[IMP-dev] internal source

13 Feb 2008

I added a directory (IMP/internal) to put files that should not be 
considered part of the IMP API. Examples include the attribute table, 
Grid3d, and the graph base classes. I plan to add a few more new files 
there.
In the process I cleaned up the includes of several files.
The directory is now not searched by doxygen so that they stay out of 
the documentation. We do have the capability later of marking them as 
internal and having them documented separately.
Index: kernel/include/IMP/ModelData.h
===================================================================

--- kernel/include/IMP/ModelData.h	(revision 368)
+++ kernel/include/IMP/ModelData.h	(working copy)
@@ -27,6 +27,8 @@
     in this structure. Float data is assumed to be potentially
     differentiable and is stored in a structure that can accomodate
     differentiation. Int and string data is stored directly in vectors.
+
+    \note ModelData should only be used in writing Optimizers.
  */
 class IMPDLLEXPORT ModelData
 {
Index: kernel/include/IMP/Model.h
===================================================================
--- kernel/include/IMP/Model.h	(revision 368)
+++ kernel/include/IMP/Model.h	(working copy)
@@ -10,16 +10,16 @@
 #define __IMP_MODEL_H
#include "IMP_config.h"
-#include "ModelData.h"
-#include "RigidBody.h"
 #include "ScoreState.h"
 #include "Object.h"
+#include "base_types.h"
namespace IMP
 {
class Particle;
 class Restraint;
+class ModelData;
//! Class for storing model, its restraints, constraints, and particles.
 /** All attribute data for particles is stored through indexing in the
Index: kernel/include/IMP/score_states/NonbondedListScoreState.h
===================================================================
--- kernel/include/IMP/score_states/NonbondedListScoreState.h	(revision 368)
+++ kernel/include/IMP/score_states/NonbondedListScoreState.h	(working copy)
@@ -13,7 +13,7 @@
 #include "BondedListScoreState.h"
 #include "MaxChangeScoreState.h"
 #include "../ScoreState.h"
-#include "../Grid3D.h"
+#include "../internal/Grid3D.h"
namespace IMP
 {
Index: kernel/include/IMP/AttributeTable.h
===================================================================
--- kernel/include/IMP/AttributeTable.h	(revision 368)
+++ kernel/include/IMP/AttributeTable.h	(working copy)
@@ -1,154 +0,0 @@
-/**
- *  \file AttributeTable.h    \brief Keys to cache lookup of attribute strings.
- *
- *  Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#ifndef __IMP_ATTRIBUTE_TABLE_H
-#define __IMP_ATTRIBUTE_TABLE_H
-
-#include <map>
-#include <vector>
-#include "base_types.h"
-#include "utility.h"
-#include "log.h"
-#include "ModelData.h"
-
-
-namespace IMP
-{
-
-class ModelData;
-
-namespace internal
-{
-
-template <class T>
-class AttributeTable
-{
-  std::vector<Index<T> > map_;
-public:
-  typedef Index<T> Value;
-  typedef Key<T> Key;
-  AttributeTable() {} 
-  const Value get_value(Key k) const {
-    IMP_check(contains(k),
-              "Attribute "" << k.get_string()
-              << "" not found in table.",
-              IndexException(std::string("Invalid attribute "")
-                             + k.get_string() + "" requested"));
-    return map_[k.get_index()];
-  }
-  void insert(Key k, Value v);
-  bool contains(Key k) const {
-    IMP_check(k != Key(), "Can't search for default key",
-              IndexException("Bad index"));
-    return k.get_index() < map_.size()
-           && map_[k.get_index()] != Value();
-  }
-  void show(std::ostream &out, const char *prefix="",
-            ModelData* md=NULL) const;
-  std::vector<Key> get_keys() const;
-};
-
-IMP_OUTPUT_OPERATOR_1(AttributeTable)
-
-
-
-
-// These really should go in the header file,
-// but I can't throw exceptions from there
-
-template <class T>
-inline void AttributeTable<T>::insert(Key k, Value v)
-{
-  IMP_check(k != Key(),
-            "Can't insert default key",
-            IndexException("bad index"));
-  IMP_assert(v != Value(),
-             "Can't add attribute with no index");
-  if (map_.size() <= k.get_index()) {
-    map_.resize(k.get_index()+1);
-  }
-  IMP_assert(map_[k.get_index()]== Value(),
-             "Trying to add attribute "" << k.get_string()
-             << "" twice");
-  map_[k.get_index()]= v;
-  IMP_assert(contains(k), "Something is broken");
-}
-
-
-template <class T>
-inline void AttributeTable<T>::show(std::ostream &out,
-                                    const char *prefix,
-                                    ModelData *md) const
-{
-  for (unsigned int i=0; i< map_.size(); ++i) {
-    if (map_[i] != Value()) {
-      out << prefix;
-      if (md != NULL) {
-        out << md->get_value(map_[i]);
-      }
-      out << std::endl;
-    }
-  }
-}
-
-
-template <class T>
-inline std::vector<typename AttributeTable<T>::Key> 
-AttributeTable<T>::get_keys() const
-{
-  std::vector<Key> ret;
-   for (unsigned int i=0; i< map_.size(); ++i) {
-     if (map_[i] != Value()) {
-       ret.push_back(Key(i));
-     }
-   }
-   return ret;
-}
-
-inline void show_attributes(std::ostream &out)
-{
-  if (attribute_key_data.size() < attribute_table_index(Float())) {
-    out << "Float attributes are ";
-    for (unsigned int i=0;
-         i< attribute_key_data[attribute_table_index(Float())].rmap.size();
-         ++i) {
-      out << """
-      << attribute_key_data[attribute_table_index(Float())].rmap[i]
-      << "" ";
-    }
-    out << std::endl;
-  }
-  if (attribute_key_data.size() < attribute_table_index(Int())) {
-    out << "Int attributes are ";
-    for (unsigned int i=0;
-         i< attribute_key_data[attribute_table_index(Int())].rmap.size();
-         ++i) {
-      out << """
-      << attribute_key_data[attribute_table_index(Int())].rmap[i]
-      << "" ";
-    }
-  }
-  if (attribute_key_data.size() < attribute_table_index(String())) {
-    out << "String attributes are ";
-    for (unsigned int i=0;
-         i< attribute_key_data[attribute_table_index(String())].rmap.size();
-         ++i) {
-      out << """
-      << attribute_key_data[attribute_table_index(String())].rmap[i]
-      << "" ";
-    }
-    out << std::endl;
-  }
-
-} 
-
-
-} // namespace internal
-
-} // namespace IMP
-
-#endif  /* __IMP_ATTRIBUTE_TABLE_H */
Index: kernel/include/IMP/RigidBody.h
===================================================================
--- kernel/include/IMP/RigidBody.h	(revision 368)
+++ kernel/include/IMP/RigidBody.h	(working copy)
@@ -1,38 +0,0 @@
-/**
- *  \file RigidBody.h   \brief Class for grouping particles into rigid bodies.
- *
- *  Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#ifndef __IMP_RIGIDBODY_H
-#define __IMP_RIGIDBODY_H
-
-#include "IMP_config.h"
-
-namespace IMP
-{
-
-//! Class for grouping particles into rigid bodies.
-class IMPDLLEXPORT RigidBody
-{
-public:
-  RigidBody();
-  ~RigidBody();
-
-  //! Set number of particles in the rigid body.
-  /** \param[in] num_particles Number of particles.
-   */
-  void set_num_particles(int num_particles);
-
-  //! Get the number of particles in the rigid body.
-  /** \return Number of particles in the body.
-   */
-  int get_num_particles() const;
-protected:
-  int num_particles_;
-};
-
-} // namespace IMP
-
-#endif  /* __IMP_RIGIDBODY_H */
Index: kernel/include/IMP/decorators/graph_base.h
===================================================================
--- kernel/include/IMP/decorators/graph_base.h	(revision 368)
+++ kernel/include/IMP/decorators/graph_base.h	(working copy)
@@ -1,105 +0,0 @@
-/**
- *  \file graph_base.h     \brief Internal use only.
- *
- *  Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#ifndef __IMP_GRAPH_DECORATORS_H
-#define __IMP_GRAPH_DECORATORS_H
-
-#include <vector>
-#include <set>
-
-#include "../Particle.h"
-#include "../Model.h"
-#include "utility.h"
-
-namespace IMP
-{
-
-namespace internal
-{
-
-struct IMPDLLEXPORT GraphData
-{
-  GraphData() {}
-  GraphData(const char *prefix): prefix_(prefix) {
-    node_keys_[0]=IntKey((prefix_+" node 0").c_str());
-    node_keys_[1]=IntKey((prefix_+" node 1").c_str());
-    num_edges_key_= IntKey((prefix_+" num edges").c_str());
-  }
-  IntKey node_keys_[2];
-  IntKey num_edges_key_;
-  mutable std::vector<IntKey> edge_keys_;
-  std::string prefix_;
-};
-
-
-IMPDLLEXPORT Particle* graph_connect(Particle* a, Particle* b,
-                                     const GraphData &d);
-
-IMPDLLEXPORT void graph_disconnect(Particle* bond,
-                                   const GraphData &d);
-
-IMPDLLEXPORT Particle* graph_get_edge(Particle* a, int i,
-                                      const GraphData &d);
-
-IMPDLLEXPORT Particle* graph_get_neighbor(Particle* a, int i,
-                                          const GraphData &d);
-
-IMPDLLEXPORT unsigned int graph_get_number_of_edges(Particle *a,
-                                                    const GraphData &d);
-
-IMPDLLEXPORT Particle* graph_get_node(Particle *a, int i,
-                                      const GraphData &d);
-
-IMPDLLEXPORT bool graph_is_edge(Particle *a, const GraphData &d);
-
-template <class F>  
-F graph_traverse(Particle *start, F f, const GraphData &d)
-{
-  std::set<Particle*> visited;
-  std::vector<Particle*> queue;
-  queue.push_back(start);
-  visited.insert(start);
-  do {
-    Particle *cur= queue.back();
-    queue.pop_back();
-    f(cur);
-    for (unsigned int i=0; i< graph_get_number_of_edges(cur, d); ++i) {
-      Particle *n= graph_get_neighbor(cur, i, d);
-      if (visited.find(n) == visited.end()) {
-        visited.insert(n);
-        queue.push_back(n);
-      }
-    }
-  } while (!queue.empty());
-  return f;
-}
-
-template <class Oit>
-struct GraphGather
-{
-  GraphGather(Oit out): out_(out){}
-  void operator()( Particle *p)
-  {
-    *out_=p;
-    ++out_;
-  }
-
-  Oit get_out() const {return out_;}
-  Oit out_;
-};
-
-template <class Oit>
-void graph_connected_component(Particle* start, const GraphData &d, Oit out)
-{
-  graph_traverse(start, GraphGather<Oit>(out), d);
-}
-
-} // namespace internal
-
-} // namespace IMP
-
-#endif  /* __IMP_GRAPH_DECORATORS_H */
Index: kernel/include/IMP/decorators/bond_decorators.h
===================================================================
--- kernel/include/IMP/decorators/bond_decorators.h	(revision 368)
+++ kernel/include/IMP/decorators/bond_decorators.h	(working copy)
@@ -12,7 +12,8 @@
 #include "../Particle.h"
 #include "../Model.h"
 #include "../DecoratorBase.h"
-#include "graph_base.h"
+#include "../internal/graph_base.h"
+#include "utility.h"
namespace IMP
 {
@@ -26,7 +27,7 @@
namespace internal
 {
-
+class GraphData;
 extern IMPDLLEXPORT  GraphData bond_graph_data_;
 extern IMPDLLEXPORT  bool bond_keys_initialized_;
 extern IMPDLLEXPORT  IntKey bond_type_key_;
Index: kernel/include/IMP/internal/AttributeTable.h
===================================================================
--- kernel/include/IMP/internal/AttributeTable.h	(revision 0)
+++ kernel/include/IMP/internal/AttributeTable.h	(working copy)
@@ -8,14 +8,14 @@
 #ifndef __IMP_ATTRIBUTE_TABLE_H
 #define __IMP_ATTRIBUTE_TABLE_H
+#include "../base_types.h"
+#include "../utility.h"
+#include "../log.h"
+#include "../ModelData.h"
+
 #include <map>
 #include <vector>
-#include "base_types.h"
-#include "utility.h"
-#include "log.h"
-#include "ModelData.h"
-
 namespace IMP
 {
Index: kernel/include/IMP/internal/graph_base.h
===================================================================
--- kernel/include/IMP/internal/graph_base.h	(revision 0)
+++ kernel/include/IMP/internal/graph_base.h	(working copy)
@@ -13,7 +13,6 @@
#include "../Particle.h"
 #include "../Model.h"
-#include "utility.h"
namespace IMP
 {
Index: kernel/include/IMP/internal/Grid3D.h
===================================================================
--- kernel/include/IMP/internal/Grid3D.h	(revision 0)
+++ kernel/include/IMP/internal/Grid3D.h	(working copy)
@@ -8,8 +8,8 @@
 #ifndef __IMP_GRID_3D_H
 #define __IMP_GRID_3D_H
-#include "base_types.h"
-#include "Vector3D.h"
+#include "../base_types.h"
+#include "../Vector3D.h"
namespace IMP
 {
Index: kernel/include/IMP/unary_functions/Linear.h
===================================================================
--- kernel/include/IMP/unary_functions/Linear.h	(revision 0)
+++ kernel/include/IMP/unary_functions/Linear.h	(revision 0)
@@ -0,0 +1,43 @@
+/**
+ *  \file Linear.h    \brief A linear function.
+ *
+ *  Copyright 2007-8 Sali Lab. All rights reserved.
+ */
+
+#ifndef __IMP_LINEAR_H
+#define __IMP_LINEAR_H
+
+#include "../UnaryFunction.h"
+
+namespace IMP
+{
+
+//! Linear function
+/** \ingroup unaryf
+    \note there is no offset since that is not meaningful for optimization
+ */
+class IMPDLLEXPORT Linear : public UnaryFunction
+{
+public:
+  Linear(Float slope) : slope_(slope) {}
+
+  virtual ~Linear() {}
+
+  virtual Float operator()(Float feature) { return feature*slope_;}
+
+  virtual Float operator()(Float feature, Float& deriv) {
+    deriv= slope_;
+    return operator()(feature);
+  }
+
+  void show(std::ostream &out=std::cout) const {
+    out << "Linear: " << slope_ << std::endl;
+  }
+
+protected:
+  Float slope_;
+};
+
+} // namespace IMP
+
+#endif  /* __IMP_HARMONIC_H */
Index: kernel/include/IMP/SConscript
===================================================================
--- kernel/include/IMP/SConscript	(revision 368)
+++ kernel/include/IMP/SConscript	(working copy)
@@ -3,11 +3,11 @@
files = ['base_types.h', 'random.h', 'Index.h', 'Model.h',
          'Particle.h', 'ScoreState.h', 'OptimizerState.h', 'IMP_config.h',
-         'ModelData.h', 'RigidBody.h', 'log.h', 'DerivativeAccumulator.h',
-         'Key.h', 'AttributeTable.h', 'utility.h', 'Restraint.h', 'Optimizer.h',
+         'log.h', 'DerivativeAccumulator.h', 'ModelData.h'
+         'Key.h', 'utility.h', 'Restraint.h', 'Optimizer.h',
          'DecoratorBase.h', 'Object.h', 'Vector3D.h', 'ScoreFuncParams.h',
          'UnaryFunction.h', 'PairScore.h', 'SingletonScore.h', 'macros.h',
-         'Grid3D.h', 'TripletScore.h']
+         'TripletScore.h']
# Install the include files:
 includedir = os.path.join(env['includedir'], 'IMP')
@@ -18,6 +18,7 @@
 SConscript('restraints/SConscript')
 SConscript('optimizers/SConscript')
 SConscript('decorators/SConscript')
+SConscript('internal/SConscript')
 SConscript('unary_functions/SConscript')
 SConscript('pair_scores/SConscript')
 SConscript('singleton_scores/SConscript')
Index: kernel/include/IMP/DerivativeAccumulator.h
===================================================================
--- kernel/include/IMP/DerivativeAccumulator.h	(revision 368)
+++ kernel/include/IMP/DerivativeAccumulator.h	(working copy)
@@ -11,7 +11,6 @@
#include "IMP_config.h"
 #include "base_types.h"
-#include "ModelData.h"
 #include <cmath>
namespace IMP
Index: kernel/include/IMP/Particle.h
===================================================================
--- kernel/include/IMP/Particle.h	(revision 368)
+++ kernel/include/IMP/Particle.h	(working copy)
@@ -16,7 +16,7 @@
 #include "Object.h"
 #include "utility.h"
 #include "Key.h"
-#include "AttributeTable.h"
+#include "internal/AttributeTable.h"
 #include "DerivativeAccumulator.h"
namespace IMP
Index: kernel/include/IMP/Grid3D.h
===================================================================
--- kernel/include/IMP/Grid3D.h	(revision 368)
+++ kernel/include/IMP/Grid3D.h	(working copy)
@@ -1,391 +0,0 @@
-/**
- *  \file Grid3D.h   \brief A class to represent a voxel grid.
- *
- *  Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#ifndef __IMP_GRID_3D_H
-#define __IMP_GRID_3D_H
-
-#include "base_types.h"
-#include "Vector3D.h"
-
-namespace IMP
-{
-
-template <class V>
-class Grid3D;
-
-template <class GI>
-class GridIndexIterator;
-
-//! Represent an index into an infinite grid
-/** The index entries can be positive or negative and do not need to correspond
-    directly to cells in the grid. They get mapped on to actual grid cells
-    by various functions.
- */
-class VirtualGridIndex
-{
-  typedef VirtualGridIndex This;
-  int d_[3];
-  bool is_default() const {
-    return d_[0]==std::numeric_limits<int>::max();
-  }
-public:
-  //! Create a grid cell from three arbitrary indexes
-  VirtualGridIndex(int x, int y, int z) {
-    d_[0]=x;
-    d_[1]=y;
-    d_[2]=z;
-  }
-  VirtualGridIndex() {
-    d_[0]=d_[1]=d_[2]=std::numeric_limits<int>::max();
-  }
-  //! Get the ith component (i=0,1,2)
-  int operator[](unsigned int i) const {
-    IMP_assert(i <3, "Bad i");
-    return d_[i];
-  }
-  IMP_COMPARISONS_3(d_[0], d_[1], d_[2]);
-  void show(std::ostream &out=std::cout) const {
-    out << "Cell(" << d_[0] << ", " << d_[1] << ", " << d_[2] << ")";
-  }
-  bool strictly_larger_than(const VirtualGridIndex &o) const {
-    return d_[0] > o.d_[0] && d_[1] > o.d_[1] && d_[2] > o.d_[2];
-  }
-};
-
-IMP_OUTPUT_OPERATOR(VirtualGridIndex);
-
-//! Iterate through grid cells in a cube
-/** The order of iteration is unspecified. 
- */
-template <class GI>
-class GridIndexIterator
-{
-  template <class V>
-  friend class Grid3D;
-  VirtualGridIndex lb_;
-  VirtualGridIndex ub_;
-  GI cur_;
-  typedef GridIndexIterator This;
-  bool is_default() const {
-    return false;
-  }
-  GridIndexIterator(VirtualGridIndex lb,
-                    VirtualGridIndex ub): lb_(lb),
-                                          ub_(ub), cur_(lb[0], lb[1], lb[2]) {
-    IMP_assert(ub_.strictly_larger_than(lb_),
-               "Invalid range in GridIndexIterator");
-  }
-public:
-  typedef const GI& reference_type;
-  typedef const GI* pointer_type;
-  typedef GI value_type;
-  typedef std::forward_iterator_tag iterator_category;
-  typedef unsigned int difference_type;
-
-  GridIndexIterator(){}
-
-  IMP_COMPARISONS_1(cur_);
-
-  This operator++() {
-    IMP_assert(cur_ >= lb_, "cur out of range");
-    IMP_assert(cur_ < ub_, "cur out of range");
-    int r[3];
-    unsigned int carry=1;
-    for (int i=2; i>=0; --i) {
-      r[i]= cur_[i]+carry;
-      if ( r[i] == ub_[i]) {
-        r[i]= lb_[i];
-        carry=1;
-      } else {
-        carry=0;
-      }
-    }
-    if (carry==1) {
-      cur_= GI();
-    } else {
-      GI nc= GI(r[0], r[1], r[2]);
-      IMP_assert(nc > cur_, "Nonfunctional increment");
-      IMP_assert(nc > lb_, "Problems advancing");
-      IMP_assert(ub_.strictly_larger_than(nc), "Problems advancing");
-      cur_= nc;
-    }
-    return *this;
-  }
-  This operator++(int) {
-    This o= *this;
-    operator++;
-    return o;
-  }
-  reference_type operator*() const {
-    return cur_;
-  }
-  pointer_type operator->() const {
-    return &cur_;
-  }
-};
-
-//! Represent a real cell in a grid
-/** These indexes represent an actual cell in the grid with no mapping.
-    They can only be constructed by the grid. 
- */
-class GridIndex: public VirtualGridIndex
-{
-public:
-  GridIndex(): VirtualGridIndex() {
-  }
-protected:
-  template <class V>
-  friend class Grid3D;
-  template <class G>
-  friend class GridIndexIterator;
-  GridIndex(int x, int y, int z): VirtualGridIndex(x,y,z) {
-    IMP_check(x>=0 && y>=0 && z>=0, "Bad indexes in grid index",
-              IndexException("Bad indexes in GridIndex"));
-  }
-};
-
-/** \brief A voxel grid in 3D space.
-    VT can be any class.
- */
-template <class VT>
-class Grid3D
-{
-public:
-  //! The type stored in each voxel.
-  typedef VT VoxelData;
-
-  //! An index that refers to a real voxel
-  typedef GridIndex Index;
-  //! An index that refers to a voxel that may or may not exist
-  /** Such an index can refer to voxels outside of the grid
-      or with negative indices.
-   */
-  typedef VirtualGridIndex VirtualIndex;
-
-private:
-  std::vector<VT> data_;
-  int d_[3];
-  Vector3D min_, max_;
-  float edge_size_[3];
-
-  void update_sizes() {
-    for (unsigned int i=0; i< 3; ++i) {
-      // hack to try to handle roundoff errors
-      // I would like to find something more reliable
-      edge_size_[i]= 1.05*(max_.get_component(i)- min_.get_component(i))/d_[i];
-    }
-    /*IMP_LOG(VERBOSE, "Grid has " << d_[0] << "x" << d_[1]
-            << "x" << d_[2] << " voxels of size "
-            << edge_size_[0] << "x" << edge_size_[1] 
-            << "x" << edge_size_[2] << std::endl);*/
-  }
-
-  unsigned int index(const Index &i) const {
-    unsigned int ii= i[2]*d_[0]*d_[1] + i[1]*d_[0]+i[0];
-    IMP_assert(ii < data_.size(), "Invalid grid index");
-    return ii;
-  }
-  template <class IndexType>
-  IndexType get_index_t(Vector3D pt) const {
-    int index[3];
-    for (unsigned int i=0; i< 3; ++i ) {
-      float d= pt.get_component(i)- min_.get_component(i);
-      index[i]= static_cast<int>(std::floor(d/edge_size_[i]));
-    }
-    return IndexType(index[0], index[1], index[2]);
-  }
-
-  int snap(int dim, int v) const {
-    if (v < 0) return 0;
-    else if (v > d_[dim]) return d_[dim];
-    else return v;
-  }
-
-  Index snap(const VirtualIndex &v) const {
-    return Index(snap(0, v[0]),
-                 snap(1, v[1]),
-                 snap(2, v[2]));
-  } 
-  std::pair<Index, VirtualIndex> empty_range() const {
-    return std::make_pair(Index(0,0,0), VirtualIndex(0,0,0));
-  }
-
-  std::pair<Index, VirtualIndex> intersect(VirtualIndex l,
-                                           VirtualIndex u) const {
-    Index rlb;
-    VirtualIndex rub;
-    for (unsigned int i=0; i< 3; ++i) {
-      if (u[i] <= 0) return empty_range();
-      if (l[i] >= d_[i]) return empty_range();
-    }
-    return std::make_pair(snap(l), snap(u));
-  }
-
-
-public:
-
-  //! Initialize the grid
-  /** \param[in] xd The number of voxels in the x direction
-      \param[in] yd The number of voxels in the y direction
-      \param[in] zd The number of voxels in the z direction
-      \param[in] minc The min coordinate of the grid
-      \param[in] maxc The max coordinate of the grid
-      \param[in] def The default value for the voxels
-   */
-  Grid3D(int xd, int yd, int zd, 
-         Vector3D minc, Vector3D maxc,
-         VoxelData def): data_(xd*yd*zd, def),
-                         min_(minc),
-                         max_(maxc) {
-    d_[0]=xd;
-    d_[1]=yd;
-    d_[2]=zd;
-    update_sizes();
-  }
-
-  //! Initialize the grid
-  /** \param[in] side The side length for the voxels
-      \param[in] minc The min coordinate of the grid
-      \param[in] maxc A lower bound for the max coordinate of the grid
-      \param[in] def The default value for the voxels
-   */
-  Grid3D(float side, 
-         Vector3D minc, Vector3D maxc,
-         VoxelData def) {
-    min_=minc;
-    float mx[3];
-    for (unsigned int i=0; i< 3; ++i ) {
-      d_[i]= std::max(static_cast<int>(std::ceil((maxc.get_component(i)
-                            - minc.get_component(i))/ side)),
-                      1);
-      mx[i]= d_[i]*side+ minc.get_component(i);
-    }
-    data_.resize(d_[0]*d_[1]*d_[2], def);
-    max_= Vector3D(mx[0], mx[1], mx[2]);
-    update_sizes();
-  }
-
-  //! An empty grid.
-  Grid3D(){
-    d_[0]=0;
-    d_[1]=0;
-    d_[2]=0;
-  }
-
-  //! Set the max corner of the grid
-  void set_min(Vector3D m) {
-    min_=m;
-    update_sizes();
-  }
-
-  //! Set the min corner of the voxel grid
-  void set_max(Vector3D m) {
-    max_=m;
-    update_sizes();
-  }
-
-  //! Get the min corner
-  const Vector3D &get_min() const {
-    return min_;
-  }
-
-  //! Get the max corner
-  const Vector3D &get_max() const {
-    return max_;
-  }
-
-  //! Return the number of voxels in a certain direction
-  unsigned int get_number_of_voxels(unsigned int i) const {
-    IMP_assert(i < 3, "Only 3D");
-    return d_[i];
-  }
-
-  //! Return the index of the voxel containing the point.
-  Index get_index(Vector3D pt) const {
-    for (unsigned int i=0; i< 3; ++i) {
-      if (pt.get_component(i) < min_.get_component(i)) return Index();
-      if (pt.get_component(i) > max_.get_component(i)) return Index();
-    }
-    return get_index_t<Index>(pt);
-  }
-
-  //! Return the index that would contain the voxel if the grid extended there
-  VirtualIndex get_virtual_index(Vector3D pt) const {
-    return get_index_t<VirtualIndex>(pt);
-  }
-
-  //! Convert a VirtualIndex into a real Index if possible
-  /** \return Index() if not possible
-   */
-  Index get_index(VirtualIndex v) const {
-    for (unsigned int i=0; i< 3; ++i) {
-      if (v[i] <0 || v[i] >= d_[i]) return Index();
-    }
-    return Index(v[0], v[1], v[2]);
-  }
-
-  //! Get the data in a particular cell
-  VoxelData& get_voxel(Index gi) {
-    return data_[index(gi)];
-  }
-
-  //! Get the data in a particular cell
-  const VoxelData& get_voxel(Index gi) const  {
-    return data_[index(gi)];
-  }
-
-  Index get_min_index() const {
-    return Index(0,0,0);
-  }
-
-  //! Return a point at the center of the voxel
-  Vector3D get_center(VirtualIndex gi) const {
-    return Vector3D(edge_size_[0]*(.5f+ gi[0]) + min_.get_component(0),
-                    edge_size_[1]*(.5f+ gi[1]) + min_.get_component(1),
-                    edge_size_[2]*(.5f+ gi[2]) + min_.get_component(2));
-  }
-
-
-  //! Iterator through the Indexes in volume
-  /** The iterator iterates though the valid indexes bounded
-      by the VirtualIndex
-   */
-  typedef GridIndexIterator<Index> IndexIterator;
-  IndexIterator indexes_begin(VirtualIndex lb, 
-                              VirtualIndex ub) const {
-    std::pair<Index, VirtualIndex> bp= intersect(lb,ub);
-    if (bp.first== bp.second) {
-      return IndexIterator();
-    } else {
-      IMP_assert(bp.second.strictly_larger_than(bp.first), "empty range");
-      return IndexIterator(bp.first, bp.second);
-    }
-  }
-  IndexIterator indexes_end(VirtualIndex, 
-                            VirtualIndex) const {
-    //IMP_assert(lb <= ub, "empty range");
-    return IndexIterator();
-  }
-
-  IndexIterator all_indexes_begin() const {
-    return indexes_begin(VirtualIndex(0,0,0),
-                         VirtualIndex(d_[0], 
-                                      d_[1],
-                                      d_[2]));
-  }
-  IndexIterator all_indexes_end() const {
-    return indexes_end(VirtualIndex(0,0,0),
-                       VirtualIndex(d_[0], 
-                                    d_[1],
-                                    d_[2]));
-  }
-};
-
-
-} // namespace IMP
-
-#endif  /* __IMP_GRID_3D_H */
Index: kernel/include/IMP.h
===================================================================
--- kernel/include/IMP.h	(revision 368)
+++ kernel/include/IMP.h	(working copy)
@@ -22,14 +22,11 @@
 #include "IMP/unary_functions/OpenCubicSpline.h"
 #include "IMP/unary_functions/Cosine.h"
 #include "IMP/ScoreFuncParams.h"
-#include "IMP/RigidBody.h"
-#include "IMP/ModelData.h"
 #include "IMP/Model.h"
 #include "IMP/PairScore.h"
 #include "IMP/SingletonScore.h"
 #include "IMP/TripletScore.h"
 #include "IMP/Vector3D.h"
-#include "IMP/Grid3D.h"
 #include "IMP/decorators/HierarchyDecorator.h"
 #include "IMP/decorators/MolecularHierarchyDecorator.h"
 #include "IMP/decorators/NameDecorator.h"
Index: kernel/doc/internal/doxygen.conf
===================================================================
--- kernel/doc/internal/doxygen.conf	(revision 368)
+++ kernel/doc/internal/doxygen.conf	(working copy)
@@ -1,1260 +1,242 @@
-# Doxyfile 1.5.2
+# Doxyfile 1.5.4
-# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project
-#
-# All text after a hash (#) is considered a comment and will be ignored
-# The format is:
-#       TAG = value [value, ...]
-# For lists items can also be appended using:
-#       TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ")
-
 #---------------------------------------------------------------------------
 # Project related configuration options
 #---------------------------------------------------------------------------
-
-# This tag specifies the encoding used for all characters in the config file that 
-# follow. The default is UTF-8 which is also the encoding used for all text before 
-# the first occurrence of this tag. Doxygen uses libiconv (or the iconv built into 
-# libc) for the transcoding. See http://www.gnu.org/software/libiconv for the list of 
-# possible encodings.
-
 DOXYFILE_ENCODING      = UTF-8
-
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
-# by quotes) that should identify the project.
-
 PROJECT_NAME           = IMP
-
-# The PROJECT_NUMBER tag can be used to enter a project or revision number. 
-# This could be handy for archiving the generated documentation or 
-# if some version control system is used.
-
 PROJECT_NUMBER         = 
-
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
-# base path where the generated documentation will be put. 
-# If a relative path is entered, it will be relative to the location 
-# where doxygen was started. If left blank the current directory will be used.
-
 OUTPUT_DIRECTORY       = .
-
-# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 
-# 4096 sub-directories (in 2 levels) under the output directory of each output 
-# format and will distribute the generated files over these directories. 
-# Enabling this option can be useful when feeding doxygen a huge amount of 
-# source files, where putting all generated files in the same directory would 
-# otherwise cause performance problems for the file system.
-
 CREATE_SUBDIRS         = NO
-
-# The OUTPUT_LANGUAGE tag is used to specify the language in which all 
-# documentation generated by doxygen is written. Doxygen will use this 
-# information to generate all constant output in the proper language. 
-# The default language is English, other supported languages are: 
-# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, 
-# Croatian, Czech, Danish, Dutch, Finnish, French, German, Greek, Hungarian, 
-# Italian, Japanese, Japanese-en (Japanese with English messages), Korean, 
-# Korean-en, Lithuanian, Norwegian, Polish, Portuguese, Romanian, Russian, 
-# Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian.
-
 OUTPUT_LANGUAGE        = English
-
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
-# include brief member descriptions after the members that are listed in 
-# the file and class documentation (similar to JavaDoc). 
-# Set to NO to disable this.
-
 BRIEF_MEMBER_DESC      = YES
-
-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend 
-# the brief description of a member or function before the detailed description. 
-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the 
-# brief descriptions will be completely suppressed.
-
 REPEAT_BRIEF           = YES
-
-# This tag implements a quasi-intelligent brief description abbreviator 
-# that is used to form the text in various listings. Each string 
-# in this list, if found as the leading text of the brief description, will be 
-# stripped from the text and the result after processing the whole list, is 
-# used as the annotated text. Otherwise, the brief description is used as-is. 
-# If left blank, the following values are used ("$name" is automatically 
-# replaced with the name of the entity): "The $name class" "The $name widget" 
-# "The $name file" "is" "provides" "specifies" "contains" 
-# "represents" "a" "an" "the"
-
 ABBREVIATE_BRIEF       = 
-
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
-# Doxygen will generate a detailed section even if there is only a brief 
-# description.
-
 ALWAYS_DETAILED_SEC    = NO
-
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all 
-# inherited members of a class in the documentation of that class as if those 
-# members were ordinary class members. Constructors, destructors and assignment 
-# operators of the base classes will not be shown.
-
 INLINE_INHERITED_MEMB  = NO
-
-# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
-# path before files name in the file list and in the header files. If set 
-# to NO the shortest path that makes the file name unique will be used.
-
 FULL_PATH_NAMES        = NO
-
-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
-# can be used to strip a user-defined part of the path. Stripping is 
-# only done if one of the specified strings matches the left-hand part of 
-# the path. The tag can be used to show relative paths in the file list. 
-# If left blank the directory from which doxygen is run is used as the 
-# path to strip.
-
 STRIP_FROM_PATH        = 
-
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of 
-# the path mentioned in the documentation of a class, which tells 
-# the reader which header file to include in order to use a class. 
-# If left blank only the name of the header file containing the class 
-# definition is used. Otherwise one should specify the include paths that 
-# are normally passed to the compiler using the -I flag.
-
 STRIP_FROM_INC_PATH    = 
-
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
-# (but less readable) file names. This can be useful is your file systems 
-# doesn't support long names like on DOS, Mac, or CD-ROM.
-
 SHORT_NAMES            = NO
-
-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
-# will interpret the first line (until the first dot) of a JavaDoc-style 
-# comment as the brief description. If set to NO, the JavaDoc 
-# comments will behave just like the Qt-style comments (thus requiring an 
-# explicit @brief command for a brief description.
-
 JAVADOC_AUTOBRIEF      = NO
-
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen 
-# treat a multi-line C++ special comment block (i.e. a block of //! or /// 
-# comments) as a brief description. This used to be the default behaviour. 
-# The new default is to treat a multi-line C++ comment block as a detailed 
-# description. Set this tag to YES if you prefer the old behaviour instead.
-
+QT_AUTOBRIEF           = NO
 MULTILINE_CPP_IS_BRIEF = NO
-
-# If the DETAILS_AT_TOP tag is set to YES then Doxygen 
-# will output the detailed description near the top, like JavaDoc.
-# If set to NO, the detailed description appears after the member 
-# documentation.
-
 DETAILS_AT_TOP         = NO
-
-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
-# member inherits the documentation from any documented member that it 
-# re-implements.
-
 INHERIT_DOCS           = YES
-
-# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce 
-# a new page for each member. If set to NO, the documentation of a member will 
-# be part of the file/class/namespace that contains it.
-
 SEPARATE_MEMBER_PAGES  = NO
-
-# The TAB_SIZE tag can be used to set the number of spaces in a tab. 
-# Doxygen uses this value to replace tabs by spaces in code fragments.
-
 TAB_SIZE               = 8
-
-# This tag can be used to specify a number of aliases that acts 
-# as commands in the documentation. An alias has the form "name=value". 
-# For example adding "sideeffect=\par Side Effects:\n" will allow you to 
-# put the command \sideeffect (or @sideeffect) in the documentation, which 
-# will result in a user-defined paragraph with heading "Side Effects:". 
-# You can put \n's in the value part of an alias to insert newlines.
-
 ALIASES                = 
-
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C 
-# sources only. Doxygen will then generate output that is more tailored for C. 
-# For instance, some of the names that are used will be different. The list 
-# of all members will be omitted, etc.
-
 OPTIMIZE_OUTPUT_FOR_C  = YES
-
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java 
-# sources only. Doxygen will then generate output that is more tailored for Java. 
-# For instance, namespaces will be presented as packages, qualified scopes 
-# will look different, etc.
-
 OPTIMIZE_OUTPUT_JAVA   = NO
-
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to 
-# include (a tag file for) the STL sources as input, then you should 
-# set this tag to YES in order to let doxygen match functions declarations and 
-# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. 
-# func(std::string) {}). This also make the inheritance and collaboration 
-# diagrams that involve STL classes more complete and accurate.
-
 BUILTIN_STL_SUPPORT    = YES
-
-# If you use Microsoft's C++/CLI language, you should set this option to YES to
-# enable parsing support.
-
 CPP_CLI_SUPPORT        = NO
-
-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
-# tag is set to YES, then doxygen will reuse the documentation of the first 
-# member in the group (if any) for the other members of the group. By default 
-# all members of a group must be documented explicitly.
-
+SIP_SUPPORT            = NO
 DISTRIBUTE_GROUP_DOC   = NO
-
-# Set the SUBGROUPING tag to YES (the default) to allow class member groups of 
-# the same type (for instance a group of public functions) to be put as a 
-# subgroup of that type (e.g. under the Public Functions section). Set it to 
-# NO to prevent subgrouping. Alternatively, this can be done per class using 
-# the \nosubgrouping command.
-
 SUBGROUPING            = YES
-
+TYPEDEF_HIDES_STRUCT   = NO
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
-
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
-# documentation are documented, even if no documentation was available. 
-# Private class members and static file members will be hidden unless 
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
-
 EXTRACT_ALL            = YES
-
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
-# will be included in the documentation.
-
 EXTRACT_PRIVATE        = NO
-
-# If the EXTRACT_STATIC tag is set to YES all static members of a file 
-# will be included in the documentation.
-
 EXTRACT_STATIC         = NO
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
-# defined locally in source files will be included in the documentation. 
-# If set to NO only classes defined in header files are included.
-
 EXTRACT_LOCAL_CLASSES  = YES
-
-# This flag is only useful for Objective-C code. When set to YES local 
-# methods, which are defined in the implementation section but not in 
-# the interface are included in the documentation. 
-# If set to NO (the default) only methods in the interface are included.
-
 EXTRACT_LOCAL_METHODS  = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
-# undocumented members of documented classes, files or namespaces. 
-# If set to NO (the default) these members will be included in the 
-# various overviews, but no documentation section is generated. 
-# This option has no effect if EXTRACT_ALL is enabled.
-
+EXTRACT_ANON_NSPACES   = NO
 HIDE_UNDOC_MEMBERS     = NO
-
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all 
-# undocumented classes that are normally visible in the class hierarchy. 
-# If set to NO (the default) these classes will be included in the various 
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
-
 HIDE_UNDOC_CLASSES     = NO
-
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all 
-# friend (class|struct|union) declarations. 
-# If set to NO (the default) these declarations will be included in the 
-# documentation.
-
 HIDE_FRIEND_COMPOUNDS  = NO
-
-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any 
-# documentation blocks found inside the body of a function. 
-# If set to NO (the default) these blocks will be appended to the 
-# function's detailed documentation block.
-
 HIDE_IN_BODY_DOCS      = NO
-
-# The INTERNAL_DOCS tag determines if documentation 
-# that is typed after a \internal command is included. If the tag is set 
-# to NO (the default) then the documentation will be excluded. 
-# Set it to YES to include the internal documentation.
-
 INTERNAL_DOCS          = NO
-
-# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate 
-# file names in lower-case letters. If set to YES upper-case letters are also 
-# allowed. This is useful if you have classes or files whose names only differ 
-# in case and if your file system supports case sensitive file names. Windows 
-# and Mac users are advised to set this option to NO.
-
 CASE_SENSE_NAMES       = YES
-
-# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen 
-# will show members with their full class and namespace scopes in the 
-# documentation. If set to YES the scope will be hidden.
-
 HIDE_SCOPE_NAMES       = NO
-
-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen 
-# will put a list of the files that are included by a file in the documentation 
-# of that file.
-
 SHOW_INCLUDE_FILES     = YES
-
-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] 
-# is inserted in the documentation for inline members.
-
 INLINE_INFO            = YES
-
-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen 
-# will sort the (detailed) documentation of file and class members 
-# alphabetically by member name. If set to NO the members will appear in 
-# declaration order.
-
 SORT_MEMBER_DOCS       = YES
-
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the 
-# brief documentation of file, namespace and class members alphabetically 
-# by member name. If set to NO (the default) the members will appear in 
-# declaration order.
-
 SORT_BRIEF_DOCS        = NO
-
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be 
-# sorted by fully-qualified names, including namespaces. If set to 
-# NO (the default), the class list will be sorted only by class name, 
-# not including the namespace part. 
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the 
-# alphabetical list.
-
 SORT_BY_SCOPE_NAME     = NO
-
-# The GENERATE_TODOLIST tag can be used to enable (YES) or 
-# disable (NO) the todo list. This list is created by putting \todo 
-# commands in the documentation.
-
 GENERATE_TODOLIST      = YES
-
-# The GENERATE_TESTLIST tag can be used to enable (YES) or 
-# disable (NO) the test list. This list is created by putting \test 
-# commands in the documentation.
-
 GENERATE_TESTLIST      = YES
-
-# The GENERATE_BUGLIST tag can be used to enable (YES) or 
-# disable (NO) the bug list. This list is created by putting \bug 
-# commands in the documentation.
-
 GENERATE_BUGLIST       = YES
-
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or 
-# disable (NO) the deprecated list. This list is created by putting 
-# \deprecated commands in the documentation.
-
 GENERATE_DEPRECATEDLIST= YES
-
-# The ENABLED_SECTIONS tag can be used to enable conditional 
-# documentation sections, marked by \if sectionname ... \endif.
-
 ENABLED_SECTIONS       = 
-
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
-# the initial value of a variable or define consists of for it to appear in 
-# the documentation. If the initializer consists of more lines than specified 
-# here it will be hidden. Use a value of 0 to hide initializers completely. 
-# The appearance of the initializer of individual variables and defines in the 
-# documentation can be controlled using \showinitializer or \hideinitializer 
-# command in the documentation regardless of this setting.
-
 MAX_INITIALIZER_LINES  = 30
-
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated 
-# at the bottom of the documentation of classes and structs. If set to YES the 
-# list will mention the files that were used to generate the documentation.
-
 SHOW_USED_FILES        = YES
-
-# If the sources in your project are distributed over multiple directories 
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy 
-# in the documentation. The default is NO.
-
 SHOW_DIRECTORIES       = NO
-
-# The FILE_VERSION_FILTER tag can be used to specify a program or script that 
-# doxygen should invoke to get the current version for each file (typically from the 
-# version control system). Doxygen will invoke the program by executing (via 
-# popen()) the command <command> <input-file>, where <command> is the value of 
-# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file 
-# provided by doxygen. Whatever the program writes to standard output 
-# is used as the file version. See the manual for examples.
-
 FILE_VERSION_FILTER    = 
-
 #---------------------------------------------------------------------------
 # configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
-
-# The QUIET tag can be used to turn on/off the messages that are generated 
-# by doxygen. Possible values are YES and NO. If left blank NO is used.
-
 QUIET                  = NO
-
-# The WARNINGS tag can be used to turn on/off the warning messages that are 
-# generated by doxygen. Possible values are YES and NO. If left blank 
-# NO is used.
-
 WARNINGS               = YES
-
-# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
-# for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
-# automatically be disabled.
-
 WARN_IF_UNDOCUMENTED   = YES
-
-# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for 
-# potential errors in the documentation, such as not documenting some 
-# parameters in a documented function, or documenting parameters that 
-# don't exist or using markup commands wrongly.
-
 WARN_IF_DOC_ERROR      = YES
-
-# This WARN_NO_PARAMDOC option can be abled to get warnings for 
-# functions that are documented, but have no documentation for their parameters 
-# or return value. If set to NO (the default) doxygen will only warn about 
-# wrong or incomplete parameter documentation, but not about the absence of 
-# documentation.
-
 WARN_NO_PARAMDOC       = NO
-
-# The WARN_FORMAT tag determines the format of the warning messages that 
-# doxygen can produce. The string should contain the $file, $line, and $text 
-# tags, which will be replaced by the file and line number from which the 
-# warning originated and the warning text. Optionally the format may contain 
-# $version, which will be replaced by the version of the file (if it could 
-# be obtained via FILE_VERSION_FILTER)
-
-WARN_FORMAT            = "$file:$line: $text"
-
-# The WARN_LOGFILE tag can be used to specify a file to which warning 
-# and error messages should be written. If left blank the output is written 
-# to stderr.
-
+WARN_FORMAT            = "$file:$line: $text "
 WARN_LOGFILE           = 
-
 #---------------------------------------------------------------------------
 # configuration options related to the input files
 #---------------------------------------------------------------------------
-
-# The INPUT tag can be used to specify the files and/or directories that contain 
-# documented source files. You may enter file names like "myfile.cpp" or 
-# directories like "/usr/src/myproject". Separate the files or directories 
-# with spaces.
-
-INPUT                  = ../../src ../../include
-
-# This tag can be used to specify the character encoding of the source files that 
-# doxygen parses. Internally doxygen uses the UTF-8 encoding, which is also the default 
-# input encoding. Doxygen uses libiconv (or the iconv built into libc) for the transcoding. 
-# See http://www.gnu.org/software/libiconv for the list of possible encodings.
-
+INPUT                  = ../../src \
+                         ../../include
 INPUT_ENCODING         = UTF-8
-
-# If the value of the INPUT tag contains directories, you can use the 
-# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
-# and *.h) to filter out the source-files in the directories. If left 
-# blank the following patterns are tested: 
-# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx 
-# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py
-
-FILE_PATTERNS          =  *.c *.cc *.cpp *.h *.dox
-
-# The RECURSIVE tag can be used to turn specify whether or not subdirectories 
-# should be searched for input files as well. Possible values are YES and NO. 
-# If left blank NO is used.
-
+FILE_PATTERNS          = *.c \
+                         *.cc \
+                         *.cpp \
+                         *.h \
+                         *.dox
 RECURSIVE              = YES
-
-# The EXCLUDE tag can be used to specify files and/or directories that should 
-# excluded from the INPUT source files. This way you can easily exclude a 
-# subdirectory from a directory tree whose root is specified with the INPUT tag.
-
-EXCLUDE                =
-
-# The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
-# directories that are symbolic links (a Unix filesystem feature) are excluded 
-# from the input.
-
+EXCLUDE                = ../../include/IMP/internal \
+                         ../../src/internal
 EXCLUDE_SYMLINKS       = NO
-
-# If the value of the INPUT tag contains directories, you can use the 
-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude 
-# certain files from those directories. Note that the wildcards are matched 
-# against the file with absolute path, so to exclude all test directories 
-# for example use the pattern */test/*
-
-EXCLUDE_PATTERNS       =  */tests/* \
-                          */imp_wrap.* \
-                          */imp2.py \
-                          ._*
-
-# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names 
-# (namespaces, classes, functions, etc.) that should be excluded from the output. 
-# The symbol name can be a fully qualified name, a word, or if the wildcard * is used, 
-# a substring. Examples: ANamespace, AClass, AClass::ANamespace, ANamespace::*Test
-
+EXCLUDE_PATTERNS       = */tests/* \
+                         */imp_wrap.* \
+                         */imp2.py \
+                         ._*
 EXCLUDE_SYMBOLS        = 
-
-# The EXAMPLE_PATH tag can be used to specify one or more files or 
-# directories that contain example code fragments that are included (see 
-# the \include command).
-
 EXAMPLE_PATH           = 
-
-# If the value of the EXAMPLE_PATH tag contains directories, you can use the 
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
-# and *.h) to filter out the source-files in the directories. If left 
-# blank all files are included.
-
 EXAMPLE_PATTERNS       = 
-
-# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be 
-# searched for input files to be used with the \include or \dontinclude 
-# commands irrespective of the value of the RECURSIVE tag. 
-# Possible values are YES and NO. If left blank NO is used.
-
 EXAMPLE_RECURSIVE      = NO
-
-# The IMAGE_PATH tag can be used to specify one or more files or 
-# directories that contain image that are included in the documentation (see 
-# the \image command).
-
 IMAGE_PATH             = 
-
-# The INPUT_FILTER tag can be used to specify a program that doxygen should 
-# invoke to filter for each input file. Doxygen will invoke the filter program 
-# by executing (via popen()) the command <filter> <input-file>, where <filter> 
-# is the value of the INPUT_FILTER tag, and <input-file> is the name of an 
-# input file. Doxygen will then use the output that the filter program writes 
-# to standard output.  If FILTER_PATTERNS is specified, this tag will be 
-# ignored.
-
 INPUT_FILTER           = 
-
-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern 
-# basis.  Doxygen will compare the file name with each pattern and apply the 
-# filter if there is a match.  The filters are a list of the form: 
-# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further 
-# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER 
-# is applied to all files.
-
 FILTER_PATTERNS        = 
-
-# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using 
-# INPUT_FILTER) will be used to filter the input files when producing source 
-# files to browse (i.e. when SOURCE_BROWSER is set to YES).
-
 FILTER_SOURCE_FILES    = NO
-
 #---------------------------------------------------------------------------
 # configuration options related to source browsing
 #---------------------------------------------------------------------------
-
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will 
-# be generated. Documented entities will be cross-referenced with these sources. 
-# Note: To get rid of all source code in the generated output, make sure also 
-# VERBATIM_HEADERS is set to NO.
-
 SOURCE_BROWSER         = NO
-
-# Setting the INLINE_SOURCES tag to YES will include the body 
-# of functions and classes directly in the documentation.
-
 INLINE_SOURCES         = NO
-
-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
-# doxygen to hide any special comment blocks from generated source code 
-# fragments. Normal C and C++ comments will always remain visible.
-
 STRIP_CODE_COMMENTS    = YES
-
-# If the REFERENCED_BY_RELATION tag is set to YES (the default) 
-# then for each documented function all documented 
-# functions referencing it will be listed.
-
 REFERENCED_BY_RELATION = YES
-
-# If the REFERENCES_RELATION tag is set to YES (the default) 
-# then for each documented function all documented entities 
-# called/used by that function will be listed.
-
 REFERENCES_RELATION    = YES
-
-# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
-# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
-# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
-# link to the source code.  Otherwise they will link to the documentstion.
-
 REFERENCES_LINK_SOURCE = YES
-
-# If the USE_HTAGS tag is set to YES then the references to source code 
-# will point to the HTML generated by the htags(1) tool instead of doxygen 
-# built-in source browser. The htags tool is part of GNU's global source 
-# tagging system (see http://www.gnu.org/software/global/global.html). You 
-# will need version 4.8.6 or higher.
-
 USE_HTAGS              = NO
-
-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen 
-# will generate a verbatim copy of the header file for each class for 
-# which an include is specified. Set to NO to disable this.
-
 VERBATIM_HEADERS       = YES
-
 #---------------------------------------------------------------------------
 # configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
-
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index 
-# of all compounds will be generated. Enable this if the project 
-# contains a lot of classes, structs, unions or interfaces.
-
 ALPHABETICAL_INDEX     = NO
-
-# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then 
-# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns 
-# in which this list will be split (can be a number in the range [1..20])
-
 COLS_IN_ALPHA_INDEX    = 5
-
-# In case all classes in a project start with a common prefix, all 
-# classes will be put under the same header in the alphabetical index. 
-# The IGNORE_PREFIX tag can be used to specify one or more prefixes that 
-# should be ignored while generating the index headers.
-
 IGNORE_PREFIX          = 
-
 #---------------------------------------------------------------------------
 # configuration options related to the HTML output
 #---------------------------------------------------------------------------
-
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will 
-# generate HTML output.
-
 GENERATE_HTML          = YES
-
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. 
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-# put in front of it. If left blank `html' will be used as the default path.
-
 HTML_OUTPUT            = html
-
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for 
-# each generated HTML page (for example: .htm,.php,.asp). If it is left blank 
-# doxygen will generate files with .html extension.
-
 HTML_FILE_EXTENSION    = .html
-
-# The HTML_HEADER tag can be used to specify a personal HTML header for 
-# each generated HTML page. If it is left blank doxygen will generate a 
-# standard header.
-
 HTML_HEADER            = 
-
-# The HTML_FOOTER tag can be used to specify a personal HTML footer for 
-# each generated HTML page. If it is left blank doxygen will generate a 
-# standard footer.
-
 HTML_FOOTER            = 
-
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
-# style sheet that is used by each HTML page. It can be used to 
-# fine-tune the look of the HTML output. If the tag is left blank doxygen 
-# will generate a default style sheet. Note that doxygen will try to copy 
-# the style sheet file to the HTML output directory, so don't put your own 
-# stylesheet in the HTML output directory as well, or it will be erased!
-
 HTML_STYLESHEET        = 
-
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
-# files or namespaces will be aligned in HTML using tables. If set to 
-# NO a bullet list will be used.
-
 HTML_ALIGN_MEMBERS     = YES
-
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files 
-# will be generated that can be used as input for tools like the 
-# Microsoft HTML help workshop to generate a compressed HTML help file (.chm) 
-# of the generated HTML documentation.
-
 GENERATE_HTMLHELP      = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can 
-# be used to specify the file name of the resulting .chm file. You 
-# can add a path in front of the file if the result should not be 
-# written to the html output directory.
-
+HTML_DYNAMIC_SECTIONS  = NO
 CHM_FILE               = 
-
-# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can 
-# be used to specify the location (absolute path including file name) of 
-# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run 
-# the HTML help compiler on the generated index.hhp.
-
 HHC_LOCATION           = 
-
-# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag 
-# controls if a separate .chi index file is generated (YES) or that 
-# it should be included in the master .chm file (NO).
-
 GENERATE_CHI           = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag 
-# controls whether a binary table of contents is generated (YES) or a 
-# normal table of contents (NO) in the .chm file.
-
 BINARY_TOC             = NO
-
-# The TOC_EXPAND flag can be set to YES to add extra items for group members 
-# to the contents of the HTML help documentation and to the tree view.
-
 TOC_EXPAND             = NO
-
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index at 
-# top of each HTML page. The value NO (the default) enables the index and 
-# the value YES disables it.
-
 DISABLE_INDEX          = NO
-
-# This tag can be used to set the number of enum values (range [1..20]) 
-# that doxygen will group on one line in the generated HTML documentation.
-
 ENUM_VALUES_PER_LINE   = 4
-
-# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
-# generated containing a tree-like index structure (just like the one that 
-# is generated for HTML Help). For this to work a browser that supports 
-# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, 
-# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are 
-# probably better off using the HTML help feature.
-
 GENERATE_TREEVIEW      = NO
-
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be 
-# used to set the initial width (in pixels) of the frame in which the tree 
-# is shown.
-
 TREEVIEW_WIDTH         = 250
-
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
-
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
-# generate Latex output.
-
 GENERATE_LATEX         = NO
-
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. 
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-# put in front of it. If left blank `latex' will be used as the default path.
-
 LATEX_OUTPUT           = latex
-
-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be 
-# invoked. If left blank `latex' will be used as the default command name.
-
 LATEX_CMD_NAME         = latex
-
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to 
-# generate index for LaTeX. If left blank `makeindex' will be used as the 
-# default command name.
-
 MAKEINDEX_CMD_NAME     = makeindex
-
-# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact 
-# LaTeX documents. This may be useful for small projects and may help to 
-# save some trees in general.
-
 COMPACT_LATEX          = NO
-
-# The PAPER_TYPE tag can be used to set the paper type that is used 
-# by the printer. Possible values are: a4, a4wide, letter, legal and 
-# executive. If left blank a4wide will be used.
-
 PAPER_TYPE             = a4wide
-
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX 
-# packages that should be included in the LaTeX output.
-
 EXTRA_PACKAGES         = 
-
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for 
-# the generated latex document. The header should contain everything until 
-# the first chapter. If it is left blank doxygen will generate a 
-# standard header. Notice: only use this tag if you know what you are doing!
-
 LATEX_HEADER           = 
-
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated 
-# is prepared for conversion to pdf (using ps2pdf). The pdf file will 
-# contain links (just like the HTML output) instead of page references 
-# This makes the output suitable for online browsing using a pdf viewer.
-
 PDF_HYPERLINKS         = NO
-
-# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of 
-# plain latex in the generated Makefile. Set this option to YES to get a 
-# higher quality PDF documentation.
-
 USE_PDFLATEX           = NO
-
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode. 
-# command to the generated LaTeX files. This will instruct LaTeX to keep 
-# running if errors occur, instead of asking the user for help. 
-# This option is also used when generating formulas in HTML.
-
 LATEX_BATCHMODE        = NO
-
-# If LATEX_HIDE_INDICES is set to YES then doxygen will not 
-# include the index chapters (such as File Index, Compound Index, etc.) 
-# in the output.
-
 LATEX_HIDE_INDICES     = NO
-
 #---------------------------------------------------------------------------
 # configuration options related to the RTF output
 #---------------------------------------------------------------------------
-
-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output 
-# The RTF output is optimized for Word 97 and may not look very pretty with 
-# other RTF readers or editors.
-
 GENERATE_RTF           = NO
-
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. 
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-# put in front of it. If left blank `rtf' will be used as the default path.
-
 RTF_OUTPUT             = rtf
-
-# If the COMPACT_RTF tag is set to YES Doxygen generates more compact 
-# RTF documents. This may be useful for small projects and may help to 
-# save some trees in general.
-
 COMPACT_RTF            = NO
-
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated 
-# will contain hyperlink fields. The RTF file will 
-# contain links (just like the HTML output) instead of page references. 
-# This makes the output suitable for online browsing using WORD or other 
-# programs which support those fields. 
-# Note: wordpad (write) and others do not support links.
-
 RTF_HYPERLINKS         = NO
-
-# Load stylesheet definitions from file. Syntax is similar to doxygen's 
-# config file, i.e. a series of assignments. You only have to provide 
-# replacements, missing definitions are set to their default value.
-
 RTF_STYLESHEET_FILE    = 
-
-# Set optional variables used in the generation of an rtf document. 
-# Syntax is similar to doxygen's config file.
-
 RTF_EXTENSIONS_FILE    = 
-
 #---------------------------------------------------------------------------
 # configuration options related to the man page output
 #---------------------------------------------------------------------------
-
-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will 
-# generate man pages
-
 GENERATE_MAN           = NO
-
-# The MAN_OUTPUT tag is used to specify where the man pages will be put. 
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-# put in front of it. If left blank `man' will be used as the default path.
-
 MAN_OUTPUT             = man
-
-# The MAN_EXTENSION tag determines the extension that is added to 
-# the generated man pages (default is the subroutine's section .3)
-
 MAN_EXTENSION          = .3
-
-# If the MAN_LINKS tag is set to YES and Doxygen generates man output, 
-# then it will generate one additional man file for each entity 
-# documented in the real man page(s). These additional files 
-# only source the real man page, but without them the man command 
-# would be unable to find the correct page. The default is NO.
-
 MAN_LINKS              = NO
-
 #---------------------------------------------------------------------------
 # configuration options related to the XML output
 #---------------------------------------------------------------------------
-
-# If the GENERATE_XML tag is set to YES Doxygen will 
-# generate an XML file that captures the structure of 
-# the code including all documentation.
-
 GENERATE_XML           = NO
-
-# The XML_OUTPUT tag is used to specify where the XML pages will be put. 
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
-# put in front of it. If left blank `xml' will be used as the default path.
-
 XML_OUTPUT             = xml
-
-# The XML_SCHEMA tag can be used to specify an XML schema, 
-# which can be used by a validating XML parser to check the 
-# syntax of the XML files.
-
 XML_SCHEMA             = 
-
-# The XML_DTD tag can be used to specify an XML DTD, 
-# which can be used by a validating XML parser to check the 
-# syntax of the XML files.
-
 XML_DTD                = 
-
-# If the XML_PROGRAMLISTING tag is set to YES Doxygen will 
-# dump the program listings (including syntax highlighting 
-# and cross-referencing information) to the XML output. Note that 
-# enabling this will significantly increase the size of the XML output.
-
 XML_PROGRAMLISTING     = YES
-
 #---------------------------------------------------------------------------
 # configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
-
-# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will 
-# generate an AutoGen Definitions (see autogen.sf.net) file 
-# that captures the structure of the code including all 
-# documentation. Note that this feature is still experimental 
-# and incomplete at the moment.
-
 GENERATE_AUTOGEN_DEF   = NO
-
 #---------------------------------------------------------------------------
 # configuration options related to the Perl module output
 #---------------------------------------------------------------------------
-
-# If the GENERATE_PERLMOD tag is set to YES Doxygen will 
-# generate a Perl module file that captures the structure of 
-# the code including all documentation. Note that this 
-# feature is still experimental and incomplete at the 
-# moment.
-
 GENERATE_PERLMOD       = NO
-
-# If the PERLMOD_LATEX tag is set to YES Doxygen will generate 
-# the necessary Makefile rules, Perl scripts and LaTeX code to be able 
-# to generate PDF and DVI output from the Perl module output.
-
 PERLMOD_LATEX          = NO
-
-# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be 
-# nicely formatted so it can be parsed by a human reader.  This is useful 
-# if you want to understand what is going on.  On the other hand, if this 
-# tag is set to NO the size of the Perl module output will be much smaller 
-# and Perl will parse it just the same.
-
 PERLMOD_PRETTY         = YES
-
-# The names of the make variables in the generated doxyrules.make file 
-# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. 
-# This is useful so different doxyrules.make files included by the same 
-# Makefile don't overwrite each other's variables.
-
 PERLMOD_MAKEVAR_PREFIX = 
-
 #---------------------------------------------------------------------------
 # Configuration options related to the preprocessor   
 #---------------------------------------------------------------------------
-
-# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will 
-# evaluate all C-preprocessor directives found in the sources and include 
-# files.
-
 ENABLE_PREPROCESSING   = YES
-
-# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro 
-# names in the source code. If set to NO (the default) only conditional 
-# compilation will be performed. Macro expansion can be done in a controlled 
-# way by setting EXPAND_ONLY_PREDEF to YES.
-
 MACRO_EXPANSION        = YES
-
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES 
-# then the macro expansion is limited to the macros specified with the 
-# PREDEFINED and EXPAND_AS_DEFINED tags.
-
 EXPAND_ONLY_PREDEF     = NO
-
-# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files 
-# in the INCLUDE_PATH (see below) will be search if a #include is found.
-
 SEARCH_INCLUDES        = YES
-
-# The INCLUDE_PATH tag can be used to specify one or more directories that 
-# contain include files that are not input files but should be processed by 
-# the preprocessor.
-
 INCLUDE_PATH           = 
-
-# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard 
-# patterns (like *.h and *.hpp) to filter out the header-files in the 
-# directories. If left blank, the patterns specified with FILE_PATTERNS will 
-# be used.
-
 INCLUDE_FILE_PATTERNS  = 
-
-# The PREDEFINED tag can be used to specify one or more macro names that 
-# are defined before the preprocessor is started (similar to the -D option of 
-# gcc). The argument of the tag is a list of macros of the form: name 
-# or name=definition (no spaces). If the definition and the = are 
-# omitted =1 is assumed. To prevent a macro definition from being 
-# undefined via #undef or recursively expanded use the := operator 
-# instead of the = operator.
-
 PREDEFINED             = 
-
-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then 
-# this tag can be used to specify a list of macro names that should be expanded. 
-# The macro definition that is found in the sources will be used. 
-# Use the PREDEFINED tag if you want to use a different macro definition.
-
 EXPAND_AS_DEFINED      = 
-
-# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then 
-# doxygen's preprocessor will remove all function-like macros that are alone 
-# on a line, have an all uppercase name, and do not end with a semicolon. Such 
-# function macros are typically used for boiler-plate code, and will confuse 
-# the parser if not removed.
-
 SKIP_FUNCTION_MACROS   = YES
-
 #---------------------------------------------------------------------------
 # Configuration::additions related to external references   
 #---------------------------------------------------------------------------
-
-# The TAGFILES option can be used to specify one or more tagfiles. 
-# Optionally an initial location of the external documentation 
-# can be added for each tagfile. The format of a tag file without 
-# this location is as follows: 
-#   TAGFILES = file1 file2 ... 
-# Adding location for the tag files is done as follows: 
-#   TAGFILES = file1=loc1 "file2 = loc2" ... 
-# where "loc1" and "loc2" can be relative or absolute paths or 
-# URLs. If a location is present for each tag, the installdox tool 
-# does not have to be run to correct the links.
-# Note that each tag file must have a unique name
-# (where the name does NOT include the path)
-# If a tag file is not located in the directory in which doxygen 
-# is run, you must also specify the path to the tagfile here.
-
 TAGFILES               = 
-
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create 
-# a tag file that is based on the input files it reads.
-
 GENERATE_TAGFILE       = 
-
-# If the ALLEXTERNALS tag is set to YES all external classes will be listed 
-# in the class index. If set to NO only the inherited external classes 
-# will be listed.
-
 ALLEXTERNALS           = NO
-
-# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed 
-# in the modules index. If set to NO, only the current project's groups will 
-# be listed.
-
 EXTERNAL_GROUPS        = YES
-
-# The PERL_PATH should be the absolute path and name of the perl script 
-# interpreter (i.e. the result of `which perl').
-
 PERL_PATH              = /usr/bin/perl
-
 #---------------------------------------------------------------------------
 # Configuration options related to the dot tool   
 #---------------------------------------------------------------------------
-
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will 
-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base 
-# or super classes. Setting the tag to NO turns the diagrams off. Note that 
-# this option is superseded by the HAVE_DOT option below. This is only a 
-# fallback. It is recommended to install and use dot, since it yields more 
-# powerful graphs.
-
 CLASS_DIAGRAMS         = YES
-
-# You can define message sequence charts within doxygen comments using the \msc 
-# command. Doxygen will then run the mscgen tool (see http://www.mcternan.me.uk/mscgen/) to 
-# produce the chart and insert it in the documentation. The MSCGEN_PATH tag allows you to 
-# specify the directory where the mscgen tool resides. If left empty the tool is assumed to 
-# be found in the default search path.
-
 MSCGEN_PATH            = 
-
-# If set to YES, the inheritance and collaboration graphs will hide 
-# inheritance and usage relations if the target is undocumented 
-# or is not a class.
-
 HIDE_UNDOC_RELATIONS   = YES
-
-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is 
-# available from the path. This tool is part of Graphviz, a graph visualization 
-# toolkit from AT&T and Lucent Bell Labs. The other options in this section 
-# have no effect if this option is set to NO (the default)
-
 HAVE_DOT               = NO
-
-# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
-# will generate a graph for each documented class showing the direct and 
-# indirect inheritance relations. Setting this tag to YES will force the 
-# the CLASS_DIAGRAMS tag to NO.
-
 CLASS_GRAPH            = YES
-
-# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen 
-# will generate a graph for each documented class showing the direct and 
-# indirect implementation dependencies (inheritance, containment, and 
-# class references variables) of the class with other documented classes.
-
 COLLABORATION_GRAPH    = YES
-
-# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen 
-# will generate a graph for groups, showing the direct groups dependencies
-
 GROUP_GRAPHS           = YES
-
-# If the UML_LOOK tag is set to YES doxygen will generate inheritance and 
-# collaboration diagrams in a style similar to the OMG's Unified Modeling 
-# Language.
-
 UML_LOOK               = NO
-
-# If set to YES, the inheritance and collaboration graphs will show the 
-# relations between templates and their instances.
-
 TEMPLATE_RELATIONS     = NO
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT 
-# tags are set to YES then doxygen will generate a graph for each documented 
-# file showing the direct and indirect include dependencies of the file with 
-# other documented files.
-
 INCLUDE_GRAPH          = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and 
-# HAVE_DOT tags are set to YES then doxygen will generate a graph for each 
-# documented header file showing the documented files that directly or 
-# indirectly include this file.
-
 INCLUDED_BY_GRAPH      = YES
-
-# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will 
-# generate a call dependency graph for every global function or class method. 
-# Note that enabling this option will significantly increase the time of a run. 
-# So in most cases it will be better to enable call graphs for selected 
-# functions only using the \callgraph command.
-
 CALL_GRAPH             = NO
-
-# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then doxygen will 
-# generate a caller dependency graph for every global function or class method. 
-# Note that enabling this option will significantly increase the time of a run. 
-# So in most cases it will be better to enable caller graphs for selected 
-# functions only using the \callergraph command.
-
 CALLER_GRAPH           = NO
-
-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen 
-# will graphical hierarchy of all classes instead of a textual one.
-
 GRAPHICAL_HIERARCHY    = YES
-
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES 
-# then doxygen will show the dependencies a directory has on other directories 
-# in a graphical way. The dependency relations are determined by the #include
-# relations between the files in the directories.
-
 DIRECTORY_GRAPH        = YES
-
-# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images 
-# generated by dot. Possible values are png, jpg, or gif
-# If left blank png will be used.
-
 DOT_IMAGE_FORMAT       = png
-
-# The tag DOT_PATH can be used to specify the path where the dot tool can be 
-# found. If left blank, it is assumed the dot tool can be found in the path.
-
 DOT_PATH               = 
-
-# The DOTFILE_DIRS tag can be used to specify one or more directories that 
-# contain dot files that are included in the documentation (see the 
-# \dotfile command).
-
 DOTFILE_DIRS           = 
-
-# The MAX_DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of 
-# nodes that will be shown in the graph. If the number of nodes in a graph 
-# becomes larger than this value, doxygen will truncate the graph, which is 
-# visualized by representing a node as a red box. Note that doxygen will always 
-# show the root nodes and its direct children regardless of this setting.
-
 DOT_GRAPH_MAX_NODES    = 50
-
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent 
-# background. This is disabled by default, which results in a white background. 
-# Warning: Depending on the platform used, enabling this option may lead to 
-# badly anti-aliased labels on the edges of a graph (i.e. they become hard to 
-# read).
-
+MAX_DOT_GRAPH_DEPTH    = 1000
 DOT_TRANSPARENT        = NO
-
-# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output 
-# files in one run (i.e. multiple -o and -T options on the command line). This 
-# makes dot run faster, but since only newer versions of dot (>1.8.10) 
-# support this, this feature is disabled by default.
-
 DOT_MULTI_TARGETS      = NO
-
-# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will 
-# generate a legend page explaining the meaning of the various boxes and 
-# arrows in the dot generated graphs.
-
 GENERATE_LEGEND        = YES
-
-# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will 
-# remove the intermediate dot files that are used to generate 
-# the various graphs.
-
 DOT_CLEANUP            = YES
-
 #---------------------------------------------------------------------------
 # Configuration::additions related to the search engine   
 #---------------------------------------------------------------------------
-
-# The SEARCHENGINE tag specifies whether or not a search engine should be 
-# used. If set to NO the values of all tags below this one will be ignored.
-
 SEARCHENGINE           = NO
Index: kernel/src/SConscript
===================================================================
--- kernel/src/SConscript	(revision 368)
+++ kernel/src/SConscript	(working copy)
@@ -14,15 +14,16 @@
 singleton_scores_files = SConscript('singleton_scores/SConscript')
 triplet_scores_files = SConscript('triplet_scores/SConscript')
 score_states_files = SConscript('score_states/SConscript')
+internal_files = SConscript('internal/SConscript')
# Source files
 files = ['base_types.cpp', 'Model.cpp', 'ModelData.cpp',
-         'Particle.cpp', 'RigidBody.cpp', 'ScoreState.cpp',
+         'Particle.cpp', 'ScoreState.cpp',
          'OptimizerState.cpp', 'Log.cpp', 'Restraint.cpp', 'Optimizer.cpp',
          'Object.cpp', 'BasicScoreFuncParams.cpp', 'random.cpp'
         ] + decorators_files + restraints_files + optimizers_files \
           + unary_functions_files + pair_scores_files + singleton_scores_files \
-          + triplet_scores_files + score_states_files
+          + triplet_scores_files + score_states_files + internal_files
# Build the shared library:
 lib = env.SharedLibrary('imp', files)
Index: kernel/src/ScoreState.cpp
===================================================================
--- kernel/src/ScoreState.cpp	(revision 368)
+++ kernel/src/ScoreState.cpp	(working copy)
@@ -5,12 +5,11 @@
  *
  */
-#include <cmath>
-
-#include "IMP/ModelData.h"
 #include "IMP/log.h"
 #include "IMP/ScoreState.h"
+#include <cmath>
+
 namespace IMP
 {
Index: kernel/src/RigidBody.cpp
===================================================================
--- kernel/src/RigidBody.cpp	(revision 368)
+++ kernel/src/RigidBody.cpp	(working copy)
@@ -1,43 +0,0 @@
-/**
- *  \file RigidBody.cpp \brief Class for grouping particles into rigid bodies.
- *
- *  Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-
-#include "IMP/RigidBody.h"
-
-namespace IMP
-{
-
-//! Constructor
-RigidBody::RigidBody()
-{
-}
-
-
-//! Destructor
-RigidBody::~RigidBody()
-{
-}
-
-
-//! Set number of particles in the rigid body.
-/** \param[in] num_particles Number of particles.
- */
-void RigidBody::set_num_particles(int num_particles)
-{
-  num_particles_ = num_particles;
-}
-
-//! Get the number of particles in the rigid body.
-/** \return Number of particles in the body.
- */
-int RigidBody::get_num_particles() const
-{
-  return num_particles_;
-}
-
-
-}  // namespace IMP
Index: kernel/src/score_states/NonbondedListScoreState.cpp
===================================================================
--- kernel/src/score_states/NonbondedListScoreState.cpp	(revision 368)
+++ kernel/src/score_states/NonbondedListScoreState.cpp	(working copy)
@@ -7,7 +7,7 @@
#include "IMP/score_states/NonbondedListScoreState.h"
 #include "IMP/decorators/XYZDecorator.h"
-#include "IMP/Grid3D.h"
+#include "IMP/internal/Grid3D.h"
 #include "IMP/score_states/MaxChangeScoreState.h"
namespace IMP
Index: kernel/src/score_states/BipartiteNonbondedListScoreState.cpp
===================================================================
--- kernel/src/score_states/BipartiteNonbondedListScoreState.cpp	(revision 368)
+++ kernel/src/score_states/BipartiteNonbondedListScoreState.cpp	(working copy)
@@ -7,7 +7,7 @@
#include "IMP/score_states/BipartiteNonbondedListScoreState.h"
 #include "IMP/decorators/XYZDecorator.h"
-#include "IMP/Grid3D.h"
+#include "IMP/internal/Grid3D.h"
namespace IMP
 {
Index: kernel/src/restraints/RestraintSet.cpp
===================================================================
--- kernel/src/restraints/RestraintSet.cpp	(revision 368)
+++ kernel/src/restraints/RestraintSet.cpp	(working copy)
@@ -6,7 +6,6 @@
  */
-#include "IMP/ModelData.h"
 #include "IMP/log.h"
 #include "IMP/restraints/RestraintSet.h"
 #include "../mystdexcept.h"
Index: kernel/src/OptimizerState.cpp
===================================================================
--- kernel/src/OptimizerState.cpp	(revision 368)
+++ kernel/src/OptimizerState.cpp	(working copy)
@@ -5,9 +5,7 @@
  *
  */
-#include <cmath>
-#include "IMP/ModelData.h"
 #include "IMP/log.h"
 #include "IMP/OptimizerState.h"
Index: kernel/src/optimizers/ConjugateGradients.cpp
===================================================================
--- kernel/src/optimizers/ConjugateGradients.cpp	(revision 368)
+++ kernel/src/optimizers/ConjugateGradients.cpp	(working copy)
@@ -10,6 +10,7 @@
 #include "IMP/log.h"
 #include "IMP/optimizers/ConjugateGradients.h"
 #include "IMP/Model.h"
+#include "IMP/ModelData.h"
 #include <limits>
namespace IMP
Index: kernel/src/optimizers/SteepestDescent.cpp
===================================================================
--- kernel/src/optimizers/SteepestDescent.cpp	(revision 368)
+++ kernel/src/optimizers/SteepestDescent.cpp	(working copy)
@@ -8,6 +8,7 @@
 #include "IMP/log.h"
 #include "IMP/optimizers/SteepestDescent.h"
 #include "IMP/Model.h"
+#include "IMP/ModelData.h"
namespace IMP
 {
Index: kernel/src/decorators/SConscript
===================================================================
--- kernel/src/decorators/SConscript	(revision 368)
+++ kernel/src/decorators/SConscript	(working copy)
@@ -1,6 +1,6 @@
 Import('env')
-files = ['AtomDecorator.cpp', 'bond_decorators.cpp', 'graph_base.cpp',
+files = ['AtomDecorator.cpp', 'bond_decorators.cpp',
          'HierarchyDecorator.cpp', 'NameDecorator.cpp', 'ResidueDecorator.cpp',
          'MolecularHierarchyDecorator.cpp', 'XYZDecorator.cpp']
Index: kernel/src/decorators/graph_base.cpp
===================================================================
--- kernel/src/decorators/graph_base.cpp	(revision 368)
+++ kernel/src/decorators/graph_base.cpp	(working copy)
@@ -1,129 +0,0 @@
-/**
- *  \file graph_base.cpp   \brief classes for implementing a graph.
- *
- *  Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#include <sstream>
-
-#include "IMP/decorators/graph_base.h"
-
-namespace IMP
-{
-
-namespace internal
-{
-
-static void graph_add_edge_key(unsigned int i, const GraphData &d)
-{
-  while (i >= d.edge_keys_.size()) {
-    std::ostringstream oss;
-    oss << d.prefix_ << " edge " << i;
-    d.edge_keys_.push_back(IntKey(oss.str().c_str()));
-  }
-}
-
-static IntKey graph_get_edge_key(unsigned int i, const GraphData &d)
-{
-  if (i >= d.edge_keys_.size()) graph_add_edge_key(i, d);
-  return d.edge_keys_[i];
-}
-
-Particle* graph_connect(Particle* a, Particle* b, const GraphData &d)
-{
-  Model *m= a->get_model();
-  Particle *p= new Particle();
-  ParticleIndex pi=m->add_particle(p);
-  p->add_attribute(d.node_keys_[0], a->get_index().get_index());
-  p->add_attribute(d.node_keys_[1], b->get_index().get_index());
-  for (int i=0; i< 2; ++i) {
-    Particle *cp=((i==0)?a:b);
-    int nc= graph_get_number_of_edges(cp, d);
-    IntKey nm=graph_get_edge_key(nc, d);
-    if (!cp->has_attribute(nm)) {
-      cp->add_attribute(nm, p->get_index().get_index());
-    } else {
-      cp->set_value(nm, p->get_index().get_index());
-    }
-    if (cp->has_attribute(d.num_edges_key_)) {
-      cp->set_value(d.num_edges_key_, nc+1);
-    } else {
-      cp->add_attribute(d.num_edges_key_, nc+1);
-    }
-  }
-
-  return a->get_model()->get_particle(pi);
-}
-
-void graph_disconnect(Particle* e, const GraphData &d)
-{
-  ParticleIndex pi=e->get_index();
-  Particle *p[2];
-  p[0]= graph_get_node(e, 0, d);
-  p[1]= graph_get_node(e, 1, d);
-  for (int i=0; i< 2; ++i) {
-    int shift=0;
-    Int nc= p[i]->get_value(d.num_edges_key_);
-    for (int j=0; j< nc; ++j) {
-      if (graph_get_edge(p[i], j, d) == e) {
-        IMP_assert(shift==0, "duplicate edges found in graph_base");
-        shift=-1;
-      } else {
-        Int v = p[i]->get_value(graph_get_edge_key(j, d));
-        p[i]->set_value(graph_get_edge_key(j+shift, d), v);
-      }
-    }
-    p[i]->set_value(graph_get_edge_key(nc-1, d), -1);
-    IMP_assert(shift==-1, "no edge found");
-    IMP_assert(nc > 0, "Too few edges");
-    p[i]->set_value(d.num_edges_key_, nc-1);
-  }
-  e->set_is_active(false);
-}
-
-
-
-Particle* graph_get_edge(Particle* a, int i, const GraphData &d)
-{
-  IntKey nm= graph_get_edge_key(i, d);
-  return a->get_model()->get_particle(ParticleIndex(a->get_value(nm)));
-}
-
-Particle* graph_get_neighbor(Particle* a, int i, const GraphData &d)
-{
-  IntKey nm= graph_get_edge_key(i, d);
-  Particle *edge= a->get_model()->get_particle(ParticleIndex(a->get_value(nm)));
-  if (graph_get_node(edge, 0, d) == a) {
-    return graph_get_node(edge, 1, d);
-  } else {
-    IMP_assert(graph_get_node(edge, 1, d) == a,
-               "Broken graph");
-    return graph_get_node(edge, 0, d);
-  }
-}
-
-unsigned int graph_get_number_of_edges(Particle *a, const GraphData &d)
-{
-  if (a->has_attribute(d.num_edges_key_)) {
-    return a->get_value(d.num_edges_key_);
-  } else {
-    return 0;
-  }
-}
-
-Particle* graph_get_node(Particle *a, int i, const GraphData &d)
-{
-  IMP_assert(i<2, "bad node requested");
-  return a->get_model()->get_particle(a->get_value(d.node_keys_[i]));
-}
-
-bool graph_is_edge(Particle *a, const GraphData &d)
-{
-  return a->has_attribute(d.node_keys_[0])
-         && a->has_attribute(d.node_keys_[1]);
-}
-
-} // namespace internal
-
-} // namespace IMP
Index: kernel/src/internal/graph_base.cpp
===================================================================
--- kernel/src/internal/graph_base.cpp	(revision 0)
+++ kernel/src/internal/graph_base.cpp	(working copy)
@@ -7,7 +7,7 @@
#include <sstream>
-#include "IMP/decorators/graph_base.h"
+#include "IMP/internal/graph_base.h"
namespace IMP
 {
Index: kernel/pyext/IMP.i
===================================================================
--- kernel/pyext/IMP.i	(revision 368)
+++ kernel/pyext/IMP.i	(working copy)
@@ -95,7 +95,6 @@
 %include "IMP/unary_functions/OpenCubicSpline.h"
 %include "IMP/unary_functions/Cosine.h"
 %include "IMP/ScoreFuncParams.h"
-%include "IMP/ModelData.h"
 %include "IMP/DerivativeAccumulator.h"
 %include "IMP/Restraint.h"
 %include "IMP/restraints/RestraintSet.h"
@@ -114,7 +113,6 @@
 %include "IMP/decorators/NameDecorator.h"
 %include "IMP/decorators/ResidueDecorator.h"
 %include "IMP/decorators/XYZDecorator.h"
-%include "IMP/decorators/graph_base.h"
 %include "IMP/decorators/bond_decorators.h"
 %include "IMP/decorators/AtomDecorator.h"
 %include "IMP/Optimizer.h"
@@ -149,7 +147,6 @@
 %include "IMP/score_states/NonbondedListScoreState.h"
 %include "IMP/score_states/BipartiteNonbondedListScoreState.h"
 %include "IMP/score_states/bonded_lists/BondDecoratorListScoreState.h"
-%include "IMP/RigidBody.h"
namespace IMP {
   %template(IntIndex) Index<Int>;

    

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