Index: kernel/include/IMP/restraints/ListRestraint.h
===================================================================
--- kernel/include/IMP/restraints/ListRestraint.h (revision 0)
+++ kernel/include/IMP/restraints/ListRestraint.h (revision 0)
@@ -0,0 +1,49 @@
+/**
+ * \file ListRestraint.h
+ * \brief Apply a SingletonScore to each particle in a list.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ *
+ */
+
+#ifndef __IMP_LIST_RESTRAINT_H
+#define __IMP_LIST_RESTRAINT_H
+
+#include <iostream>
+
+#include "../IMP_config.h"
+#include "../Restraint.h"
+
+namespace IMP
+{
+
+class SingletonScore;
+
+//! Applies a SingletonScore to each Particle in a list.
+/**
+ \ingroup restraint
+ */
+class IMPDLLEXPORT ListRestraint : public Restraint
+{
+public:
+ //! Create the list restraint.
+ /** \param[in] ps The list of particles to use in the restraint.
+ \param[in] ss The function to apply to each particle.
+ */
+ ListRestraint(const Particles &ps, SingletonScore *ss);
+ virtual ~ListRestraint(){}
+
+ IMP_RESTRAINT("0.5", "Daniel Russel");
+
+ //! Set the list of particles
+ void set_particles(const Particles &ps) {
+ Restraint::set_particles(ps);
+ }
+
+protected:
+ std::auto_ptr<SingletonScore> ss_;
+};
+
+} // namespace IMP
+
+#endif /* __IMP_LIST_RESTRAINT_H */
Index: kernel/include/IMP/SingletonScore.h
===================================================================
--- kernel/include/IMP/SingletonScore.h (revision 0)
+++ kernel/include/IMP/SingletonScore.h (revision 0)
@@ -0,0 +1,41 @@
+/**
+ * \file SingletonScore.h \brief A Score on a single particle.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ */
+
+#ifndef __IMP_SINGLETON_SCORE_H
+#define __IMP_SINGLETON_SCORE_H
+
+#include "IMP_config.h"
+#include "base_types.h"
+#include "Object.h"
+#include "DerivativeAccumulator.h"
+
+namespace IMP
+{
+
+class Particle;
+
+/**
+ \ingroup restraint
+ \addtogroup singleton Score functions on one particle
+ Score functions to by applied to a single particle. These can be
+ used to make more flexible restraints.
+ */
+
+//! Abstract score function for a single particle.
+class IMPDLLEXPORT SingletonScore : public Object
+{
+public:
+ SingletonScore() {}
+ virtual ~SingletonScore() {}
+ //! Compute the score for the pair and the derivative if needed.
+ virtual Float evaluate(Particle *a,
+ DerivativeAccumulator *da) = 0;
+ virtual void show(std::ostream &out=std::cout) const = 0;
+};
+
+} // namespace IMP
+
+#endif /* __IMP_SINGLETON_SCORE_H */
Index: kernel/include/IMP/singleton_scores/DistanceToSingletonScore.h
===================================================================
--- kernel/include/IMP/singleton_scores/DistanceToSingletonScore.h (revision 0)
+++ kernel/include/IMP/singleton_scores/DistanceToSingletonScore.h (revision 0)
@@ -0,0 +1,35 @@
+/**
+ * \file DistanceToSingletonScore.h
+ * \brief A Score on the distance between to a fixed point.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ */
+
+#ifndef __IMP_DISTANCE_TO_SINGLETON_SCORE_H
+#define __IMP_DISTANCE_TO_SINGLETON_SCORE_H
+
+#include "../SingletonScore.h"
+#include "../Vector3D.h"
+namespace IMP
+{
+
+class UnaryFunction;
+
+//! Apply a function to the distance to a fixed point.
+/** \ingroup singleton
+ */
+class IMPDLLEXPORT DistanceToSingletonScore : public SingletonScore
+{
+ std::auto_ptr<UnaryFunction> f_;
+ Vector3D pt_;
+public:
+ DistanceToSingletonScore(const Vector3D& pt, UnaryFunction *f);
+ virtual ~DistanceToSingletonScore(){}
+ virtual Float evaluate(Particle *a,
+ DerivativeAccumulator *da);
+ virtual void show(std::ostream &out=std::cout) const;
+};
+
+} // namespace IMP
+
+#endif /* __IMP_DISTANCE_TO_SINGLETON_SCORE_H */
Index: kernel/include/IMP/singleton_scores/SConscript
===================================================================
--- kernel/include/IMP/singleton_scores/SConscript (revision 0)
+++ kernel/include/IMP/singleton_scores/SConscript (revision 0)
@@ -0,0 +1,9 @@
+import os.path
+Import('env')
+
+files = ['DistanceToSingletonScore.h']
+
+# Install the include files:
+includedir = os.path.join(env['includedir'], 'IMP', 'singleton_scores')
+inst = env.Install(includedir, files)
+env.Alias('install', inst)
Index: kernel/src/singleton_scores/SConscript
===================================================================
--- kernel/src/singleton_scores/SConscript (revision 0)
+++ kernel/src/singleton_scores/SConscript (revision 0)
@@ -0,0 +1,6 @@
+Import('env')
+
+files = ['DistanceToSingletonScore.cpp']
+
+files = [File(x) for x in files]
+Return('files')
Index: kernel/src/singleton_scores/DistanceToSingletonScore.cpp
===================================================================
--- kernel/src/singleton_scores/DistanceToSingletonScore.cpp (revision 0)
+++ kernel/src/singleton_scores/DistanceToSingletonScore.cpp (revision 0)
@@ -0,0 +1,86 @@
+/**
+ * \file DistanceToSingletonScore.cpp
+ * \brief A Score on the distance to a fixed point.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ */
+
+#include "IMP/singleton_scores/DistanceToSingletonScore.h"
+#include "IMP/decorators/XYZDecorator.h"
+#include "IMP/UnaryFunction.h"
+
+namespace IMP
+{
+
+namespace internal
+{
+
+static const Float MIN_DISTANCE = .00001;
+Float evaluate_distance_to_singleton_score(const Vector3D &v,
+ Particle *b,
+ DerivativeAccumulator *da,
+ UnaryFunction *f,
+ Float offset,
+ Float scale)
+{
+ IMP_CHECK_OBJECT(f);
+ IMP_CHECK_OBJECT(b);
+
+ Float d2 = 0, delta[3];
+ Float score;
+
+ XYZDecorator d1 = XYZDecorator::cast(b);
+ if (!d1.get_coordinates_are_optimized()) {
+ IMP_WARN("DistanceToSingletonScore called on non optimized particle"
+ << *b <<std::endl);
+ return 0;
+ }
+ for (int i = 0; i < 3; ++i) {
+ delta[i] = v.get_component(i) - d1.get_coordinate(i);
+ d2 += square(delta[i]);
+ }
+
+ Float distance = std::sqrt(d2);
+
+ Float shifted_distance = scale*(distance - offset);
+
+ // if needed, calculate the partial derivatives of the scores with respect
+ // to the particle attributes
+ // avoid division by zero if the distance is too small
+ if (da && distance >= MIN_DISTANCE) {
+ Float deriv;
+
+ score = (*f)(shifted_distance, deriv);
+
+ for (int i = 0; i < 3; ++i) {
+ Float d = delta[i] / distance * deriv;
+ d1.add_to_coordinate_derivative(i, -d, *da);
+ }
+ } else {
+ // calculate the score based on the distance feature
+ score = (*f)(shifted_distance);
+ }
+
+ return score;
+}
+
+} // namespace internal
+
+ DistanceToSingletonScore::DistanceToSingletonScore(const Vector3D &v,
+ UnaryFunction *f): f_(f),
+ pt_(v){}
+
+Float DistanceToSingletonScore::evaluate(Particle *b,
+ DerivativeAccumulator *da)
+{
+ return internal::evaluate_distance_to_singleton_score(pt_,b, da,
+ f_.get(), 0,1);
+}
+
+void DistanceToSingletonScore::show(std::ostream &out) const
+{
+ out << "DistanceToSingletScore using ";
+ f_->show(out);
+}
+
+} // namespace IMP
Index: kernel/src/restraints/ListRestraint.cpp
===================================================================
--- kernel/src/restraints/ListRestraint.cpp (revision 0)
+++ kernel/src/restraints/ListRestraint.cpp (revision 0)
@@ -0,0 +1,47 @@
+/**
+ * \file ListRestraint.cpp
+ * \brief Apply a score fgunction toa list of particles.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ *
+ */
+
+#include <cmath>
+
+#include "IMP/SingletonScore.h"
+#include "IMP/log.h"
+#include "IMP/restraints/ListRestraint.h"
+
+namespace IMP
+{
+
+ListRestraint::ListRestraint(const Particles &ps,
+ SingletonScore *s) : ss_(s)
+{
+ set_particles(ps);
+}
+
+
+Float ListRestraint::evaluate(DerivativeAccumulator *accum)
+{
+
+ IMP_CHECK_OBJECT(ss_);
+
+ Float score=0;
+
+ for (unsigned int i=0; i< number_of_particles(); ++i) {
+ score += ss_->evaluate(get_particle(i), accum);
+ }
+
+ return score;
+}
+
+
+void ListRestraint::show(std::ostream& out) const
+{
+ out << "List restraint with score function ";
+ ss_->show(out);
+ out << std::endl;
+}
+
+} // namespace IMP
Index: kernel/test/restraints/test_list.py
===================================================================
--- kernel/test/restraints/test_list.py (revision 0)
+++ kernel/test/restraints/test_list.py (revision 0)
@@ -0,0 +1,60 @@
+import unittest
+import IMP, IMP.test
+
+class OneSingle(IMP.SingletonScore):
+ def __init__(self):
+ IMP.SingletonScore.__init__(self)
+ def evaluate(self, pa, da):
+ return 1
+ def last_modified_by(self):
+ return "Me"
+ def version(self):
+ return "0.5"
+ def show(self, t):
+ print "One Singleton"
+
+class Linear(IMP.UnaryFunction):
+ def __init__(self):
+ IMP.UnaryFunction.__init__(self)
+ def __call__(self, *args):
+ return args[0]
+ def show(self, *args):
+ print "identity"
+
+class TestList(IMP.test.TestCase):
+ def setUp(self):
+ IMP.set_log_level(IMP.VERBOSE)
+
+ def test_it(self):
+ """Test the singleton restraint"""
+ m= IMP.Model()
+ for i in range(0,10):
+ p= IMP.Particle()
+ m.add_particle(p)
+ os= OneSingle()
+ s= IMP.ListRestraint(m.get_particles(), os)
+ m.add_restraint(s)
+ score= m.evaluate(False)
+ self.assertEqual(score, 10, "Wrong score")
+
+ def test_ss(self):
+ """Test the distanceto score"""
+ m= IMP.Model()
+ p= IMP.Particle()
+ m.add_particle(p)
+ d=IMP.XYZDecorator.create(p)
+ d.set_x(0)
+ d.set_y(1)
+ d.set_z(1)
+ d.set_coordinates_are_optimized(True)
+ v= IMP.Vector3D(3,1,5)
+ l= Linear()
+ s= IMP.DistanceToSingletonScore(v, l)
+ r= IMP.ListRestraint(m.get_particles(), s)
+ m.add_restraint(r)
+ e= m.evaluate(False)
+ self.assertEqual(e,5, "Wrong distance in score")
+
+
+if __name__ == '__main__':
+ unittest.main()
Index: kernel/pyext/IMP.i
===================================================================
--- kernel/pyext/IMP.i (revision 345)
+++ kernel/pyext/IMP.i (working copy)
@@ -49,13 +49,22 @@
%pythonprepend NonbondedRestraint::NonbondedRestraint %{
args[1].thisown=0
%}
%pythonprepend BondDecoratorRestraint::BondDecoratorRestraint %{
args[1].thisown=0
%}
- %pythonprepend DistancePairScore::DistancePairScore %{
+ %pythonprepend ListRestraint::ListRestraint %{
args[1].thisown=0
%}
- %pythonprepend SphericalDistancePairScore::SphericalDistancePairScore %{
+ %pythonprepend DistancePairScore::DistancePairScore %{
+ args[0].thisown=0
+ %}
+ %pythonprepend SphereDistancePairScore::SphereDistancePairScore %{
+ args[0].thisown=0
+ %}
+ %pythonprepend DistanceToSingletonScore::DistanceToSingletonScore %{
args[1].thisown=0
%}
}
@@ -82,6 +91,7 @@
%include "IMP/Restraint.h"
%include "IMP/restraints/RestraintSet.h"
%include "IMP/ScoreState.h"
+%include "IMP/SingletonScore.h"
%include "IMP/OptimizerState.h"
%include "IMP/log.h"
%include "IMP/Model.h"
@@ -104,6 +114,7 @@
%include "IMP/optimizers/states/VRMLLogOptimizerState.h"
%include "IMP/pair_scores/DistancePairScore.h"
%include "IMP/pair_scores/SphereDistancePairScore.h"
+%include "IMP/singleton_scores/DistanceToSingletonScore.h"
%include "IMP/restraints/DistanceRestraint.h"
%include "IMP/restraints/AngleRestraint.h"
%include "IMP/restraints/DihedralRestraint.h"
@@ -115,6 +126,7 @@
%include "IMP/restraints/ExclusionVolumeRestraint.h"
%include "IMP/restraints/NonbondedRestraint.h"
%include "IMP/restraints/BondDecoratorRestraint.h"
+%include "IMP/restraints/ListRestraint.h"
%include "IMP/score_states/BondedListScoreState.h"
%include "IMP/score_states/NonbondedListScoreState.h"
%include "IMP/score_states/BipartiteNonbondedListScoreState.h"
@@ -135,7 +147,7 @@
%template(StringKey) Key<String>;
%template(AtomType) Key<AtomTypeTag>;
%template(ResidueType) Key<ResidueTypeTag>;
- %template(show_named_nierarchy) show<NameDecorator>;
+ %template(show_named_hierarchy) show<NameDecorator>;
%template(show_molecular_hierarchy) show<MolecularHierarchyDecorator>;
%template(Particles) ::std::vector<Particle*>;
%template(Restraints) ::std::vector<Restraint*>;
Index: kernel/include/IMP.h
===================================================================
--- kernel/include/IMP.h (revision 345)
+++ kernel/include/IMP.h (working copy)
@@ -25,6 +25,7 @@
#include "IMP/ModelData.h"
#include "IMP/Model.h"
#include "IMP/PairScore.h"
+#include "IMP/SingletonScore.h"
#include "IMP/Vector3D.h"
#include "IMP/decorators/HierarchyDecorator.h"
#include "IMP/decorators/MolecularHierarchyDecorator.h"
@@ -39,6 +40,7 @@
#include "IMP/optimizers/states/VRMLLogOptimizerState.h"
#include "IMP/pair_scores/DistancePairScore.h"
#include "IMP/pair_scores/SphereDistancePairScore.h"
+#include "IMP/singleton_scores/DistanceToSingletonScore.h"
#include "IMP/restraints/RestraintSet.h"
#include "IMP/restraints/DistanceRestraint.h"
#include "IMP/restraints/AngleRestraint.h"
@@ -50,6 +52,7 @@
#include "IMP/restraints/PairConnectivityRestraint.h"
#include "IMP/restraints/ExclusionVolumeRestraint.h"
#include "IMP/restraints/NonbondedRestraint.h"
+#include "IMP/restraints/ListRestraint.h"
#include "IMP/restraints/BondDecoratorRestraint.h"
#include "IMP/score_states/BipartiteNonbondedListScoreState.h"
#include "IMP/score_states/NonbondedListScoreState.h"
Index: kernel/include/IMP/SConscript
===================================================================
--- kernel/include/IMP/SConscript (revision 345)
+++ kernel/include/IMP/SConscript (working copy)
@@ -6,7 +6,7 @@
'ModelData.h', 'RigidBody.h', 'log.h', 'DerivativeAccumulator.h',
'Key.h', 'AttributeTable.h', 'utility.h', 'Restraint.h', 'Optimizer.h',
'DecoratorBase.h', 'Object.h', 'Vector3D.h', 'ScoreFuncParams.h',
- 'UnaryFunction.h', 'PairScore.h']
+ 'UnaryFunction.h', 'PairScore.h', 'SingletonScore.h', 'Grid3D.h']
# Install the include files:
includedir = os.path.join(env['includedir'], 'IMP')
@@ -19,4 +19,5 @@
SConscript('decorators/SConscript')
SConscript('unary_functions/SConscript')
SConscript('pair_scores/SConscript')
+SConscript('singleton_scores/SConscript')
SConscript('score_states/SConscript')
Index: kernel/src/SConscript
===================================================================
--- kernel/src/SConscript (revision 345)
+++ kernel/src/SConscript (working copy)
@@ -11,6 +11,7 @@
unary_functions_files = SConscript('unary_functions/SConscript')
score_states_files = SConscript('score_states/SConscript')
pair_scores_files = SConscript('pair_scores/SConscript')
+singleton_scores_files = SConscript('singleton_scores/SConscript')
score_states_files = SConscript('score_states/SConscript')
# Source files
@@ -19,7 +20,8 @@
'OptimizerState.cpp', 'Log.cpp', 'Restraint.cpp', 'Optimizer.cpp',
'Object.cpp', 'BasicScoreFuncParams.cpp'
] + decorators_files + restraints_files + optimizers_files \
- + unary_functions_files + pair_scores_files + score_states_files
+ + unary_functions_files + pair_scores_files + score_states_files\
+ + singleton_scores_files
# Build the shared library:
lib = env.SharedLibrary('imp', files)
Index: kernel/src/restraints/SConscript
===================================================================
--- kernel/src/restraints/SConscript (revision 345)
+++ kernel/src/restraints/SConscript (working copy)
@@ -5,7 +5,8 @@
'SphericalRestraint.cpp', 'RestraintSet.cpp',
'DistanceRestraint.cpp', 'AngleRestraint.cpp', 'DihedralRestraint.cpp',
'TorusRestraint.cpp', 'ExclusionVolumeRestraint.cpp',
- 'NonbondedRestraint.cpp', 'BondDecoratorRestraint.cpp']
+ 'NonbondedRestraint.cpp', 'BondDecoratorRestraint.cpp',
+ 'ListRestraint.cpp']
files = [File(x) for x in files]
Return('files')