Index: kernel/test/restraints/test_tunnel.py
===================================================================
--- kernel/test/restraints/test_tunnel.py	(revision 0)
+++ kernel/test/restraints/test_tunnel.py	(revision 0)
@@ -0,0 +1,62 @@
+import unittest
+import IMP
+import IMP.test
+import IMP.utils
+import math
+
+class TunnelTest(IMP.test.TestCase):
+    """Tests for tunnel restraints"""
+
+    def test_score(self):
+        """Test derivatives and score of tunnel restraint"""
+        IMP.set_log_level(IMP.VERBOSE)
+        m= IMP.Model()
+        p= IMP.Particle()
+        m.add_particle(p)
+        d= IMP.XYZDecorator.create(p)
+        rk= IMP.FloatKey("radiusk")
+        p.add_attribute(rk, 1, False)
+        f= IMP.HarmonicLowerBound(0, 1)
+        tr= IMP.TunnelRestraint(f, rk)
+        tr.set_height(10)
+        tr.set_radius(5)
+        tr.set_center(IMP.Vector3D(10,10,10))
+        tr.add_particle(p)
+        tr.set_coordinate(2)
+        m.add_restraint(tr)
+        m.evaluate(True)
+        d.set_coordinates(IMP.Vector3D(10,10,10))
+        self.assertEqual(m.evaluate(True), 0)
+
+        print "Test left"
+        d.set_coordinates(IMP.Vector3D(4, 10, 10))
+        self.assert_(m.evaluate(True)>0)
+        self.assertEqual(d.get_coordinate_derivative(2), 0)
+        self.assertEqual(d.get_coordinate_derivative(1), 0)
+        print d.get_coordinate_derivative(0)
+        self.assert_(d.get_coordinate_derivative(0) > 0)
+
+        print "Test above"
+        d.set_coordinates(IMP.Vector3D(10, 4, 10))
+        self.assert_(m.evaluate(True)>0)
+        self.assertEqual(d.get_coordinate_derivative(2), 0)
+        self.assertEqual(d.get_coordinate_derivative(0), 0)
+        print d.get_coordinate_derivative(1)
+        self.assert_(d.get_coordinate_derivative(1) > 0)
+
+        print "Test bottom"
+        d.set_coordinates(IMP.Vector3D(30, 30, 3))
+        self.assert_(m.evaluate(True)>0)
+        self.assertEqual(d.get_coordinate_derivative(0), 0)
+        self.assertEqual(d.get_coordinate_derivative(1), 0)
+        self.assert_(d.get_coordinate_derivative(2) < 0)
+
+        print "Test top"
+        d.set_coordinates(IMP.Vector3D(30, 30, 17))
+        self.assert_(m.evaluate(True)>0)
+        self.assertEqual(d.get_coordinate_derivative(0), 0)
+        self.assertEqual(d.get_coordinate_derivative(1), 0)
+        self.assert_(d.get_coordinate_derivative(2) > 0)
+
+if __name__ == '__main__':
+    unittest.main()
Index: kernel/include/IMP/restraints/TunnelRestraint.h
===================================================================
--- kernel/include/IMP/restraints/TunnelRestraint.h	(revision 0)
+++ kernel/include/IMP/restraints/TunnelRestraint.h	(revision 0)
@@ -0,0 +1,82 @@
+/**
+ *  \file TunnelRestraint.h    \brief Tunnel restraint.
+ *
+ *  Just return a constant.
+ *
+ *  Copyright 2007-8 Sali Lab. All rights reserved.
+ *
+ */
+
+#ifndef __IMP_TUNNEL_RESTRAINT_H
+#define __IMP_TUNNEL_RESTRAINT_H
+
+#include "../IMP_config.h"
+#include "../Restraint.h"
+#include "../Vector3D.h"
+#include "../UnaryFunction.h"
+#include "../internal/kernel_version_info.h"
+
+namespace IMP
+{
+class PairScore;
+
+//! Restrain particles to a tunnel.
+/** Particles with x,y,z coordinates and an optional radius are
+    prevented from being in a volume destribed by a slab from
+    (center[i]-height) to (center+height) on the ith coordinate with a
+    tunnel of radius r centered at center. To set which coordinate
+    is used use the get/set _coordinate functions.
+
+    Note that the UnaryFunction should look like a lower bound with 0
+    meaning that the particle is just touching the tunnel.
+
+    \ingroup restraint
+ */
+class IMPDLLEXPORT TunnelRestraint : public Restraint
+{
+  int coordinate_;
+  Vector3D center_;
+  Float height_;
+  Float radius_;
+  internal::ObjectPointer<UnaryFunction, true> f_;
+  FloatKey rk_;
+public:
+  TunnelRestraint(UnaryFunction* f, FloatKey rk);
+
+  void set_center(Vector3D c){
+    center_=c;
+  }
+  void set_height(Float h){
+    IMP_check(h >= 0,
+              "Height can't be negative",
+              ValueException);
+    height_=h;
+  }
+  void set_radius(Float h){
+    IMP_check(h >= 0,
+              "Radius can't be negative",
+              ValueException);
+    radius_=h;
+  }
+  void set_coordinate(unsigned int i) {
+    IMP_check(i < 3,
+              "Invalid coordinate value",
+              ValueException);
+    coordinate_=i;
+  }
+  unsigned int get_coordinate() const {
+    return coordinate_;
+  }
+
+  using Restraint::add_particles;
+  using Restraint::add_particle;
+  using Restraint::set_particles;
+  using Restraint::clear_particles;
+  using Restraint::erase_particle;
+
+  IMP_RESTRAINT(internal::kernel_version_info)
+};
+
+} // namespace IMP
+
+#endif /* __IMP_CONSTANT_RESTRAINT_H */
Index: kernel/include/IMP/restraints/SConscript
===================================================================
--- kernel/include/IMP/restraints/SConscript	(revision 611)
+++ kernel/include/IMP/restraints/SConscript	(working copy)
@@ -1,15 +1,21 @@
+Import('env')
 import os.path
-Import('env')
-
-files = ['ConnectivityRestraint.h',
-         'DistanceRestraint.h', 'AngleRestraint.h',
-         'DihedralRestraint.h', 'RestraintSet.h',
-         'NonbondedRestraint.h', 'BondDecoratorRestraint.h',
-         'SingletonListRestraint.h', 'PairListRestraint.h',
-         'TripletChainRestraint.h', 'PairChainRestraint.h',
-         'ConstantRestraint.h']
-
-# Install the include files:
-includedir = os.path.join(env['includedir'], 'IMP', 'restraints')
+files=[
+       'AngleRestraint.h',
+       'BondDecoratorRestraint.h',
+       'ConnectivityRestraint.h',
+       'ConstantRestraint.h',
+       'DihedralRestraint.h',
+       'DistanceRestraint.h',
+       'NonbondedRestraint.h',
+       'PairChainRestraint.h',
+       'PairListRestraint.h',
+       'RestraintSet.h',
+       'SingletonListRestraint.h',
+       'SymmetryRestraint.h',
+       'TripletChainRestraint.h',
+       'TunnelRestraint.h',
+      ]
+includedir = os.path.join(env['includedir'], 'IMP', 'restraints' )
 inst = env.Install(includedir, files)
 env.Alias('install', inst)
Index: kernel/src/restraints/TunnelRestraint.cpp
===================================================================
--- kernel/src/restraints/TunnelRestraint.cpp	(revision 0)
+++ kernel/src/restraints/TunnelRestraint.cpp	(revision 0)
@@ -0,0 +1,103 @@
+/**
+ *  \file TunnelRestraint.cpp \brief Don't restrain anything.
+ *
+ *  Copyright 2007-8 Sali Lab. All rights reserved.
+ *
+ */
+
+#include "IMP/restraints/TunnelRestraint.h"
+#include "IMP/decorators/XYZDecorator.h"
+
+namespace IMP
+{
+
+TunnelRestraint::TunnelRestraint(UnaryFunction *f, FloatKey r) : f_(f),
+                                                                rk_(r){
+  coordinate_=0;
+  center_=Vector3D(0,0,0);
+  height_=0;
+  radius_=0;
+}
+
+
+
+Float TunnelRestraint::evaluate(DerivativeAccumulator *accum)
+{
+  Float ret=0;
+  for (Restraint::ParticleIterator it= Restraint::particles_begin();
+       it != Restraint::particles_end(); ++it) {
+    XYZDecorator d(*it);
+    Float radius=0;
+    if (rk_ != FloatKey() && (*it)->has_attribute(rk_)) {
+      radius= (*it)->get_value(rk_);
+    }
+    IMP_LOG(VERBOSE, "Tunnel restraint on particle " << d << std::endl);
+    Float hr= height_+radius;
+    if (d.get_coordinate(coordinate_) < center_[coordinate_] + hr
+        && d.get_coordinate(coordinate_) > center_[coordinate_] - hr) {
+      Float sd=0;
+      for (int i=1; i< 3; ++i) {
+        int oc= (i+coordinate_)%3;
+        sd+= square(d.get_coordinate(oc)- center_[oc]);
+      }
+      sd= std::sqrt(sd);
+      IMP_LOG(VERBOSE, "The distance is " << sd << " and radius "
+              << radius_ << std::endl);
+      if (sd > radius_-radius) {
+        Float rd= sd-radius_;
+        Float hdu= center_[coordinate_] + height_
+          - d.get_coordinate(coordinate_);
+        Float hdd=  d.get_coordinate(coordinate_)
+          + height_- center_[coordinate_];
+        Vector3D deriv(0,0,0);
+        Float score=0;
+        Float deriv_scalar=0;
+        /*! \todo Clean up these tests so I am not dependent on two expressions
+          being the same and evaluating to the same thing */
+        // look below if changed
+        Float dist= -std::min(std::min(rd, hdu), hdd) - radius;
+        if (accum) {
+          score= f_->evaluate_deriv(dist, deriv_scalar);
+        } else {
+          score= f_->evaluate(dist);
+        }
+
+        // kind if evil
+        if (dist== -rd -radius) {
+          Vector3D v= (d.get_vector() - center_).get_unit_vector();
+          for (int i=0; i< 2; ++i) {
+            int oc= (i+coordinate_+1)%3;
+            deriv[oc]= v[oc]*deriv_scalar;
+          }
+        } else {
+          // kind of evil
+          if (dist == -hdu -radius) deriv_scalar= -deriv_scalar;
+          deriv[coordinate_]= deriv_scalar;
+        }
+
+        if (accum) {
+          for (unsigned int i=0; i< 3; ++i) {
+            d.add_to_coordinate_derivative(i, deriv[i], *accum);
+          }
+        }
+        ret+= score;
+      } else {
+        IMP_LOG(VERBOSE, "Particle " << (*it)->get_index()
+                << " is in channel" << std::endl);
+      }
+    } else {
+      IMP_LOG(VERBOSE, "Particle " << (*it)->get_index()
+              << " is outside of slab" << std::endl);
+    }
+  }
+  return ret;
+}
+
+void TunnelRestraint::show(std::ostream& out) const
+{
+  out << "Tunnel restraint :" << f_ 
+      << " " << center_ << " " << height_ << " " 
+      << coordinate_ << std::endl;
+}
+
+}  // namespace IMP
Index: kernel/src/restraints/SConscript
===================================================================
--- kernel/src/restraints/SConscript	(revision 611)
+++ kernel/src/restraints/SConscript	(working copy)
@@ -1,11 +1,16 @@
-Import('env')
-
-files = ['ConnectivityRestraint.cpp', 'RestraintSet.cpp',
-         'DistanceRestraint.cpp', 'AngleRestraint.cpp', 'DihedralRestraint.cpp',
-         'NonbondedRestraint.cpp', 'BondDecoratorRestraint.cpp',
-         'SingletonListRestraint.cpp', 'PairListRestraint.cpp',
-         'TripletChainRestraint.cpp', 'PairChainRestraint.cpp',
-         'ConstantRestraint.cpp']
-
-files = [File(x) for x in files]
+files=[
+        File( 'AngleRestraint.cpp' ),
+        File( 'BondDecoratorRestraint.cpp' ),
+        File( 'ConnectivityRestraint.cpp' ),
+        File( 'ConstantRestraint.cpp' ),
+        File( 'DihedralRestraint.cpp' ),
+        File( 'DistanceRestraint.cpp' ),
+        File( 'NonbondedRestraint.cpp' ),
+        File( 'PairChainRestraint.cpp' ),
+        File( 'PairListRestraint.cpp' ),
+        File( 'RestraintSet.cpp' ),
+        File( 'SingletonListRestraint.cpp' ),
+        File( 'TripletChainRestraint.cpp' ),
+        File( 'TunnelRestraint.cpp' ),
+      ]
 Return('files')
Index: kernel/pyext/IMP.i
===================================================================
--- kernel/pyext/IMP.i	(revision 611)
+++ kernel/pyext/IMP.i	(working copy)
@@ -42,6 +42,9 @@
   %pythonprepend NonbondedListScoreState::add_bonded_list %{
         args[1].thisown=0
   %}
+  %pythonprepend TunnelRestraint::TunnelRestraint %{
+        args[0].thisown=0
+  %}
   %pythonprepend DistanceRestraint::DistanceRestraint %{
         args[0].thisown=0
   %}
@@ -234,6 +237,7 @@
 %include "IMP/restraints/RestraintSet.h"
 %include "IMP/restraints/SingletonListRestraint.h"
 %include "IMP/restraints/TripletChainRestraint.h"
+%include "IMP/restraints/TunnelRestraint.h"
 
 namespace IMP {
   %template(ParticleIndex) Index<ParticleTag>;
Index: kernel/include/IMP.h
===================================================================
--- kernel/include/IMP.h	(revision 611)
+++ kernel/include/IMP.h	(working copy)
@@ -1,88 +1,108 @@
 /**
- *  \file IMP.h   \brief IMP, an Integrative Modeling Platform.
- *
- *  Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
+*  ile IMP.h   rief IMP, an Integrative Modeling Platform.
+*
+*  Copyright 2007-8 Sali Lab. All rights reserved.
+*
+*/
 #ifndef __IMP_H
 #define __IMP_H
-
-#include "IMP/IMP_config.h"
-#include "IMP/log.h"
-#include "IMP/random.h"
-#include "IMP/base_types.h"
-#include "IMP/Particle.h"
-#include "IMP/Optimizer.h"
-#include "IMP/Restraint.h"
-#include "IMP/exception.h"
-#include "IMP/UnaryFunction.h"
-#include "IMP/unary_functions/Harmonic.h"
-#include "IMP/unary_functions/HarmonicLowerBound.h"
-#include "IMP/unary_functions/HarmonicUpperBound.h"
-#include "IMP/unary_functions/OpenCubicSpline.h"
-#include "IMP/unary_functions/ClosedCubicSpline.h"
-#include "IMP/unary_functions/Cosine.h"
-#include "IMP/unary_functions/Linear.h"
-#include "IMP/unary_functions/WormLikeChain.h"
-#include "IMP/Model.h"
-#include "IMP/PairScore.h"
-#include "IMP/SingletonScore.h"
-#include "IMP/TripletScore.h"
-#include "IMP/Vector3D.h"
-#include "IMP/VersionInfo.h"
-#include "IMP/ParticleRefiner.h"
-#include "IMP/particle_refiners/BondCoverParticleRefiner.h"
-#include "IMP/particle_refiners/ChildrenParticleRefiner.h"
-#include "IMP/decorators/HierarchyDecorator.h"
-#include "IMP/decorators/MolecularHierarchyDecorator.h"
-#include "IMP/decorators/NameDecorator.h"
-#include "IMP/decorators/AtomDecorator.h"
-#include "IMP/decorators/ResidueDecorator.h"
-#include "IMP/decorators/XYZDecorator.h"
-#include "IMP/decorators/bond_decorators.h"
-#include "IMP/optimizers/SteepestDescent.h"
-#include "IMP/optimizers/ConjugateGradients.h"
-#include "IMP/optimizers/MolecularDynamics.h"
-#include "IMP/optimizers/BrownianDynamics.h"
-#include "IMP/optimizers/MonteCarlo.h"
-#include "IMP/optimizers/Mover.h"
-#include "IMP/optimizers/MoverBase.h"
-#include "IMP/optimizers/movers/BallMover.h"
-#include "IMP/optimizers/movers/NormalMover.h"
-#include "IMP/optimizers/states/VRMLLogOptimizerState.h"
-#include "IMP/optimizers/states/CMMLogOptimizerState.h"
-#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"
-#include "IMP/restraints/RestraintSet.h"
-#include "IMP/restraints/ConstantRestraint.h"
-#include "IMP/restraints/DistanceRestraint.h"
-#include "IMP/restraints/AngleRestraint.h"
-#include "IMP/restraints/DihedralRestraint.h"
-#include "IMP/restraints/ConnectivityRestraint.h"
-#include "IMP/restraints/NonbondedRestraint.h"
-#include "IMP/restraints/BondDecoratorRestraint.h"
-#include "IMP/restraints/SingletonListRestraint.h"
-#include "IMP/restraints/PairListRestraint.h"
-#include "IMP/restraints/TripletChainRestraint.h"
-#include "IMP/restraints/PairChainRestraint.h"
-#include "IMP/score_states/BipartiteNonbondedListScoreState.h"
-#include "IMP/score_states/MaxChangeScoreState.h"
-#include "IMP/score_states/NonbondedListScoreState.h"
-#include "IMP/score_states/BondedListScoreState.h"
-#include "IMP/score_states/BondDecoratorListScoreState.h"
-#include "IMP/score_states/AllNonbondedListScoreState.h"
-#include "IMP/score_states/GravityCenterScoreState.h"
-#include "IMP/score_states/CoverBondsScoreState.h"
-
-
-/**
-   \namespace IMP The IMP namespace.
- */
-
+#include <IMP/base_types.h>
+#include <IMP/DecoratorBase.h>
+#include <IMP/DerivativeAccumulator.h>
+#include <IMP/exception.h>
+#include <IMP/IMP_config.h>
+#include <IMP/Index.h>
+#include <IMP/Key.h>
+#include <IMP/log.h>
+#include <IMP/macros.h>
+#include <IMP/Model.h>
+#include <IMP/Optimizer.h>
+#include <IMP/OptimizerState.h>
+#include <IMP/PairScore.h>
+#include <IMP/Particle.h>
+#include <IMP/ParticleRefiner.h>
+#include <IMP/random.h>
+#include <IMP/Restraint.h>
+#include <IMP/ScoreState.h>
+#include <IMP/SingletonScore.h>
+#include <IMP/TripletScore.h>
+#include <IMP/UnaryFunction.h>
+#include <IMP/utility.h>
+#include <IMP/Vector3D.h>
+#include <IMP/VersionInfo.h>
+#include <IMP/decorators/AtomDecorator.h>
+#include <IMP/decorators/bond_decorators.h>
+#include <IMP/decorators/HierarchyDecorator.h>
+#include <IMP/decorators/macros.h>
+#include <IMP/decorators/MolecularHierarchyDecorator.h>
+#include <IMP/decorators/NameDecorator.h>
+#include <IMP/decorators/ResidueDecorator.h>
+#include <IMP/decorators/utility.h>
+#include <IMP/decorators/XYZDecorator.h>
+#include <IMP/internal/ArrayOnAttributesHelper.h>
+#include <IMP/internal/AttributeTable.h>
+#include <IMP/internal/bbox_nbl_helpers.h>
+#include <IMP/internal/constants.h>
+#include <IMP/internal/ExponentialNumber.h>
+#include <IMP/internal/graph_base.h>
+#include <IMP/internal/Grid3D.h>
+#include <IMP/internal/kernel_version_info.h>
+#include <IMP/internal/ObjectContainer.h>
+#include <IMP/internal/Object.h>
+#include <IMP/internal/ObjectPointer.h>
+#include <IMP/internal/ParticleGrid.h>
+#include <IMP/internal/RefCountedObject.h>
+#include <IMP/internal/Unit.h>
+#include <IMP/internal/units.h>
+#include <IMP/internal/utility.h>
+#include <IMP/internal/Vector.h>
+#include <IMP/optimizers/BrownianDynamics.h>
+#include <IMP/optimizers/ConjugateGradients.h>
+#include <IMP/optimizers/MolecularDynamics.h>
+#include <IMP/optimizers/MonteCarlo.h>
+#include <IMP/optimizers/MoverBase.h>
+#include <IMP/optimizers/Mover.h>
+#include <IMP/optimizers/SteepestDescent.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/restraints/AngleRestraint.h>
+#include <IMP/restraints/BondDecoratorRestraint.h>
+#include <IMP/restraints/ConnectivityRestraint.h>
+#include <IMP/restraints/ConstantRestraint.h>
+#include <IMP/restraints/DihedralRestraint.h>
+#include <IMP/restraints/DistanceRestraint.h>
+#include <IMP/restraints/NonbondedRestraint.h>
+#include <IMP/restraints/PairChainRestraint.h>
+#include <IMP/restraints/PairListRestraint.h>
+#include <IMP/restraints/RestraintSet.h>
+#include <IMP/restraints/SingletonListRestraint.h>
+#include <IMP/restraints/TripletChainRestraint.h>
+#include <IMP/restraints/TunnelRestraint.h>
+#include <IMP/score_states/AllNonbondedListScoreState.h>
+#include <IMP/score_states/BipartiteNonbondedListScoreState.h>
+#include <IMP/score_states/BondDecoratorListScoreState.h>
+#include <IMP/score_states/BondedListScoreState.h>
+#include <IMP/score_states/CoverBondsScoreState.h>
+#include <IMP/score_states/GravityCenterScoreState.h>
+#include <IMP/score_states/MaxChangeScoreState.h>
+#include <IMP/score_states/NonbondedListScoreState.h>
+#include <IMP/singleton_scores/AttributeSingletonScore.h>
+#include <IMP/singleton_scores/DistanceToSingletonScore.h>
+#include <IMP/triplet_scores/AngleTripletScore.h>
+#include <IMP/unary_functions/ClosedCubicSpline.h>
+#include <IMP/unary_functions/Cosine.h>
+#include <IMP/unary_functions/Harmonic.h>
+#include <IMP/unary_functions/HarmonicLowerBound.h>
+#include <IMP/unary_functions/HarmonicUpperBound.h>
+#include <IMP/unary_functions/Linear.h>
+#include <IMP/unary_functions/OpenCubicSpline.h>
+#include <IMP/unary_functions/WormLikeChain.h>
+#include <IMP/optimizers/movers/BallMover.h>
+#include <IMP/optimizers/movers/NormalMover.h>
+#include <IMP/optimizers/states/CMMLogOptimizerState.h>
+#include <IMP/optimizers/states/VelocityScalingOptimizerState.h>
+#include <IMP/optimizers/states/VRMLLogOptimizerState.h>
 #endif  /* __IMP_H */