Add missing docs

modules/algebra/include/Rotation3D.h

@@ -277,6 +277,7 @@ class IMPALGEBRAEXPORT Rotation3D : public GeometricPrimitiveD<3> {
       more efficient to call that function if all columns are needed.
 
       \param[in] v vector to be rotated by rotation \f$R(q)\f$
+      \param[in] i the quaternion element
       \param[in] wrt_unnorm Gradient is computed wrt unnormalized quaternion.
                             Rotation includes a normalization operation, and
                             the gradient is projected to the tangent space at

modules/core/include/BallMover.h

@@ -53,7 +53,8 @@ class IMPCOREEXPORT BallMover : public MonteCarloMover {
   BallMover(Model *m, ParticleIndex pi, double radius);
 
   //! Move specified variables of particles within a ball of specified radius
-  /** \param[in] pis The set of particles to perturb.
+  /** \param[in] m The model containing the particles.
+      \param[in] pis The set of particles to perturb.
       \param[in] vars The variables to use (normally the keys for x,y,z)
       \param[in] radius The radius deviation to use.
    */
@@ -62,6 +63,7 @@ class IMPCOREEXPORT BallMover : public MonteCarloMover {
 
   //! Move the x,y,z coordinates of pis within a ball of specified radius
   /** The x,y,z coordinates of each particle are perturbed within a ball.
+      \param[in] m The model containing the particles.
       \param[in] pis The set of particles to perturb.
       \param[in] radius The radius deviation to use.
    */

modules/em/include/DensityMap.h

@@ -381,17 +381,21 @@ class IMPEMEXPORT DensityMap : public IMP::Object {
   //! Create and return a new cropped map based on particles
   /** The map is cropped based on voxel proximity to a set of particles.
       All voxel centers farther than [distance] away from any
-      particle center in [ps] will have their density value set to 0.0.
-      
-      setting inverse to true will set all voxel centers within
-      [distance] of a particle to 0.0.
+      particle center in [ps] will have their density value set to 0.0,
+      unless inverse is set to true in which case all voxel centers *within*
+      [distance] of a particle will be set to 0.0.
 
       \param[in] ps List of particles used to crop map
       \param[in] distance Distance from particles at which to crop map
-      \param[in] inverse Set to true to crop the particle volume of the map
+      \param[in] inverse If true, remove nearby density rather than distant
+                 density
+      \param[in] keep_map_dimensions If false, crop the map to remove as many
+                 voxels set to 0.0 as possible; otherwise, return a map the
+		 same size as the input.
       \return the new cropped map.
    */
-  DensityMap *get_cropped(Particles ps, double distance, bool inverse = false, bool keep_map_dimensions = false);
+  DensityMap *get_cropped(Particles ps, double distance, bool inverse=false,
+		          bool keep_map_dimensions=false);
 
   //! Create and return a new cropped map with the given bounding box extent
   /** \param[in] bb the bounding box