Index: kernel/src/restraints/AnglesRestraint.cpp
===================================================================
--- kernel/src/restraints/AnglesRestraint.cpp (revision 0)
+++ kernel/src/restraints/AnglesRestraint.cpp (revision 0)
@@ -0,0 +1,91 @@
+/**
+ * \file AnglesRestraint.cpp \brief Angles restraint.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ *
+ */
+
+#include "IMP/restraints/AnglesRestraint.h"
+#include "IMP/decorators/XYZDecorator.h"
+#include "IMP/Particle.h"
+#include "IMP/Model.h"
+#include "IMP/log.h"
+#include "IMP/Vector3D.h"
+#include "IMP/UnaryFunction.h"
+
+#include <cmath>
+
+namespace IMP
+{
+
+AnglesRestraint::AnglesRestraint(UnaryFunction* score_func)
+{
+ score_func_ = std::auto_ptr<UnaryFunction>(score_func);
+ clear_chains();
+}
+
+void AnglesRestraint::add_chain(const Particles &ps)
+{
+ if (ps.size() <3) {
+ IMP_WARN("Adding a chain of length 2 or less to the AnglesRestraint"
+ << " doesn't accomplish anything."<< std::endl);
+ } else {
+ Restraint::add_particles(ps);
+ chain_splits_.back()= Restraint::number_of_particles();
+ chain_splits_.push_back(Restraint::number_of_particles());
+ }
+}
+
+Float AnglesRestraint::evaluate(DerivativeAccumulator *accum)
+{
+ int cur_break=0;
+ unsigned int i=2;
+ float score=0;
+ while (i < Restraint::number_of_particles()) {
+ /*IMP_LOG(VERBOSE, "Chain eval on "
+ << Restraint::get_particle(i-2)->get_index()
+ << Restraint::get_particle(i-1)->get_index()
+ << Restraint::get_particle(i)->get_index()
+ << " split is " << chain_splits_[cur_break]
+ << std::endl);*/
+ score += internal::evaluate_angle_restraint(Restraint::get_particle(i-2),
+ Restraint::get_particle(i-1),
+ Restraint::get_particle(i),
+ score_func_.get(),
+ accum);
+ if (chain_splits_[cur_break] == i) {
+ i+=3;
+ ++cur_break;
+ } else {
+ ++i;
+ }
+ }
+ return score;
+}
+
+void AnglesRestraint::clear_chains() {
+ Restraint::clear_particles();
+ chain_splits_.clear();
+ chain_splits_.push_back(0);
+}
+
+
+//! Show the current restraint.
+/** \param[in] out Stream to send restraint description to.
+ */
+void AnglesRestraint::show(std::ostream& out) const
+{
+ if (get_is_active()) {
+ out << "angles restraint (active):" << std::endl;
+ } else {
+ out << "angles restraint (inactive):" << std::endl;
+ }
+
+ out << " version: " << version() << " ";
+ out << " last_modified_by: " << last_modified_by() << std::endl;
+ out << " " << chain_splits_.size()-1 << " chains" << std::endl;
+ score_func_->show(out);
+ out << std::endl;
+}
+
+} // namespace IMP
Index: kernel/include/IMP/restraints/AnglesRestraint.h
===================================================================
--- kernel/include/IMP/restraints/AnglesRestraint.h (revision 0)
+++ kernel/include/IMP/restraints/AnglesRestraint.h (revision 0)
@@ -0,0 +1,51 @@
+/**
+ * \file AnglesRestraint.h \brief Restraint the angles between particles.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ *
+ */
+
+#ifndef __IMP_ANGLES_RESTRAINT_H
+#define __IMP_ANGLES_RESTRAINT_H
+
+#include "../IMP_config.h"
+#include "../Restraint.h"
+#include "AngleRestraint.h"
+#include <vector>
+
+namespace IMP
+{
+
+class UnaryFunction;
+
+//! Restraint the angles between particles
+/** Currently the particles can be added as chains and the angle
+ of each three successive particles in the chain is restrained.
+ \ingroup restraint
+ */
+class IMPDLLEXPORT AnglesRestraint : public Restraint
+{
+public:
+ //! Create the angle restraint.
+ /** \param[in] score_func Scoring function for the restraint.
+ */
+ AnglesRestraint(UnaryFunction* score_func);
+ virtual ~AnglesRestraint(){}
+
+ IMP_RESTRAINT("0.5", "Daniel Russel");
+
+ //! Add a chain of particles
+ /** Each three successive particles are restrained*/
+ void add_chain(const Particles &ps);
+
+ //! Clear all the stored chains
+ void clear_chains();
+
+protected:
+ std::auto_ptr<UnaryFunction> score_func_;
+ std::vector<unsigned int> chain_splits_;
+};
+
+} // namespace IMP
+
+#endif /* __IMP_ANGLES_RESTRAINT_H */
Index: kernel/test/restraints/test_angles.py
===================================================================
--- kernel/test/restraints/test_angles.py (revision 0)
+++ kernel/test/restraints/test_angles.py (revision 0)
@@ -0,0 +1,76 @@
+import unittest
+import IMP
+import IMP.test
+import IMP.utils
+import math
+
+class One(IMP.UnaryFunction):
+ def __init__(self):
+ IMP.UnaryFunction.__init__(self)
+ def __call__(self, *args):
+ return 1
+ def show(self, *args):
+ print "identity"
+
+
+class AngleRestraintTests(IMP.test.TestCase):
+ """Tests for angle restraints"""
+ def setUp(self):
+ # for some reason objects get destroyed even though
+ # python doesn't own them
+ self.stupid_hack=[]
+
+ def create_particles(self, m, n):
+ l0=IMP.Particles()
+ for i in range(0,n):
+ p= IMP.Particle()
+ m.add_particle(p)
+ d= IMP.XYZDecorator.create(p)
+ l0.append(p)
+ self.randomize_particles(l0, 20)
+ return l0
+
+ def create_angle_r(self, s, ps):
+ print s.thisown
+ for i in range(2, len(ps)):
+ print str(i)
+ l= One()
+ self.stupid_hack.append(l)
+ r= IMP.AngleRestraint(ps[i-2],ps[i-1], ps[i], l)
+ s.add_restraint(r)
+ #print r.evaluate(None)
+ #print r.thisown
+ #print l.thisown
+ #print s.evaluate(None)
+ print s.evaluate(None)
+
+ def test_score(self):
+ """Check score of angles restraints"""
+ IMP.set_log_level(IMP.VERBOSE)
+ m=IMP.Model()
+ l0= self.create_particles(m, 3)
+ l1= self.create_particles(m, 10)
+ l2= self.create_particles(m, 2)
+ l= One()
+ r= IMP.AnglesRestraint(l)
+ r.add_chain(l0)
+ r.add_chain(l1)
+ r.add_chain(l2)
+ m.add_restraint(r)
+ s= IMP.RestraintSet("angle restraints")
+ m.add_restraint(s)
+ print "creating angle restraints"
+ self.create_angle_r(s, l0)
+ self.create_angle_r(s, l1)
+ self.create_angle_r(s, l2)
+ ss= s.evaluate(None)
+ rs= r.evaluate(None)
+ diff = ss-rs
+ print ss
+ print rs
+ if (diff <0): diff=-diff
+ self.assert_(diff < .001, "The restraints are not equal")
+
+
+if __name__ == '__main__':
+ unittest.main()