Index: kernel/test/particle_refiners/test_refine_once_ps.py
===================================================================
--- kernel/test/particle_refiners/test_refine_once_ps.py	(revision 0)
+++ kernel/test/particle_refiners/test_refine_once_ps.py	(revision 0)
@@ -0,0 +1,35 @@
+import unittest
+import IMP
+import IMP.test
+
+rk = IMP.FloatKey("radius")
+
+class Test(IMP.test.TestCase):
+    """Tests for bond refiner"""
+
+
+    def test_rops(self):
+        """Make sure that bond cover coordinates are correct"""
+        IMP.set_log_level(IMP.VERBOSE)
+        m= IMP.Model()
+        pp= IMP.Particle()
+        m.add_particle(pp)
+        hpp= IMP.HierarchyDecorator.create(pp)
+        c=[]
+        for i in range(0,10):
+            p= IMP.Particle()
+            m.add_particle(p)
+            hp= IMP.HierarchyDecorator.create(p)
+            hpp.add_child(hp)
+            c.append(p)
+        pr= IMP.ChildrenParticleRefiner()
+        cps= IMP.test.ConstPairScore(1)
+        rps= IMP.RefineOncePairScore(pr, cps)
+        self.assertEqual(rps.evaluate(pp, pp, None), 100)
+
+       
+
+
+
+if __name__ == '__main__':
+    unittest.main()
Index: kernel/src/pair_scores/RefineOncePairScore.cpp
===================================================================
--- kernel/src/pair_scores/RefineOncePairScore.cpp	(revision 0)
+++ kernel/src/pair_scores/RefineOncePairScore.cpp	(revision 0)
@@ -0,0 +1,62 @@
+/**
+ *  \file RefineOncePairScore.cpp
+ *  \brief A bond cover pair score.
+ *
+ *  Copyright 2007-8 Sali Lab. All rights reserved.
+ */
+
+#include "IMP/pair_scores/RefineOncePairScore.h"
+#include "IMP/decorators/bond_decorators.h"
+#include "IMP/decorators/XYZDecorator.h"
+#include "IMP/internal/constants.h"
+
+#include <cmath>
+
+namespace IMP
+{
+
+RefineOncePairScore::RefineOncePairScore(ParticleRefiner *r, 
+                                         PairScore *f): r_(r), f_(f) {}
+
+Float RefineOncePairScore::evaluate(Particle *a, Particle *b,
+                                  DerivativeAccumulator *da)
+{
+  Particle* p[2]={a,b};
+  Particles ps[2];
+  for (unsigned int i=0; i< 2; ++i) {
+    if (r_->get_can_refine(p[i])) {
+      ps[i]= r_->get_refined(p[i]);
+    } else {
+      ps[i].push_back(p[i]);
+    }
+    IMP_LOG(VERBOSE, "Refining " << p[i]->get_index()
+            << " resulted in " << ps[i].size() << " particles"
+            << std::endl);
+  }
+
+  Float ret=0;
+  for (unsigned int i=0; i< ps[0].size(); ++i) {
+    for (unsigned int j=0; j< ps[1].size(); ++j) {
+      ret+=f_->evaluate(ps[0][i], ps[1][j], da);
+    }
+  }
+
+  for (unsigned int i=0; i< 2; ++i) {
+    if (ps[i].size() != 1 || ps[i].size()==1 && ps[i][0] != p[i]) {
+      IMP_LOG(VERBOSE, "Refining " << p[i]->get_index()
+              << " resulted in " << ps[i].size() << " particles"
+              << std::endl);
+      r_->cleanup_refined(p[i], ps[i], da);
+    }
+  }
+  return ret;
+}
+
+void RefineOncePairScore::show(std::ostream &out) const
+{
+  out << "RefineOncePairScore using ";
+  f_->show(out);
+  r_->show(out);
+}
+
+} // namespace IMP
Index: kernel/include/IMP/pair_scores/RefineOncePairScore.h
===================================================================
--- kernel/include/IMP/pair_scores/RefineOncePairScore.h	(revision 0)
+++ kernel/include/IMP/pair_scores/RefineOncePairScore.h	(revision 0)
@@ -0,0 +1,44 @@
+/**
+ *  \file RefineOncePairScore.h    
+ *  \brief For particles that are bonds, exand the pairticle
+ *     into several so as to conserve the volume.
+ *
+ *  Copyright 2007-8 Sali Lab. All rights reserved.
+ */
+
+#ifndef __IMP_REFINE_ONCE_PAIR_SCORE_H
+#define __IMP_REFINE_ONCE_PAIR_SCORE_H
+
+#include "../PairScore.h"
+#include "../UnaryFunction.h"
+#include "../ParticleRefiner.h"
+#include "../internal/ObjectPointer.h"
+
+namespace IMP
+{
+
+//! Refine the input particles at most once with the ParticleRefiner.
+/** Each passed particle is refined once before the resulting pairs
+    have the pair score called on them.
+
+    \ingroup pairscore
+ */
+class IMPDLLEXPORT RefineOncePairScore : public PairScore
+{
+  internal::ObjectPointer<ParticleRefiner, true> r_;
+  internal::ObjectPointer<PairScore, true> f_;
+
+public:
+  /** \param[in] r The ParticleRefiner to call on each particle
+      \param[in] f The pair score to apply to the generated pairs
+*/
+  RefineOncePairScore(ParticleRefiner *r, PairScore *f);
+  virtual ~RefineOncePairScore(){}
+  virtual Float evaluate(Particle *a, Particle *b,
+                         DerivativeAccumulator *da);
+  virtual void show(std::ostream &out=std::cout) const;
+};
+
+} // namespace IMP
+
+#endif  /* __IMP_REFINE_ONCE_PAIR_SCORE_H */
Index: kernel/include/IMP.h
===================================================================
--- kernel/include/IMP.h	(revision 606)
+++ kernel/include/IMP.h	(working copy)
@@ -55,6 +55,7 @@
 #include "IMP/optimizers/states/VelocityScalingOptimizerState.h"
 #include "IMP/pair_scores/DistancePairScore.h"
 #include "IMP/pair_scores/SphereDistancePairScore.h"
+#include "IMP/pair_scores/RefineOncePairScore.h"
 #include "IMP/singleton_scores/DistanceToSingletonScore.h"
 #include "IMP/singleton_scores/AttributeSingletonScore.h"
 #include "IMP/triplet_scores/AngleTripletScore.h"
Index: kernel/src/pair_scores/SConscript
===================================================================
--- kernel/src/pair_scores/SConscript	(revision 606)
+++ kernel/src/pair_scores/SConscript	(working copy)
@@ -1,6 +1,7 @@
 Import('env')
 
-files = ['DistancePairScore.cpp', 'SphereDistancePairScore.cpp']
+files = ['DistancePairScore.cpp', 'SphereDistancePairScore.cpp',
+            'RefineOncePairScore.cpp']
 
 files = [File(x) for x in files]
 Return('files')
Index: kernel/pyext/IMP.i
===================================================================
--- kernel/pyext/IMP.i	(revision 606)
+++ kernel/pyext/IMP.i	(working copy)
@@ -78,9 +78,16 @@
   %pythonprepend DistancePairScore::DistancePairScore %{
         args[0].thisown=0
   %}
+  %pythonprepend BondCoverPairScore::BondCoverPairScore %{
+        args[0].thisown=0
+  %}
   %pythonprepend SphereDistancePairScore::SphereDistancePairScore %{
         args[0].thisown=0
   %}
+  %pythonprepend RefineOncePairScore::RefineOncePairScore %{
+        args[0].thisown=0
+        args[1].thisown=0
+  %}
   %pythonprepend DistanceToSingletonScore::DistanceToSingletonScore %{
         args[0].thisown=0
   %}
@@ -96,6 +103,9 @@
   %pythonprepend MonteCarlo::set_local_optimizer %{
         args[1].thisown=0
   %}
+  %pythonprepend VRMLLogOptimizerState::add_particle_refiner %{
+        args[1].thisown=0
+  %}
   %pythonprepend Particle::get_value %{
         check_particle(args[0], args[1])
   %}
@@ -167,6 +177,7 @@
 %include "IMP/log.h"
 %include "IMP/Model.h"
 %include "IMP/PairScore.h"
+%include "IMP/ParticleRefiner.h"
 %include "IMP/SingletonScore.h"
 %include "IMP/TripletScore.h"
 %include "IMP/Particle.h"
@@ -196,7 +207,10 @@
 %include "IMP/optimizers/states/CMMLogOptimizerState.h"
 %include "IMP/optimizers/states/VelocityScalingOptimizerState.h"
 %include "IMP/pair_scores/DistancePairScore.h"
+%include "IMP/pair_scores/RefineOncePairScore.h"
 %include "IMP/pair_scores/SphereDistancePairScore.h"
+%include "IMP/particle_refiners/BondCoverParticleRefiner.h"
+%include "IMP/particle_refiners/ChildrenParticleRefiner.h"
 %include "IMP/singleton_scores/DistanceToSingletonScore.h"
 %include "IMP/singleton_scores/AttributeSingletonScore.h"
 %include "IMP/triplet_scores/AngleTripletScore.h"