[IMP-dev] bye, bye SphericalRestraint

[Daniel Russel <>]

Index: kernel/include/IMP/restraints/SphericalRestraint.h
===================================================================
--- kernel/include/IMP/restraints/SphericalRestraint.h	(revision 363)
+++ kernel/include/IMP/restraints/SphericalRestraint.h	(working copy)
@@ -1,49 +0,0 @@
-/**
- *  \file SphericalRestraint.h   \brief Absolute position restraint.
- *
- *  Optimize based on distance from an absolute position.
- *
- *  Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#ifndef __IMP_SPHERICAL_RESTRAINT_H
-#define __IMP_SPHERICAL_RESTRAINT_H
-
-#include <list>
-
-#include "../IMP_config.h"
-#include "../UnaryFunction.h"
-#include "../Restraint.h"
-
-namespace IMP
-{
-
-//! Restrict particle position based on its distance to a point.
-class IMPDLLEXPORT SphericalRestraint : public Restraint
-{
-public:
-  // Create the SphericalRestraint.
-  /**
-     \param[in] p The particle to restrict.
-     \param[in] x The x coordinate to take distance to.
-     \param[in] y The y coordinate to take distance to.
-     \param[in] z The z coordinate to take distance to.
-     \param[in] score_func The scoring function. It is deleted in the
-                           destructor.
-   */
-  SphericalRestraint(Particle* p,
-                     Float x, Float y, Float z,
-                     UnaryFunction* score_func);
-  virtual ~SphericalRestraint();
-
-  IMP_RESTRAINT("0.5", "Daniel Russel");
-
-protected:
-  Float center_[3];
-  UnaryFunction* score_func_;
-};
-
-} // namespace IMP
-
-#endif /* __IMP_COORDINATE_RESTRAINT_H */
Index: kernel/src/restraints/SphericalRestraint.cpp
===================================================================
--- kernel/src/restraints/SphericalRestraint.cpp	(revision 363)
+++ kernel/src/restraints/SphericalRestraint.cpp	(working copy)
@@ -1,91 +0,0 @@
-/**
- *  \file SphericalRestraint.cpp \brief Absolute position restraint.
- *
- *  Optimize based on distance from an absolute position.
- *
- *  Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#include <cmath>
-
-#include "IMP/Model.h"
-#include "IMP/Particle.h"
-#include "IMP/log.h"
-#include "IMP/restraints/SphericalRestraint.h"
-#include "IMP/decorators/XYZDecorator.h"
-
-namespace IMP
-{
-
-static const float MIN_DISTANCE_SQUARED=.001;
-
-
-
-SphericalRestraint::SphericalRestraint(Particle* p,
-                                       Float x, Float y, Float z,
-                                       UnaryFunction* score_func)
-{
-  add_particle(p);
-  center_[0]=x;
-  center_[1]=y;
-  center_[2]=z;
-  score_func_ =score_func;
-}
-
-SphericalRestraint::~SphericalRestraint()
-{
-  delete score_func_;
-}
-
-
-
-Float SphericalRestraint::evaluate(DerivativeAccumulator *accum)
-{
-  IMP_CHECK_OBJECT(score_func_);
-
-  Float d2=0;
-  Float diff[3];
-  XYZDecorator xyzd= XYZDecorator::cast(get_particle(0));
-  for (unsigned int i=0; i< 3; ++i) {
-    diff[i] =xyzd.get_coordinate(i) - center_[i];
-    d2+= diff[i]*diff[i];
-  }
-  Float d= std::sqrt(d2);
-  if (d2 < MIN_DISTANCE_SQUARED) {
-    return 0;
-  } 
-
-  Float ret=0;
-  if (accum) {
-    Float deriv;
-    ret= (*score_func_)(d, deriv);
-    for (unsigned int i=0; i< 3; ++i) {
-      Float dd= deriv*diff[i]/d;
-      xyzd.add_to_coordinate_derivative(i, dd, *accum);
-    }
-  } else {
-    ret= (*score_func_)(d);
-  }
-  return ret;
-}
-
-
-void SphericalRestraint::show(std::ostream& out) const
-{
-  if (get_is_active()) {
-    out << "Spherical restraint (active):" << std::endl;
-  } else {
-    out << "Spherical restraint (inactive):" << std::endl;
-  }
-
-  out << "  version: " << version() << "  ";
-  out << "  last_modified_by: " << last_modified_by() << std::endl;
-  out << "  particle: " << get_particle(0)->get_index();
-  out << "  ";
-  score_func_->show(out);
-  out << std::endl;
-  out << std::endl;
-}
-
-}  // namespace IMP
Index: kernel/test/coordinate/test_coordinate.py
===================================================================
--- kernel/test/coordinate/test_coordinate.py	(revision 363)
+++ kernel/test/coordinate/test_coordinate.py	(working copy)
@@ -1,69 +0,0 @@
-import unittest
-import os
-import IMP
-import IMP.test
-import IMP.utils
-
-class CoordinateTests(IMP.test.TestCase):
-    """Test various absolute position restraints"""
-
-    def setUp(self):
-        self.model = IMP.Model()
-        p= IMP.Particle()
-        self.pi= self.model.add_particle(p);
-        d= IMP.XYZDecorator.create(p)
-        d.set_coordinates_are_optimized(True)
-        pc= IMP.Particle()
-        self.pic= self.model.add_particle(pc);
-        dc= IMP.XYZDecorator.create(pc)
-
-        self.opt = IMP.SteepestDescent()
-        self.opt.set_model(self.model)
-        #self.opt.set_threshold(1e-5)
-
-
-    def _do_test(self, center, sf):
-        """All coordinate values should be greater than the set minimum"""
-
-        r= IMP.SphericalRestraint(self.model.get_particle(self.pi),
-                                  center[0], center[1], center[2],
-                                  sf)
-        ri=self.model.add_restraint(r)
-
-        self.opt.optimize(55)
-        self.model.get_restraint(ri).set_is_active(False)
-
-    def _get_center(self):
-        v= IMP.Floats()
-        d= IMP.XYZDecorator.cast(self.model.get_particle(self.pic))
-        v.append(d.get_x())
-        v.append(d.get_y())
-        v.append(d.get_z())
-        return v
-
-    def test_in_ball(self):
-        """Testing that restraint keeps point in ball"""
-        self.randomize_particles(self.model.get_particles(), 50.0)
-        f= IMP.HarmonicUpperBound(10,.1)
-        c= self._get_center()
-        self._do_test(c, f)
-        pd= IMP.XYZDecorator.cast(self.model.get_particle(self.pi))
-        cd= IMP.XYZDecorator.cast(self.model.get_particle(self.pic))
-        d= IMP.distance(pd, cd)
-        self.assert_(d < 11)
-
-    def test_on_ball(self):
-        """Testing that restraint keeps point on sphere"""
-        self.randomize_particles(self.model.get_particles(), 50.0)
-        f= IMP.Harmonic(10,.1)
-        c= self._get_center()
-        self._do_test( c, f)
-        pd= IMP.XYZDecorator.cast(self.model.get_particle(self.pi))
-        cd= IMP.XYZDecorator.cast(self.model.get_particle(self.pic))
-        d= IMP.distance(pd, cd)
-        self.assert_(d < 11)
-        self.assert_(d > 9)
-
-
-if __name__ == '__main__':
-    unittest.main()