it used to take a prefix also, which was often ignored).
1300 Anyone who implemented a decorator will have to delete the second argument of their show function.
1304 - Containers now have methods IMP::SingletonContainer::evaluate(), IMP::PairContainer::evaluate(),
1305 IMP::SingletonContainer::apply() and IMP::PairContainer::apply(). Using these can be significantly
1306 faster than looping over the particles externally. Similarly, there is IMP::SingletonScore::evaluate(),
1307 IMP::PairScore::evaluate(), IMP::SingletonModifier::apply(), IMP::PairModifier::apply().
1309 - The decorator functions have been renamed to IMP::Decorator::setup_particle(), IMP::Decorator::decorate_particle()
1310 and IMP::Decorator::particle_is_instance(). A shell script \c tools/update-decorators is provided which
1311 updates the names in all code in subdirectories of the current directory. Please backup things first.
1313 - a function, IMP::Restraint::safe_evaluate() has been added to be used
1314 when requesting the value of restraints outside of the IMP::Model::evaluate().
1318 - The atom::BondPairContainer has been renamed to atom::BondPairFilter
1319 since it wasn't a real container. A real atom::BondPairContainer has
1322 - Out of source builds mostly works. To do an out of source build, make a link
1323 to \c scons_tools and \c SConstruct from the source directory in the build
1324 directory and then add the line \command{repository="../path_to_src_dir"} in
1325 the \c config.py in the build directory. Then running \c scons in the build
1326 directory will put generated files there. This allows you to make both a
1327 \c release and \c fast build off of the same set of sources. Proper docs
1330 - The SConscript setup for a module has been greatly simplified so it should
1331 be easy enough for users to maintain their own module and updates to the
1332 build system shouldn't involve changes to user SConscripts any more. This does
1333 mean that any non-svn modules need to be updated. Look at IMP.core or another
1334 module and copy what is there. Again, proper docs will be added soon.
1339 - Per Javi's suggestion, the conventions have been split into
1340 "Coding conventions" and "API conventions" and linked from the main page.
1342 - benchmarks got moved to their own module, IMP::benchmark and will
1343 now be tracked over time
1347 - FilteredListSingletonContainer and FilteredPairSingletonContainer
1348 went away as there was too much hard to factor code shared with
1349 IMP::core::ListSingletonContainer and IMP::core::PairSingletonContainer. The
1350 IMP::core::ClosePairsScoreState is now handled by a list of filters
1351 on the class itself. That is, do
1352 IMP::core::ClosePairsScoreState::add_close_pair_filter() to add a
1355 - Hooks have been added to allow actions to be taken on an assertion
1356 or check failure. See IMP::HandleFailure and its descendants for
1359 - IMP::display::CGOWriter has been much improved and now allows
1360 provides lots of display-time control and easy building of
1363 - Generic optimizer states have been added
1364 (IMP::core::SingletonsOptimizerState and
1365 IMP::core::PairsOptimizerState).
1369 - box distributions (IMP::algebra::random_vector_on_box(),
1370 IMP::algebra::random_vector_in_box()) take bounding boxes
1372 - IMP::em::DensityMap are now IMP::Object objects. Some current
1373 allocations on the stack may need to be changed (since ref counted
1374 objects can't be stack allocated).
1376 - IMP::em::DensityMap::Read() is now deprecated (as is
1377 IMP::em::DensityMap::Write) as they violated a slew of
1378 conventions. Use IMP::em::read_map() and IMP::em::write_map()
1384 - new methods IMP::atom::add_radii() and IMP::atom::add_bonds();
1386 - Hierarchys to IMP::atom::Hierarchies
1388 - IMP::Particles has been changed to a new type. It no longer plays
1389 quite so well with Python lists (you can't create one from an
1390 arbitrary Python list).
1392 - The containers for multiple decorators have been revised to make them
1393 more useful. See IMP::Decorators. You can now implicitly convert,
1394 for %example, a IMP::core::XYZs to an IMP::Particles (as well as use
1395 IMP::Decorators::get_particles()). All methods that take a
1396 collection of particles with a certain type now instead take a
1399 - A method that has expectations about the particles it takes should
1400 take decorators rather than particles. That is, anything which
1401 expects IMP::core::XYZ particles, should take an IMP::core::XYZs
1402 instead of IMP::Particles.
1404 - IMP_LIST() now takes an extra argument (the name of the plural
1407 - In C++ IMP::Decorator objects are implicitly convertible to
1408 IMP::Particle* objects. Unfortunately, making this work in Python is
1411 - More methods take and return decorators rather than
1412 IMP::Particles. This means it is clearer what their expectations are
1413 and what they produce.
1417 - The IMP::helper module was added and various functionality moved
1418 there. See its documentation page for a list of what is there.
1420 - IMP::algebra::SphericalCoords was renamed to
1421 IMP::algebra::SphericalVector3D to be consistent with other algebra
1424 - IMP::algebra::Rotation2D is now IMP::InvalidDefault to be consistent
1425 with the other similar classes.
1427 - We are trying to be a bit more specific about what is expected from
1428 a IMP::atom::Hierarchy. Towards that end, there are two methods for
1429 extracting a representation from a hierarchy,
1430 IMP::atom::get_detailed_representation(), and
1431 IMP::atom::get_simplified_representation()
1433 - A method has been added to produce a simplified copy of an
1434 IMP::atom::Hierarchy. The method is still a bit crude and could
1435 benefit from other people inspecting the output and saying how it
1438 - There is now an IMP::algebra::BoundingBoxD (and
1439 IMP::algebra::BoundingBox3D) to track bounding boxes. There are
1440 methods like IMP::algebra::bound_box(Sphere3D) which gets the
1441 bounding box of a sphere.
1443 - Each IMP::Object has its own log level. If
1444 IMP::Object::set_log_level() is called with a value other than
1445 IMP::DEFAULT, the value is used for code within and called by the
1446 object. To support this in your objects you need to add
1447 IMP_OBJECT_LOG to the start of each major method. It has been added
1448 to some of the core objects.
1452 - IMP::atom::MolecularHierarchy has been renamed to
1453 IMP::atom::Hierarchy. Use \command{sed -i.old
1454 "s\#MolecularHierarchy\#Hierarchy\#g" my_files}
1456 - the long-deprecated Name(Decorator) was removed
1458 - The decorator suffix has been removed from decorator names.
1460 - Unit conventions have been established and documented for distance,
1461 energy, force and angle.
1463 - there is a function IMP::atom::create_protein() to create a coarse
1464 grained protein. The function is crude so far, but the idea is that
1465 we should have standard ways of generating such things so that
1466 everyone can benefit from best practices.
1468 - a class IMP::atom::BondGraph has been added so Boost.Graph
1469 algorithms can be used with bond graphs
1471 - the IMP-specific doxygen commands have been documented.
1473 - the doxygen commands unstable{name} and untested{name} have been
1474 added to doxygen to be used for marking methods and functions as
1475 likely to change or not well tested. Pass the name of the class or
1478 - bonds can now be added to molecular hierarchies automatically see
1479 IMP::atom::add_bonds()
1483 - There is a IMP::Rotation2D
1485 - You can now extract fixed Euler ZYZ angles from a
1486 IMP::Rotation3D. This code can serve as a template for extracting
1487 other Euler angle conventions if they are needed.
1489 - IMP::algebra::rotation_between_two_vectors() changed to
1490 IMP::algebra::rotation_taking_first_to_second() to make it clear
1491 which direction the rotation goes.
1495 - IMP::Decorator derived objects are now convertible to bool. So code
1496 like \code if (d) { blah } \endcode works.
1498 - IMP::Decorator::cast now returns a null decorator (\c
1499 DecoratorName()) rather than throwing an exception. This might make
1502 - New IMP::statistics module for statistical methods
1507 - Support for taking advantage of rigid bodies in collision detection
1508 has been added via the IMP::core::RigidClosePairsFinder.
1510 - All IMP::core::ClosePairsScoreState-related functionality has been
1511 optimized and should be noticeably faster.
1513 - The EMBED project has been merged into the IMP::em module. Thus, it
1514 is no longer necessary to obtain EMBED separately to build IMP::em.
1516 - All C++ methods which work with std::istream or std::ostream
1517 arguments should now be usable from Python: any Python file-like
1520 - The SWIG interface now ties in to the reference counting mechanism
1521 used in the C++ code, for all classes derived from
1522 IMP::RefCounted. So, for %example, deleting a Python object should
1523 not free the underlying C++ object if another C++ object holds a
1524 reference to it, and unrefing a C++ object should not delete it if a
1525 Python object still holds a reference to it. There should be no
1526 further need to manually keep references to Python objects to
1527 prevent things from being prematurely cleaned up. This should be
1528 transparent to the user; please report any problems.
1530 - IMP::atom::AtomDecorator no longer inherits from
1531 IMP::core::XYZDecorator.
1535 - The decorators IMP::atom::AtomDecorator, IMP::atom::ChainDecorator,
1536 IMP::atom::ResidueDecorator etc. now inherit from
1537 IMP::atom::MolecularHierarchyDecorator. This means they can set
1538 their IMP::atom::MolecularHierarchyDecorator::Type properly and
1539 saves a lot of typing in the common case. We can always make
1540 hierarchy decorators zero memory overhead if we find that the cost
1543 - The base classes IMP::Comparable, IMP::NullDefault,
1544 IMP::ValidDefault and IMP::UninitializedDefault were added to
1545 document what the default constructors do for various objects in
1550 - IMP::Object now defines pure virtual methods
1551 IMP::Object::get_version_info() and IMP::Object::show(). All
1552 non-abstract classes which inherit from IMP::Object must implement
1553 them. Doing this means they are more uniformly implemented and are
1554 documented in one place.
1556 - IMP::Object is now reference counted (the only objects this changes
1557 are IMP::Model and IMP::Optimizer). As a result optimizers and
1558 IMP::Model objects must be created on the heap.
1560 - IMP::RefCounted has had its name changed and no longer inherits from
1561 IMP::Object. This makes it easier to use independently.
1563 - the docs for reference counting (IMP::RefCounted) and and IMP::Decorator
1566 - running doxygen produces no warnings. Let's try to keep it that
1567 way. Run \command{scons doc > /dev/null} before you check in large
1568 blocks of new code to make sure that you didn't introduce warnings.
1570 - Helper classes have been added to make SingletonModifier and
1571 PairModifier objects look like functors for C++ and Python. This
1572 makes it so you can use \c map in Python and \c for_each in C++. See
1573 IMP::SingletonFunctor and IMP::PairFunctor for more information.
1575 - The recent changes page has moved to a doxygen page to make it
1576 easier to link changes back to the relevant source code.
1578 ## Week of March 20:
1580 - create_rigid_body(), create_rigid_bodies(), create_centroid()
1581 etc. now require you to add the score state to the model
1582 yourself. Whether the rigid body is enforced or not can be
1583 controlled by adding or removing the returned IMP::ScoreState.
1585 - All previously deprecated code has been removed. This includes
1586 indexes in particles, the no-argument constructor for particles and
1587 the functionality that was moved from core to atom.
1589 - The IMP::core::RigidBodyDecorator and
1590 IMP::core::RigidMemberDecorator have been simplified by removing the
1591 traits classes. There is now only one type of rigid body and it
1592 stores the list of member particles internally.
1594 - IMP::core::NameDecorator has been deprecated as IMP::Particles have
1595 built in names (use IMP::Particle::get_name(),
1596 IMP::Particle::set_name()).
1598 - IMP::atom::ChainDecorator has been added
1600 ## Week of March 13:
1602 - A new IMP::display::Writer, IMP::display::ChimeraWriter has been
1603 added which exports geometry to native Chimera constructs. It
1604 probably should be used instead of bild and cmm for most purposes as
1605 it combines the best of both types.
1607 - compose() for transformation is now a free function so
1608 compose(rotation, vector) will work via promotions.
1610 - the geometry classes have been cleaned up and are now more
1611 consistent with IMP standards (and more likely to do what their
1612 names/comments suggest). See IMP::algebra::Sphere3D,
1613 IMP::algebra::Cylinder3D, IMP::algebra::Segment3D,
1614 IMP::algebra::Plane3D etc.
1616 - ParticleRefiner has been renamed to IMP::Refiner since the Particle
1617 was long and unnecessary.
Array< 4, WeakPointer< Particle >, Particle * > ParticleQuad
Index< ParticleIndexTag > ParticleIndex
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
Array< 3, WeakPointer< Particle >, Particle * > ParticleTriplet
bool get_is_valid() const
Array< 2, WeakPointer< Particle >, Particle * > ParticlePair
