Merge for 2.6.2 release.

ChangeLog.md

@@ -1,6 +1,12 @@
 ChangeLog {#changelog}
 =========
 
+# 2.6.2 - 2016-05-25 # {#changelog_2_6_2}
+- Add support for SWIG 3.0.8.
+- Add support for Ubuntu 16.04, Xenial Xerus.
+- Minor documentation fixes.
+- Bugfix: fix detection of termini in IMP::atom::Selection.
+
 # 2.6.1 - 2016-04-14 # {#changelog_2_6_1}
 - The 'cluster' binary is now called 'rmsd_cluster' to avoid conflicts with
   other packages (e.g. graphviz also provides a 'cluster' binary).

VERSION

@@ -1 +1 @@
-2.6.1
+2.6.2

doc/manual/install_windows.md

@@ -13,7 +13,7 @@ that you're going to use to build %IMP. The basic procedure is as follows:
   - Install Microsoft Visual Studio Express (it is free, but registration with
     Microsoft is required).
   - Get and install [cmake](http://www.cmake.org).
-  - Get [Python 2](http://www.python.org) (not Python 3)
+  - Get [Python](http://www.python.org)
     (make sure you get the
     32-bit version if you're going to build %IMP for 32-bit Windows).
   - Get and install the

doc/manual/installation.md

@@ -27,8 +27,7 @@ In order to build %IMP from source, you will need:
 - [HDF5](http://www.hdfgroup.org/HDF5/) (1.8 or later)
 - [Python](http://www.python.org) (2.6 or later, or any version of Python 3)
 - [SWIG](http://www.swig.org) (1.3.40 or later; 2.0.4 or later is needed
-  if you want to use Python 3; note that 3.0.8 does not
-  [currently work](https://github.com/swig/swig/issues/583))
+  if you want to use Python 3)
 
 The following prerequisites are _optional_; without them some parts of %IMP
 will not build, and some will not function optimally.

modules/algebra/include/Cylinder3D.h

@@ -1,6 +1,6 @@
 /**
  *  \file IMP/algebra/Cylinder3D.h
- *  \brief stores a cylinder
+ *  \brief Represent a cylinder in 3D.
  *
  *  Copyright 2007-2016 IMP Inventors. All rights reserved.
  */

modules/algebra/include/GeometricPrimitiveD.h

@@ -1,5 +1,6 @@
 /**
- *  \file IMP/algebra/GeometricPrimitiveD.h    \brief Basic types used by IMP.
+ *  \file IMP/algebra/GeometricPrimitiveD.h
+ *  \brief Base class for geometric types.
  *
  *  Copyright 2007-2016 IMP Inventors. All rights reserved.
  *

modules/algebra/include/ParabolicFit.h

@@ -1,6 +1,6 @@
 /**
  * \file IMP/algebra/ParabolicFit.h
- * \brief fit the data with parabola
+ * \brief Fit data with parabola
  *
  * Copyright 2007-2016 IMP Inventors. All rights reserved.
  *

modules/algebra/include/ReferenceFrame3D.h

@@ -1,5 +1,6 @@
 /**
- *  \file IMP/algebra/ReferenceFrame3D.h   \brief Simple 3D rotation class.
+ *  \file IMP/algebra/ReferenceFrame3D.h
+ *  \brief A reference frame in 3D.
  *
  *  Copyright 2007-2016 IMP Inventors. All rights reserved.
  *
@@ -13,7 +14,7 @@
 
 IMPALGEBRA_BEGIN_NAMESPACE
 
-//!  A reference frame in 3D.
+//! A reference frame in 3D.
 /**
     \geometry
 */
@@ -32,10 +33,11 @@ class IMPALGEBRAEXPORT ReferenceFrame3D {
  public:
   IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(ReferenceFrame3D);
   //! Create the default reference frame
-  /** That is, the origin with x,y,z axis as the principal axes.*/
+  /** That is, the origin with x,y,z axis as the principal axes. */
   ReferenceFrame3D()
       : tr_(get_identity_transformation_3d()), has_inverse_(true), tri_(tr_) {}
-  //! a reference frame specified by a transformation matrix
+
+  //! A reference frame specified by a transformation matrix
   /** Constructs a reference frame using transformation tr
 
       @param tr a transformation from local coordinates in this

modules/algebra/include/Reflection3D.h

@@ -15,8 +15,6 @@
 IMPALGEBRA_BEGIN_NAMESPACE
 
 //! Reflect about a plane in 3D
-/**
-*/
 class Reflection3D : public GeometricPrimitiveD<3> {
   Plane3D pl_;
 

modules/algebra/include/Rotation2D.h

@@ -1,6 +1,6 @@
 /**
  *  \file IMP/algebra/Rotation2D.h
- *  \brief Classes and operations related with rotations
+ *  \brief Represent a rotation in 2D space.
  *
  *  Copyright 2007-2016 IMP Inventors. All rights reserved.
 */
@@ -25,7 +25,7 @@ class Rotation2D;
 Rotation2D compose(const Rotation2D &a, const Rotation2D &b);
 #endif
 
-//! Stores a 2D rotation matrix
+//! Represent a rotation in 2D space.
 /**
   \note This class requires the angles to be given in radians, and the
   convention used is that the rotations are performed rotating counterclockwise
@@ -37,10 +37,10 @@ class Rotation2D : public GeometricPrimitiveD<2> {
  public:
   Rotation2D() : angle_(std::numeric_limits<double>::quiet_NaN()) {};
 
-  //! Builds the matrix for the given angle
+  //! Build the matrix for the given angle
   Rotation2D(double angle) { set_angle(angle); }
 
-  //! rotates a 2D point
+  //! Rotate a 2D point
   /**
   * \param[in] o a 2D vector to be rotated
   */
@@ -50,21 +50,21 @@ class Rotation2D : public GeometricPrimitiveD<2> {
     return get_rotated(o[0], o[1]);
   }
 
-  //! rotates a 2D point
+  //! Rotate a 2D point
   Vector2D get_rotated(const double x, const double y) const {
     IMP_INTERNAL_CHECK(!IMP::isnan(angle_),
                        "Attempting to use uninitialized rotation");
     return Vector2D(c_ * x - s_ * y, s_ * x + c_ * y);
   }
 
-  //! Returns the matrix for the inverse rotation
+  //! Return the matrix for the inverse rotation
   Rotation2D get_inverse() const {
     IMP_INTERNAL_CHECK(!IMP::isnan(angle_),
                        "Attempting to use uninitialized rotation");
     return Rotation2D(-angle_);
   }
 
-  //! sets the angle for the rotation
+  //! Set the angle for the rotation
   /**
   * \param[in] angle the angle
   */
@@ -74,10 +74,10 @@ class Rotation2D : public GeometricPrimitiveD<2> {
     s_ = sin(angle);
   }
 
-  //! gets the angle
+  //! Get the angle
   double get_angle() const { return angle_; }
 
-  //! Prints the angle
+  //! Print the angle
   IMP_SHOWABLE_INLINE(Rotation2D, out << "Rotation2D (radians): " << angle_;);
 
  private:
@@ -86,22 +86,22 @@ class Rotation2D : public GeometricPrimitiveD<2> {
   double s_;      // sine of the angle
 };
 
-//! Builds an identity rotation in 2D
+//! Build an identity rotation in 2D
 inline Rotation2D get_identity_rotation_2d() { return Rotation2D(0.0); }
 
-//! Builds an identity rotation in 2D
+//! Build an identity rotation in 2D
 inline Rotation2D get_random_rotation_2d() {
   return Rotation2D(2 * PI *
                     boost::uniform_01<>()(random_number_generator));
 }
 
-//! Builds the rotation that transforms the vector X of the origin
+//! Build the rotation that transforms the vector X of the origin
 //! of coordinates into the given vector
 inline Rotation2D get_rotation_to_x_axis(const Vector2D &v) {
   return Rotation2D(atan2(v[1], v[0]));
 }
 
-//! compose two rotations a and b
+//! Compose two rotations a and b.
 /**
   For any vector v (a*b)*v = a*(b*v).
 */
@@ -114,4 +114,5 @@ inline Rotation2D compose(const Rotation2D &a, const Rotation2D &b) {
 IMP_VALUES(Rotation2D, Rotation2Ds);
 
 IMPALGEBRA_END_NAMESPACE
+
 #endif /* IMPALGEBRA_ROTATION_2D_H */

modules/algebra/include/Rotation3D.h

@@ -75,7 +75,7 @@ class IMPALGEBRAEXPORT Rotation3D : public GeometricPrimitiveD<3> {
   IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(Rotation3D);
 
   //! Create a rotation from a vector of 4 quaternion coefficients.
-  //! @note: use assume_normalize with care - inputting an unnormalized
+  //! @note: use assume_normalized with care - inputting an unnormalized
   //!        vector would result in unexpected results if it is true
   explicit Rotation3D(const VectorD<4> &v,
                       bool assume_normalized=false)
@@ -120,7 +120,7 @@ class IMPALGEBRAEXPORT Rotation3D : public GeometricPrimitiveD<3> {
                 o[2]);
   }
 
-  //! Gets only the requested rotation coordinate of the vector
+  //! Get only the requested rotation coordinate of the vector
   double get_rotated_one_coordinate_no_cache(const Vector3D &o,
                                              unsigned int coord) const {
     IMP_USAGE_CHECK(get_is_valid(),
@@ -158,7 +158,7 @@ class IMPALGEBRAEXPORT Rotation3D : public GeometricPrimitiveD<3> {
     return Vector3D(o * matrix_[0], o * matrix_[1], o * matrix_[2]);
   }
 
-  //! Gets only the requested rotation coordinate of the vector
+  //! Get only the requested rotation coordinate of the vector
   double get_rotated_one_coordinate(const Vector3D &o,
                                     unsigned int coord) const {
     IMP_USAGE_CHECK(get_is_valid(),
@@ -195,7 +195,7 @@ class IMPALGEBRAEXPORT Rotation3D : public GeometricPrimitiveD<3> {
     return v_;
   }
 
-  //! multiply two rotations
+  //! Multiply two rotations
   Rotation3D operator*(const Rotation3D &q) const {
     IMP_USAGE_CHECK(get_is_valid(),
                     "Attempting to compose uninitialized rotation");
@@ -220,7 +220,7 @@ class IMPALGEBRAEXPORT Rotation3D : public GeometricPrimitiveD<3> {
   */
   const Vector3D get_derivative(const Vector3D &o, unsigned int i) const;
 
-  /** returns true is the rotation is valid, false if
+  /** Return true is the rotation is valid, false if
       invalid or not initialized (e.g., only initialized by
       the empty constructor)
   */

modules/algebra/include/Segment3D.h

@@ -25,15 +25,13 @@ class IMPALGEBRAEXPORT Segment3D : public GeometricPrimitiveD<3> {
  public:
   Segment3D() {}
   Segment3D(const Vector3D &start, const Vector3D &end);
-  //! Get the start=0/end=1 point of the segment
+  //! Get the start (i==0) or end (i==1) point of the segment
   const Vector3D &get_point(unsigned int i) const {
     IMP_INTERNAL_CHECK(i < 2, "Invalid point index");
     return p_[i];
   }
   Vector3D get_middle_point() const { return .5 * p_[0] + .5 * p_[1]; }
-  /** \brief Get a normalized direction vector pointing from
-      get_point(0) to get_point(1).
-  */
+  //! Get a normalized direction vector from get_point(0) to get_point(1).
   Vector3D get_direction() const { return (p_[1] - p_[0]).get_unit_vector(); }
   double get_length() const;
   IMP_SHOWABLE_INLINE(Segment3D,
@@ -47,15 +45,14 @@ IMP_LINEAR_GEOMETRY_METHODS(Segment3D, segment_3d,
                             return BoundingBoxD<3>(g.get_point(0)) +
                                    BoundingBoxD<3>(g.get_point(1)));
 
-/**  Returns f, the 'relative' projection of a point p onto the line
-     that contains s.
-     Formally, the projection of p onto the line through s is s[0]+f*(s[1]-s[0])
-     f is in the range [0..1] if the projection of p is inside s.
+//! Return the 'relative' projection of a point p onto the line that contains s.
+/** Formally, the projection of p onto the line through s is s[0]+f*(s[1]-s[0])
+    f is in the range [0..1] if the projection of p is inside s.
 
-     @param s segment in 3D
-     @param p point in 3D
+    @param s segment in 3D
+    @param p point in 3D
 
-     @return the 'relative' project of p onto the line containing s
+    @return the 'relative' projection of p onto the line containing s
 */
 IMPALGEBRAEXPORT double get_relative_projection_on_segment(
     const Segment3D &s, const algebra::Vector3D &p);

modules/algebra/include/Sphere3D.h

@@ -38,22 +38,20 @@ inline double get_ball_radius_from_volume_3d(double volume) {
 }
 
 #ifdef IMP_ALGEBRA_USE_IMP_CGAL
-/** Return the surface area and volume of the union of the balls
-    bounded by the spheres. This method requires CGAL to work.
-*/
+//! Get surface area & volume of the union of the balls bounded by the spheres.
+/** This method requires CGAL to work.
+ */
 IMPALGEBRAEXPORT FloatPair
     get_surface_area_and_volume(const algebra::Sphere3Ds &ss);
 #endif
 
-/** Return a set of balls that approximates the surface of the passed set within
- * the error tolerance.
- *
- * The any point in the old surface will be within
- * roughly maximum_allowed_error_angstroms of a point in the new surface and any
- * point outside the old volume will be within roughly
- * maximum_allowed_error_angstroms of a point outside the new volume.
- *
- * \note The name may change if someone thinks up a better one.
+//! Get a set of balls that approximates the surface of the passed set.
+/** Any point in the old surface will be within roughly
+    maximum_allowed_error_angstroms of a point in the new surface and any
+    point outside the old volume will be within roughly
+    maximum_allowed_error_angstroms of a point outside the new volume.
+
+    \note The name may change if someone thinks up a better one.
  */
 IMPALGEBRAEXPORT Sphere3Ds
     get_simplified_from_volume(Sphere3Ds in,

modules/algebra/include/SphericalVector3D.h

@@ -32,15 +32,13 @@ class IMPALGEBRAEXPORT SphericalVector3D : public GeometricPrimitiveD<3> {
  public:
   SphericalVector3D() {};
 
-  //! Constructor that directly converts to spherical coordinates from a vector
-  //! v in Cartesian coordinates
+  //! Construct from a Cartesian coordinate vector
   SphericalVector3D(const Vector3D& v) { set_cartesian_coordinates(v); }
 
-  //! Direct Constructor. A check for the validity of the coords is done
-  //! by default
-  /**
-    Set apply_check to false if you do not want the check
-  **/
+  //! Construct from provided spherical coordinates.
+  /** A check for the validity of the coords is done by default.
+      Set apply_check to false if you do not want the check.
+   */
   SphericalVector3D(double r, double theta, double psi,
                     bool apply_check = true) {
     if (apply_check) {