Merge for 2.9.0 release

.gitignore

@@ -22,5 +22,4 @@ applications/*/CMakeLists.txt
 tools/build/cmake_files/MakeContainers.cmake
 Files.cmake
 .DS_Store
-modules/npctransport/
 .#*

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "modules/npctransport"]
+	path = modules/npctransport
+	url = https://github.com/salilab/npctransport.git
+[submodule "components/pathway_mapping"]
+	path = components/pathway_mapping
+	url = https://github.com/salilab/pathway_mapping.git

.travis.yml

@@ -48,7 +48,7 @@ git:
 
 before_install:
  - sudo apt-get update -qq
- - sudo apt-get install -qq libboost$BOOST-all-dev swig libhdf5-serial-dev
+ - sudo apt-get install -qq libboost$BOOST-all-dev swig libhdf5-serial-dev libeigen3-dev
  - ./setup_git.py
 
 script:

CMakeLists.txt

@@ -64,9 +64,7 @@ cmake_policy(SET CMP0017 NEW)
 endif(POLICY CMP0017)
 
 # Don't set MACOSX_RPATH by default
-if(POLICY CMP0042)
-cmake_policy(SET CMP0042 OLD)
-endif(POLICY CMP0042)
+set(CMAKE_MACOSX_RPATH 0)
 
 # Stop cmake warning about files in the build directory it didn't create
 # (see issue #909)
@@ -277,6 +275,12 @@ if(NOT IMP_STATIC)
   find_package(OpenMP3)
 endif()
 
+find_package(Eigen3 3.0 REQUIRED)
+# Add Eigen3 to 'system' include path. Amongst other things, this will suppress
+# many compiler warnings about Eigen code which a) clutter the output and
+# b) we're not going to fix, since Eigen isn't our code.
+include_directories(SYSTEM ${EIGEN3_INCLUDE_DIR})
+
 add_custom_target("IMP-version"
                   COMMAND ${CMAKE_SOURCE_DIR}/tools/build/make_version.py --source=${CMAKE_SOURCE_DIR}
                   WORKING_DIRECTORY ${CMAKE_BINARY_DIR}

ChangeLog.md

@@ -1,6 +1,47 @@
 ChangeLog {#changelog}
 =========
 
+# 2.9.0 - 2018-07-02 # {#changelog_2_9_0}
+- [Eigen](https://eigen.tuxfamily.org/) is now required to build IMP.
+- The Windows .exe IMP installer no longer supports Python 2.6. Python 2.7,
+  3.4, 3.5, and 3.6 are supported by this installer.
+- A binary package is now provided for Ubuntu 18.04 LTS, Bionic Beaver.
+- The IMP::atom::setup_as_rigid_body() function has been removed.
+  Use IMP::atom::create_rigid_body() instead.
+- Constructors for IMP::container classes, IMP::core::BallMover,
+  IMP::core::RigidBodyMover, and IMP::core::IncrementalScoringFunction taking
+  a RigidBody or Particles have been removed. Use constructors taking
+  ParticleIndexes instead.
+- The IMP::core::ConnectivityRestraint::get_connected_pairs() method has been
+  removed. Use get_connected_index_pairs() instead.
+- The stats() profiling method has been removed from
+  IMP::isd::GaussianProcessInterpolationRestraint and
+  IMP::isd::MultivariateFNormalSufficient. Use a third party package (such as
+  gperftools) for profiling instead.
+- Scores in IMP.saxs (and FoXS) now use the chi-square value rather than chi.
+- New applications of IMP are now available:
+  - [Modeling of the entire yeast nuclear pore complex](https://salilab.org/npc2018), as well as
+    [modeling of the flexible FG regions](https://salilab.org/npc_fg_2018) and
+    modeling of the individual [Nup133](https://salilab.org/nup133),
+    [Nup82](https://salilab.org/nup82), and
+    [Pom152](https://salilab.org/pom152) subcomplexes.
+  - [Modeling of the Ecm29-proteasome complex](https://salilab.org/ecm29)
+- The new modules IMP::npc and IMP::npctransport provide specialized
+  restraints and other functionality for modeling static nuclear pore complex
+  structures and transport through these structures, respectively, although
+  may also be useful for other modeling applications.
+- IMP's mmCIF support for deposition of models in
+  [PDB-Dev](https://pdb-dev.wwpdb.org/), in the IMP::pmi and IMP::mmcif modules,
+  now utilizes the [python-ihm](https://github.com/ihmwg/python-ihm) library,
+  a copy of which is included with IMP.
+- RMF files now store additional metadata, such as the primary sequence of
+  each chain, software used, information on each restraint (such as fit values),
+  and provenance (classes derived from IMP::core::Provenance) that describes
+  transformations of the system, such as initial input from a PDB file,
+  sampling, clustering, and filtering.
+- The new experimental IMP::mmcif module allows generating basic mmCIF files
+  directly from an IMP::Model and/or RMF files.
+
 # 2.8.0 - 2017-08-16 # {#changelog_2_8_0}
 - New applications of IMP are now available:
   - [Modeling of the yeast Spindle Pole Body core](https://salilab.org/spb/)
@@ -32,7 +73,7 @@ ChangeLog {#changelog}
 - Memory and CPU performance improvements across the code, particularly
   in IMP::pmi.
 - Preview of mmCIF support for deposition of integrative models in
-  [PDB-dev](https://pdb-dev.rcsb.rutgers.edu/). See the IMP::pmi::mmcif
+  [PDB-Dev](https://pdb-dev.wwpdb.org/). See the IMP::pmi::mmcif
   module for more details.
 - This will be the last release that includes packages for RedHat Enterprise
   Linux 5 (and variants, such as CentOS 5), since RHEL 5 has reached end
@@ -50,7 +91,7 @@ ChangeLog {#changelog}
   Use IMP::core::create_rigid_body() instead.
 - IMP::test:TempDir and IMP::test::RunInTempDir are deprecated in favor
   of similar functions that work as Python context managers
-  (IMP::test::temporary_directory() and IMP::Test::temporary_working_directory()
+  (IMP::test::temporary_directory() and IMP::test::temporary_working_directory()
   respectively).
 
 # 2.6.2 - 2016-05-25 # {#changelog_2_6_2}

README.md

@@ -31,7 +31,7 @@ new shell.
 Copyright and License information
 =================================
 
-IMP is Copyright 2007-2017 IMP Inventors. The IMP Inventors are
+IMP is Copyright 2007-2018 IMP Inventors. The IMP Inventors are
 Andrej Sali, Ben Webb, Daniel Russel, Keren Lasker, Dina Schneidman,
 Javier Velázquez-Muriel, Friedrich Förster, Elina Tjioe, Hao Fan,
 Seung Joong Kim, Yannick Spill, Riccardo Pellarin.

VERSION

@@ -1 +1 @@
-2.8.0
+2.9.0

components/README.md

@@ -0,0 +1,2 @@
+This directory contains additional components for integrative modeling
+that are not IMP modules.

doc/manual/biosystem.md

@@ -23,13 +23,19 @@ We recommend the following contents for your repository (see the
 for an example):
 
  - subdirectories containing
-   - your modeling protocol (generally one or more Python scripts)
+   - your modeling protocol (generally one or more Python scripts).
    - input files (e.g. PDB files, EM density maps, lists of crosslinks),
-     especially if these files aren't in a database somewhere already
+     especially if these files aren't in a database somewhere already.
+     If these inputs are derived in some fashion (e.g. you use a PDB file as
+     input that's a comparative model or docking result, or you use an EM map
+     that's been segmented) then this needs to be described somewhere, with
+     links to the original unmodified files (e.g. PDB IDs for templates of any
+     comparative models, alignment files, Modeller scripts).
    - outputs (trajectories, clusters, analysis). Where this isn't possible
      due to size, we can host the larger files, such as trajectories, elsewhere
      (e.g. as a dataset in [Zenodo](https://zenodo.org)) and link to them
-     from the repository.
+     from the repository. Aim to keep the repository below 1GB in size so that
+     it's manageable.
  - a top-level `%README.md` file describing the system and explaining how to
    run the protocol.
  - a top-level `LICENSE` file with the license for the data files and scripts.

doc/manual/cnmultifit_groel.dox

@@ -97,7 +97,7 @@ It also generates a file <tt>multifit.output</tt> that shows the
 transformation needed to place the subunit in the density.
 
 The optional <tt>--chimera</tt> parameter requests the same transformation
-output in a \external{http://www.cgl.ucsf.edu/chimera/,Chimera}-compatible
+output in a \external{https://www.cgl.ucsf.edu/chimera/,Chimera}-compatible
 format. To generate PDB files from the Chimera output file, use:
 
 \code{.sh}

doc/manual/design.md

@@ -17,7 +17,7 @@ The next parts of the manual will cover the use of the various parts of
  - [Chimera tools/web services](@ref web_services):
    we provide a number of web services that
    use %IMP at [https://salilab.org/](https://salilab.org). Additionally,
-   the [UCSF Chimera](http://www.cgl.ucsf.edu/chimera/) software includes
+   the [UCSF Chimera](https://www.cgl.ucsf.edu/chimera/) software includes
    several tools that use %IMP. These are the simplest to use because they
    do not require an %IMP installation.
 

doc/manual/installation.md

@@ -24,6 +24,7 @@ In order to build %IMP from source, you will need:
 
 - [CMake](https://cmake.org) (2.8 or later)
 - [Boost](http://www.boost.org) (1.41 or later)
+- [Eigen](https://eigen.tuxfamily.org/) (3.0 or later)
 - [HDF5](https://support.hdfgroup.org/HDF5/) (1.8 or later; 1.10 should also
   work)
 - [Python](https://www.python.org) (2.6 or later, or any version of Python 3)
@@ -41,7 +42,7 @@ will not build, and some will not function optimally.
   nonbonded lists.
 - [Google perf tools](\ref perf): needed only for profiling %IMP code.
 - [ANN](\ref ANN): certain data structures will be faster if it is available.
-- [GSL](\ref GSL): needed to use the IMP.gsl module.
+- [GSL](\ref GSL) (1.13 or later): needed to use the IMP.gsl module.
 - [OpenCV](\ref OpenCV) (2.1 or later): needed to use the IMP.em2d module or the
   [idock](@ref idock_pcsk9) and [emagefit](@ref emagefit_3sfd) command
   line tools.
@@ -50,6 +51,8 @@ will not build, and some will not function optimally.
 - [libTAU](https://integrativemodeling.org/libTAU.html): needed to use the
   IMP.cnmultifit module or the [cnmultifit](@ref cnmultifit_groel) command
   line tool.
+- [Protobuf](https://github.com/google/protobuf): needed to use the
+  IMP.npctransport module.
 - An [MPI](@ref IMP::mpi) library is needed to use the IMP.mpi module.
 - The [numpy, scipy](http://www.scipy.org/scipylib/download.html),
   [scikit-learn](http://scikit-learn.org/stable/install.html),
@@ -80,7 +83,7 @@ such as
 
         brew tap homebrew/science
         brew tap salilab/salilab
-        brew install boost gmp google-perftools cgal graphviz gsl cmake doxygen hdf5 swig fftw mpfr opencv libtau
+        brew install boost gmp google-perftools cgal graphviz gsl cmake doxygen hdf5 swig fftw mpfr opencv libtau eigen
 
   to install everything %IMP finds useful (or that you will want for installing various useful Python libs that %IMP finds useful). On older Macs, you may also need to `brew install git` if you want to use git (newer Macs include git).
 - [Macports](http://www.macports.org/) If you use MacPorts, you must add `/opt/local/bin` to your path (either by modifying your shell's

doc/manual/licenses.md

@@ -1,7 +1,7 @@
 Copyright and licenses {#licenses}
 ======================
 
-%IMP is Copyright 2007-2017 %IMP Inventors. The %IMP Inventors are
+%IMP is Copyright 2007-2018 %IMP Inventors. The %IMP Inventors are
 Andrej Sali, Ben Webb, Daniel Russel, Keren Lasker, Dina Schneidman,
 Javier Velázquez-Muriel, Friedrich Förster, Elina Tjioe, Hao Fan,
 Seung Joong Kim, Yannick Spill, Riccardo Pellarin.

doc/manual/mainpage.dox

@@ -93,7 +93,6 @@ complex might want to skip ahead to
    - [Close pairs lists](@ref close_pairs)
    - [RMF](@ref rmf)
    - [Building](@ref building)
-   - [Eigen](@ref eigen)
    - [git submodules and subtrees](@ref subtree)
 
  - [Copyright and licenses](@ref licenses)

doc/manual/multi_foxs.dox

@@ -33,10 +33,10 @@ print(IMP.multi_foxs.get_example_path('rpa'))</tt>'.
 \section multi_foxs_calc Calculation
 
 The structure of the RPA in complex with ssDNA is available in the
-\external{http://www.pdb.org,RCSB Protein Data Bank (PDB)} as code
-\external{http://www.pdb.org/pdb/explore/explore.do?structureId=1JMC,1jmc}
+\external{https://www.rcsb.org/,RCSB Protein Data Bank (PDB)} as code
+\external{https://www.rcsb.org/structure/1JMC,1jmc}
 (file <tt>1jmc.pdb</tt>), the unbound RPA structures are available as code
-\external{http://www.pdb.org/pdb/explore/explore.do?structureId=1FGU,1fgu}
+\external{https://www.rcsb.org/structure/1FGU,1fgu}
 (file <tt>1fguA.pdb</tt>, <tt>1fguB.pdb</tt>), while the SAXS profile is given in the <tt>weighted.dat</tt> file. The SAXS profile was simulated from the 3 structures with the following weights:
 
 \verbatim

doc/manual/multifit_3sfd.dox

@@ -118,7 +118,7 @@ each Gaussian. For example, with 50 residues per Gaussian, a 170-residue
 protein should use 3 Gaussians and a 260-residue protein should use
 5 Gaussians.) The reduced representation is written out as a PDB file
 containing fake CA atoms, where each CA corresponds to a single anchor point,
-and also as a \external{http://www.cgl.ucsf.edu/chimera/,Chimera} cmm file.
+and also as a \external{https://www.cgl.ucsf.edu/chimera/,Chimera} cmm file.
 
 \section multifit_3sfd_fit_fft Fit each protein to the map
 

doc/manual/rnapolii_stalk.dox

@@ -32,7 +32,7 @@ packages installed in addition to [IMP itself](@ref installation):
 - [Chimera](https://www.cgl.ucsf.edu/chimera/download.html)
   for visualization of results
 
-(If you are using [Anaconda Python](https://store.continuum.io/cshop/anaconda/),
+(If you are using [Anaconda Python](https://www.anaconda.com/download/),
 you can get the Python packages above by simply running
 `conda install numpy scipy scikit-learn matplotlib`.
 On a Mac you can get them using the

doc/manual/web_services.md

@@ -6,11 +6,11 @@ They are the simplest to use because they do not require an %IMP installation.
 
 # Chimera tools
 
-The [UCSF Chimera](http://www.cgl.ucsf.edu/chimera/) software includes
+The [UCSF Chimera](https://www.cgl.ucsf.edu/chimera/) software includes
 several tools that use %IMP:
 
- - [Small-Angle X-Ray Profile](http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/saxs/saxs.html): calculate a theoretical small-angle X-ray scattering (SAXS) profile from a set of atoms
- - [MultiFit](http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multifit/multifit.html): perform simultaneous rigid fitting of multiple atomic-resolution structures into density maps at resolutions as low as 25 Å.
+ - [Small-Angle X-Ray Profile](https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/saxs/saxs.html): calculate a theoretical small-angle X-ray scattering (SAXS) profile from a set of atoms
+ - [MultiFit](https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multifit/multifit.html): perform simultaneous rigid fitting of multiple atomic-resolution structures into density maps at resolutions as low as 25 Å.
 
 In addition, UCSF Chimera is able to read [RMF files](https://integrativemodeling.org/rmf/)
 generated by %IMP.

modules/algebra/README.md

@@ -58,9 +58,6 @@ straightforward, it is not available as a package for common platforms.
 In addition, ANN must be built as a shared library rather than a static
 library.
 
-# Eigen # {#Eigen}
-We ship a copy of Eigen as part of IMP as Eigen support varies quite considerably across platforms and it is header-only  and so easy to ship. Our version of Eigen has been patched to move everything to the `IMP_Eigen` namespace and preprocessor symbols to start with `IMP_EIGEN_` so that things do not conflict with system installs of Eigen.
-
 # Info
 
 _Author(s)_: Daniel Russel, Keren Lasker, Ben Webb, Javier Angel Velázquez-Muriel

modules/algebra/benchmark/benchmark_grid_traversal.cpp

@@ -1,5 +1,5 @@
 /**
- * Copyright 2007-2017 IMP Inventors. All rights reserved.
+ * Copyright 2007-2018 IMP Inventors. All rights reserved.
  */
 #include <IMP/benchmark/benchmark_config.h>
 #include <IMP/benchmark/benchmark_macros.h>

modules/algebra/benchmark/benchmark_knn.cpp

@@ -1,5 +1,5 @@
 /**
- * Copyright 2007-2017 IMP Inventors. All rights reserved.
+ * Copyright 2007-2018 IMP Inventors. All rights reserved.
  */
 
 #include <IMP/algebra.h>

modules/algebra/benchmark/benchmark_rotate.cpp

@@ -1,5 +1,5 @@
 /**
- * Copyright 2007-2017 IMP Inventors. All rights reserved.
+ * Copyright 2007-2018 IMP Inventors. All rights reserved.
  */
 #include <IMP/algebra.h>
 #include <boost/timer.hpp>

modules/algebra/benchmark/benchmark_surface.cpp

@@ -1,5 +1,5 @@
 /**
- * Copyright 2007-2017 IMP Inventors. All rights reserved.
+ * Copyright 2007-2018 IMP Inventors. All rights reserved.
  */
 
 #include <IMP/algebra/connolly_surface.h>

modules/algebra/examples/grid.cpp

@@ -2,7 +2,7 @@
  *  \example grid.cpp
  *  \brief Show some of the basics of using a grid from C++.
  *
- *  Copyright 2007-2017 IMP Inventors. All rights reserved.
+ *  Copyright 2007-2018 IMP Inventors. All rights reserved.
  *
  */
 #include <IMP/algebra/standard_grids.h>

modules/algebra/include/BoundingBoxD.h

@@ -1,7 +1,7 @@
 /**
  *  \file IMP/algebra/BoundingBoxD.h   \brief A bounding box in D dimensions.
  *
- *  Copyright 2007-2017 IMP Inventors. All rights reserved.
+ *  Copyright 2007-2018 IMP Inventors. All rights reserved.
  *
  */
 

modules/algebra/include/Cone3D.h

@@ -2,7 +2,7 @@
  *  \file IMP/algebra/Cone3D.h
  *  \brief Represent a cone in 3D.
  *
- *  Copyright 2007-2017 IMP Inventors. All rights reserved.
+ *  Copyright 2007-2018 IMP Inventors. All rights reserved.
  */
 
 #ifndef IMPALGEBRA_CONE_3D_H

modules/algebra/include/Cylinder3D.h

@@ -2,7 +2,7 @@
  *  \file IMP/algebra/Cylinder3D.h
  *  \brief Represent a cylinder in 3D.
  *
- *  Copyright 2007-2017 IMP Inventors. All rights reserved.
+ *  Copyright 2007-2018 IMP Inventors. All rights reserved.
  */
 
 #ifndef IMPALGEBRA_CYLINDER_3D_H

modules/algebra/include/Ellipsoid3D.h

@@ -1,7 +1,7 @@
 /**
  *  \file IMP/algebra/Ellipsoid3D.h   \brief Simple 3D ellipsoid class.
  *
- *  Copyright 2007-2017 IMP Inventors. All rights reserved.
+ *  Copyright 2007-2018 IMP Inventors. All rights reserved.
  *
  */