Merge for 2.14.0 release

CMakeLists.txt

@@ -13,6 +13,11 @@ if(POLICY CMP0094)
 cmake_policy(SET CMP0094 NEW)
 endif(POLICY CMP0094)
 
+# Use new-style variables/escapes
+if(POLICY CMP0053)
+cmake_policy(SET CMP0053 NEW)
+endif(POLICY CMP0053)
+
 include(${CMAKE_SOURCE_DIR}/modules/rmf/dependency/RMF/cmake_modules/IMPFindPython.cmake)
 imp_find_python()
 
@@ -409,11 +414,13 @@ if(IMP_DOXYGEN_FOUND)
     COMMAND ${IMP_DOXYGEN_EXECUTABLE} doxygen/ref.html
     COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_show_warnings.py --warn=${CMAKE_BINARY_DIR}/doxygen/ref-warnings.txt
     COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_fix_links.py ${CMAKE_BINARY_DIR}/doc/ref
+    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_fix_php.py ${CMAKE_BINARY_DIR}/doc/ref
     COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_add_ref_nav.py ${CMAKE_SOURCE_DIR}
     # Rebuild manual so that it can link to the refguide tags
     COMMAND ${IMP_DOXYGEN_EXECUTABLE} doxygen/manual.html
     COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_show_warnings.py --warn=${CMAKE_BINARY_DIR}/doxygen/manual-warnings.txt
     COMMAND patch -p1 < ${CMAKE_SOURCE_DIR}/doc/doxygen/search.patch
+    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_fix_php.py ${CMAKE_BINARY_DIR}/doc/manual
     COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_add_nav.py ${CMAKE_SOURCE_DIR} . doc/manual tools
     COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/tools/build/doxygen_spell_check.py doxygen/manual/xml ${CMAKE_SOURCE_DIR}/doc/standards_exceptions
     WORKING_DIRECTORY ${CMAKE_BINARY_DIR}

ChangeLog.md

@@ -1,6 +1,21 @@
 ChangeLog {#changelog}
 =========
 
+# 2.14.0 - 2020-12-02 # {#changelog_2_14_0}
+- All IMP.parallel worker classes are now subclasses of IMP.parallel.Worker;
+  the old class names still exist as aliases, but are deprecated.
+- The IMP.kinematics module has had a major overhaul.
+- The Windows .exe installer now supports Python 3.9, and has dropped support
+  for Python 3.5.
+- New applications of IMP are now available:
+  - [Integrative structures of the Nef-CD4-AP2 complex](https://salilab.org/Nef_CD4_AP2/)
+  - [Integrative Modeling of Yeast Exocyst Complex](https://salilab.org/exocyst/)
+  - [Integrative threading of protein structure using secondary structure elements](https://salilab.org/SSEThread/)
+- Bugfix: fix near-infinite loop in FoXS JavaScript output when no models
+  are fit.
+- Bugfix: IMP.saxs.Restraint should now work correctly when some or all
+  particles are members of rigid bodies.
+
 # 2.13.0 - 2020-05-14 # {#changelog_2_13_0}
 - Ubuntu .deb packages now use Python 3 by default (install the imp-python2
   package if you want to use Python 2) and support MPI (install the

VERSION

@@ -1 +1 @@
-2.13.0
+2.14.0

doc/manual/cmake_config.md

@@ -84,7 +84,7 @@ For example, on a Mac with Homebrew, where `python` is Homebrew's
 `/usr/local/bin/python`, old versions of CMake will often find Apple's Python
 headers. This can be resolved (if you cannot upgrade CMake to 3.14 or later)
 by telling CMake where the Homebrew Python headers and library
-are, by addinng to your CMake invocation something like
+are, by adding to your CMake invocation something like
 `-DPYTHON_LIBRARY=/usr/local/opt/python@2/Frameworks/Python.framework/Versions/Current/lib/libpython2.7.dylib -DPYTHON_INCLUDE_DIR=/usr/local/opt/python@2/Frameworks/Python.framework/Versions/Current/Headers`
 
 ## CMake reports that it found a dependency but then reports failed {#cmake_compile}

doc/manual/kinematics_rrt.dox

@@ -22,7 +22,7 @@ First, obtain the input files used in this example and put them in the
 current directory, by typing:
 
 \code{.sh}
-cp <imp_example_path>/kinematics/antibody/* .
+cp "<imp_example_path>"/kinematics/antibody/*.* .
 \endcode
 
 (On a Windows machine, use `copy` rather than `cp`.) Here, `<imp_example_path>`
@@ -33,8 +33,8 @@ print(IMP.kinematics.get_example_path('antibody'))</tt>'.
 \section kinematics_rrt_calc Calculation
 
 The structure of the antibody 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=1IGT,1igt}
+\external{https://www.rcsb.org/,RCSB Protein Data Bank (PDB)} as code
+\external{https://www.rcsb.org/structure/1IGT,1igt}
 (file <tt>1igt.pdb</tt>). The atomic structure can be sampled by running <tt>rrt_sample</tt>. First, we need to define the linker regions (residues 229-235 in chains B and D). These residues are listed in the input file <tt>linker.txt</tt>. Since the antibody contains four chains (A-D), we would like to connect them into a single rigid body using '-c' connect_chains option. We do that for the antibody structure using the S-S bonds between the chains. Therefore, the file <tt>conect_chains.txt</tt> specifies atom numbers for the two chains we want to connect.
 
 \code{.sh}

doc/manual/outoftree.md

@@ -4,7 +4,7 @@ Building modules out of tree {#outoftree}
 Normally to build an %IMP module it is placed in the `modules` subdirectory
 together with the rest of the %IMP source code and then all of %IMP is
 built, as per the [installation instructions](@ref installation_source).
-However, this makes builing a module an expensive process (as the build
+However, this makes building a module an expensive process (as the build
 system needs to check whether any part of %IMP has changed, not just the
 module itself) and it is awkward to build a module against multiple
 versions of %IMP, for example against both the latest stable release and

doc/manual/rmf.md

@@ -34,7 +34,7 @@ atom::Hierarchy data is stored as RMF::REPRESENTATION nodes in the file.
 
 There is exactly one node in the RMF file per IMP::Particle in the hierarchy.
 The link classes are implemented in terms of a bunch of helper classes,
-each of whichs handle a particular type of data.
+each of which handles a particular type of data.
 
 The main tricky part is handling rigid bodies. In particular, the particles
 defining the rigid body are not always part of the %IMP hierarchy, and

modules/EMageFit/doc/scripts.dox

@@ -99,7 +99,7 @@ called from DominoModel.
 IMP.em2d.sampling - Sets the positions and orientations for the components of
 the assembly before combining them using DOMINO. In the EMageFit benchmark the
 set of Monte Carlo solutions was used as input to DOMINO, but
-any other combination of positions and orientations for the the subunits
+any other combination of positions and orientations for the subunits
 could be used.
 
 IMP.em2d.solutions_io - Contains the class <tt>ResultsDB</tt> for managing

modules/EMageFit/pyext/src/imp_general/alignments.py

@@ -14,7 +14,7 @@
 def get_reference_frames_from_chain_alignment(reference_rbs, reference_index,
                                               rbs_to_align, index_to_align):
     """
-        Align the rigid bodies rbs_to_align to the the reference frames of
+        Align the rigid bodies rbs_to_align to the reference frames of
         reference_rbs. The rb with index_to_align is aligned to the reference rb
         with reference_index. The function returns the reference frames to
         apply to the rbs_to_align.

modules/EMageFit/pyext/src/solutions_io.py

@@ -77,7 +77,7 @@ def gather_best_solution_results(fns, fn_output, max_number=50000,
             raising an error. This option is to tolerate some files
             of the databases being broken because the cluster fails,
             fill the disks, etc
-       @param orderby Criterion used to sort the the records
+       @param orderby Criterion used to sort the records
        NOTE:
        Makes sure to reorder all column names if necessary before merging
        The record for the native solution is only added once (from first file).
@@ -588,7 +588,7 @@ def get_native_rank(self, orderby):
 
     def get_nth_largest_cluster(self, position, table_name="clusters"):
         """
-            Recover the the information about the n-th largest cluster
+            Recover the information about the n-th largest cluster
             @param position Cluster position (by size) requested
             (1 is the largest cluster)
             @param table_name Table where the information about the

modules/algebra/test/test_inverse.py

@@ -14,7 +14,7 @@ def setUp(self):
         self.v2 = IMP.algebra.Vector3D(-41.472, 8.922, -63.657)
 
     def test_inverse(self):
-        """Check that the the inverse of a transformation works"""
+        """Check that the inverse of a transformation works"""
         rt = IMP.algebra.get_rotation_from_fixed_xyz(0.2, 0.8, -0.4)
         t = IMP.algebra.Transformation3D(
             rt, IMP.algebra.Vector3D(20.0, -12.4, 18.6))

modules/algebra/test/test_sphere_cover.py

@@ -30,7 +30,7 @@ def test_get_uniform_surface_cover(self):
                                delta=4 * radius / numpts ** .5)
 
     def test_get_uniform_surface_cover_not_on_000(self):
-        """Check uniform cover when the the center is not on (0,0,0)"""
+        """Check uniform cover when the center is not on (0,0,0)"""
         # IMP.random_number_generator.seed(1)
         center = IMP.algebra.Vector3D(4.0, 5.0, -9.0)
         radius = 5.0

modules/atom/include/CHARMMParameters.h

@@ -227,19 +227,30 @@ class IMPATOMEXPORT CHARMMParameters : public ForceFieldParameters {
     CHARMMDihedralParametersList param;
     internal::CHARMMDihedralNames types =
         internal::CHARMMDihedralNames(type1, type2, type3, type4);
-    // Get the first match, using wildcards
+    // Look for matches without wildcards
     DihedralParameters::const_iterator match = find_dihedral(
-        dihedral_parameters_.begin(), dihedral_parameters_.end(), types, true);
+        dihedral_parameters_.begin(), dihedral_parameters_.end(), types, false);
     if (match != dihedral_parameters_.end()) {
-      // If it matched, look for duplicate dihedral terms (this time the
-      // match must be exactly the same as the first match)
       param.push_back(match->second);
       while ((match = find_dihedral(match + 1, dihedral_parameters_.end(),
                                     match->first, false)) !=
              dihedral_parameters_.end()) {
         param.push_back(match->second);
       }
+    } else {
+      // If no matches, try again with wildcards
+      match = find_dihedral(
+        dihedral_parameters_.begin(), dihedral_parameters_.end(), types, true);
+      if (match != dihedral_parameters_.end()) {
+        param.push_back(match->second);
+        while ((match = find_dihedral(match + 1, dihedral_parameters_.end(),
+                                      match->first, true)) !=
+               dihedral_parameters_.end()) {
+          param.push_back(match->second);
+        }
+      }
     }
+
     if (param.size() == 0) {
       IMP_THROW("No CHARMM parameters found for dihedral "
                     << type1 << "-" << type2 << "-" << type3 << "-" << type4,

modules/atom/include/DihedralSingletonScore.h

@@ -17,7 +17,7 @@ IMPATOM_BEGIN_NAMESPACE
 //! Score the dihedral angle.
 /** This scores the dihedral using information stored in its Dihedral
     decorator. The form of the score is \f[
-        \frac{1}{2} s|s| (1.0 + \cos(\chi m - \chi_i))
+        \frac{1}{2} s|s| + s^2\cos(\chi m + \chi_i))
     \f] where \f$s\f$ is the stiffness, \f$m\f$ the multiplicity, \f$\chi_i\f$
     the ideal value of the dihedral, and \f$\chi\f$ the actual value.
 

modules/atom/include/ImproperSingletonScore.h

@@ -28,7 +28,7 @@ IMPATOM_BEGIN_NAMESPACE
     as the angle between the plane in which the first three atoms lie and
     the plane in which the last three atoms lie.
 
-    \note The multiplicity of the the Dihedral is not used.
+    \note The multiplicity of the Dihedral is not used.
 
     \see CHARMMTopology::add_impropers(), Dihedral.
  */

modules/atom/include/LoopStatisticalPairScore.h

@@ -0,0 +1,60 @@
+/**
+ *  \file IMP/atom/LoopStatisticalPairScore.h
+ *  \brief Fiser/Melo loop modeling statistical potential
+ *
+ *  Copyright 2007-2020 IMP Inventors. All rights reserved.
+ *
+ */
+
+#ifndef IMPATOM_LOOP_STATISTICAL_PAIR_SCORE_H
+#define IMPATOM_LOOP_STATISTICAL_PAIR_SCORE_H
+
+#include <IMP/atom/atom_config.h>
+#include "Hierarchy.h"
+#include <IMP/score_functor/LoopStatistical.h>
+#include <IMP/score_functor/DistancePairScore.h>
+#include <IMP/core/StatisticalPairScore.h>
+
+IMPATOM_BEGIN_NAMESPACE
+
+/** \name Fiser/Melo loop modeling statistical potential
+
+    \imp provides the Fiser/Melo loop modeling statistical potential.
+
+    \note These are quite large objects as they store the whole
+    lookup table. It is much better to share them between
+    restraints than to create separate instances.
+
+ */
+class LoopStatisticalPairScore;
+typedef score_functor::LoopStatisticalType LoopStatisticalType;
+
+//! Score atoms based on the Fiser/Melo loop modeling statistical potential
+/**
+    See Fiser et al, Modeling of loops in protein structures.
+    Protein Science 9, 1753-1773, 2000.
+
+    Like DOPE, this potential should not be applied to two atoms from
+    the same residue. You may need to use the SameResiduePairFilter
+    to filter these out.
+*/
+class LoopStatisticalPairScore
+    : public score_functor::DistancePairScore<score_functor::LoopStatistical> {
+  typedef score_functor::DistancePairScore<score_functor::LoopStatistical> P;
+
+ public:
+  LoopStatisticalPairScore(
+    double threshold = std::numeric_limits<double>::max())
+      : P(score_functor::LoopStatistical(threshold)) {}
+  LoopStatisticalPairScore(double threshold, TextInput data_file)
+      : P(score_functor::LoopStatistical(threshold, data_file)) {}
+};
+
+/** Add the Fiser/Melo loop modeling atom types to the atoms in the hierarchy.
+ */
+IMPATOMEXPORT void add_loop_statistical_score_data(atom::Hierarchy h);
+
+/** @} */
+IMPATOM_END_NAMESPACE
+
+#endif /* IMPATOM_LOOP_STATISTICAL_PAIR_SCORE_H */

modules/atom/include/MolecularDynamics.h

@@ -23,23 +23,16 @@ IMPATOM_BEGIN_NAMESPACE
 class IMPATOMEXPORT LinearVelocity : public Decorator {
   static void do_setup_particle(Model *m, ParticleIndex pi,
                      const algebra::Vector3D v = algebra::Vector3D(0, 0, 0)) {
-    m->add_attribute(get_velocity_key(0), pi, v[0]);
-    m->add_attribute(get_velocity_key(1), pi, v[1]);
-    m->add_attribute(get_velocity_key(2), pi, v[2]);
+    m->add_attribute(get_velocities_key(), pi, v.get_coordinates());
   }
-
-public:
-  static FloatKey get_velocity_key(unsigned int i) {
-    IMP_USAGE_CHECK(i < 3, "Out of range coordinate");
-    static const FloatKey keys[] = {FloatKey("vx"), FloatKey("vy"),
-                                    FloatKey("vz")};
-    return keys[i];
+  static FloatsKey get_velocities_key() {
+    static const FloatsKey key("linvel");
+    return key;
   }
 
+public:
   static bool get_is_setup(Model *m, ParticleIndex pi) {
-    return m->get_has_attribute(get_velocity_key(0), pi)
-           && m->get_has_attribute(get_velocity_key(1), pi)
-           && m->get_has_attribute(get_velocity_key(2), pi);
+    return m->get_has_attribute(get_velocities_key(), pi);
   }
 
   IMP_DECORATOR_METHODS(LinearVelocity, Decorator);
@@ -49,17 +42,13 @@ class IMPATOMEXPORT LinearVelocity : public Decorator {
   void set_velocity(const algebra::Vector3D &v) {
     Model *m = get_model();
     ParticleIndex pi = get_particle_index();
-    m->set_attribute(get_velocity_key(0), pi, v[0]);
-    m->set_attribute(get_velocity_key(1), pi, v[1]);
-    m->set_attribute(get_velocity_key(2), pi, v[2]);
+    m->set_attribute(get_velocities_key(), pi, v.get_coordinates());
   }
 
   algebra::Vector3D get_velocity() const {
     Model *m = get_model();
     ParticleIndex pi = get_particle_index();
-    return algebra::Vector3D(m->get_attribute(get_velocity_key(0), pi),
-                             m->get_attribute(get_velocity_key(1), pi),
-                             m->get_attribute(get_velocity_key(2), pi));
+    return algebra::Vector3D(m->get_attribute(get_velocities_key(), pi));
   }
 };
 
@@ -71,25 +60,17 @@ class IMPATOMEXPORT LinearVelocity : public Decorator {
 class IMPATOMEXPORT AngularVelocity : public Decorator {
   static void do_setup_particle(Model *m, ParticleIndex pi,
                    const algebra::Vector4D v = algebra::Vector4D(0, 0, 0, 0)) {
-    m->add_attribute(get_velocity_key(0), pi, v[0]);
-    m->add_attribute(get_velocity_key(1), pi, v[1]);
-    m->add_attribute(get_velocity_key(2), pi, v[2]);
-    m->add_attribute(get_velocity_key(3), pi, v[3]);
+    m->add_attribute(get_velocities_key(), pi, v.get_coordinates());
+  }
+  static FloatsKey get_velocities_key() {
+    static const FloatsKey key("angvel");
+    return key;
   }
 
 public:
-  static FloatKey get_velocity_key(unsigned int i) {
-    IMP_USAGE_CHECK(i < 4, "Out of range coordinate");
-    static const FloatKey keys[] = {FloatKey("angvel0"), FloatKey("angvel1"),
-                                    FloatKey("angvel2"), FloatKey("angvel3")};
-    return keys[i];
-  }
 
   static bool get_is_setup(Model *m, ParticleIndex pi) {
-    return m->get_has_attribute(get_velocity_key(0), pi)
-           && m->get_has_attribute(get_velocity_key(1), pi)
-           && m->get_has_attribute(get_velocity_key(2), pi)
-           && m->get_has_attribute(get_velocity_key(3), pi);
+    return m->get_has_attribute(get_velocities_key(), pi);
   }
 
   IMP_DECORATOR_METHODS(AngularVelocity, Decorator);
@@ -99,19 +80,13 @@ class IMPATOMEXPORT AngularVelocity : public Decorator {
   void set_velocity(const algebra::Vector4D &v) {
     Model *m = get_model();
     ParticleIndex pi = get_particle_index();
-    m->set_attribute(get_velocity_key(0), pi, v[0]);
-    m->set_attribute(get_velocity_key(1), pi, v[1]);
-    m->set_attribute(get_velocity_key(2), pi, v[2]);
-    m->set_attribute(get_velocity_key(3), pi, v[3]);
+    m->set_attribute(get_velocities_key(), pi, v.get_coordinates());
   }
 
   algebra::Vector4D get_velocity() const {
     Model *m = get_model();
     ParticleIndex pi = get_particle_index();
-    return algebra::Vector4D(m->get_attribute(get_velocity_key(0), pi),
-                             m->get_attribute(get_velocity_key(1), pi),
-                             m->get_attribute(get_velocity_key(2), pi),
-                             m->get_attribute(get_velocity_key(3), pi));
+    return algebra::Vector4D(m->get_attribute(get_velocities_key(), pi));
   }
 };
 

modules/atom/include/Representation.h

@@ -39,7 +39,7 @@ enum RepresentationType {
 class IMPATOMEXPORT Representation : public Hierarchy {
   static IntsKey get_types_key();
   static ParticleIndexesKey get_representations_key();
-  static FloatKey get_resolution_key(unsigned int index);
+  static FloatsKey get_resolutions_key();
   static FloatKey get_base_resolution_key();
 
   static void do_setup_particle(Model *m, ParticleIndex pi,
@@ -81,6 +81,12 @@ class IMPATOMEXPORT Representation : public Hierarchy {
   //! Get all resolutions that are available for a specific RepresentationType.
   Floats get_resolutions(RepresentationType type = BALLS) const;
 
+  //! Remove the given representation.
+  /** The representation is only removed from the Representation
+      decorator; it is not destroyed. For that, use IMP::atom::destroy().
+   */
+  void remove_representation(ParticleIndexAdaptor rep);
+
   //! If you've changed the parent, update all the resolutions
   void update_parents();
 };