Index: include/IMP/restraints/DistanceRestraint.h
===================================================================
--- include/IMP/restraints/DistanceRestraint.h (revision 651)
+++ include/IMP/restraints/DistanceRestraint.h (working copy)
@@ -28,23 +28,18 @@
class IMPDLLEXPORT DistanceRestraint : public Restraint
{
public:
-
- DistanceRestraint(Model* model, Particle* p1, Particle* p2,
+ //! Create the distance restraint.
+ /** \param[in] p1 Pointer to first particle in distance restraint.
+ \param[in] p2 Pointer to second particle in distance restraint.
+ \param[in] score_func Scoring function for the restraint.
+ */
+ DistanceRestraint(Particle* p1, Particle* p2,
ScoreFunc* score_func);
virtual ~DistanceRestraint();
IMP_RESTRAINT("0.5", "Daniel Russel")
protected:
- //! Do set up for the distance restraint constructors.
- /** \param[in] model Pointer to the model.
- \param[in] p1 Pointer to first particle in distance restraint.
- \param[in] p2 Pointer to second particle in distance restraint.
- \param[in] score_func Scoring function for the restraint.
- */
- void set_up(Model* model, Particle* p1, Particle* p2,
- ScoreFunc* score_func);
-
//! scoring function for this restraint
ScoreFunc* score_func_;
};
Index: include/IMP/restraints/SphericalRestraint.h
===================================================================
--- include/IMP/restraints/SphericalRestraint.h (revision 651)
+++ include/IMP/restraints/SphericalRestraint.h (working copy)
@@ -22,8 +22,8 @@
class IMPDLLEXPORT SphericalRestraint : public Restraint
{
public:
+ // Create the SphericalRestraint.
/**
- \param[in] model
\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.
@@ -31,7 +31,7 @@
\param[in] score_func The scoring function. It is deleted in the
destructor.
*/
- SphericalRestraint(Model* model, Particle* p,
+ SphericalRestraint(Particle* p,
Float x, Float y, Float z,
ScoreFunc* score_func);
virtual ~SphericalRestraint();
Index: src/restraints/ProximityRestraint.cpp
===================================================================
--- src/restraints/ProximityRestraint.cpp (revision 651)
+++ src/restraints/ProximityRestraint.cpp (working copy)
@@ -39,7 +39,7 @@
// create the restraint
ScoreFunc *sf = score_func_params->create_score_func();
- dist_rsrs_[idx] = new DistanceRestraint(model, get_particle(i),
+ dist_rsrs_[idx] = new DistanceRestraint(get_particle(i),
get_particle(j),
sf);
idx++;
@@ -84,8 +84,7 @@
IMP_LOG(VERBOSE, i << " " << j << " add distance: " << actual_mean);
score_func_params->set_mean(actual_mean);
ScoreFunc *sf = score_func_params->create_score_func();
- dist_rsrs_[idx] = new DistanceRestraint(model,
- get_particle(i),
+ dist_rsrs_[idx] = new DistanceRestraint(get_particle(i),
get_particle(j),
sf);
idx++;
Index: src/restraints/DistanceRestraint.cpp
===================================================================
--- src/restraints/DistanceRestraint.cpp (revision 651)
+++ src/restraints/DistanceRestraint.cpp (working copy)
@@ -19,29 +19,9 @@
//! particles must be at least this far apart to calculate the restraint
static const Float MIN_DISTANCE = 0.0000001;
-//! Constructor - set up the restraint using a given mean.
-/** \param[in] model Pointer to the model.
- \param[in] p1 Pointer to first particle in distance restraint.
- \param[in] p2 Pointer to second particle in distance restraint.
- \param[in] score_func Scoring function for the restraint.
- */
-DistanceRestraint::DistanceRestraint(Model* model, Particle* p1, Particle* p2,
+DistanceRestraint::DistanceRestraint(Particle* p1, Particle* p2,
ScoreFunc* score_func)
{
- set_up(model, p1, p2, score_func);
-}
-
-
-//! Do set up for the distance restraint constructors.
-/** \param[in] model Pointer to the model.
- \param[in] p1 Pointer to first particle in distance restraint.
- \param[in] p2 Pointer to second particle in distance restraint.
- \param[in] score_func_params Score function parameters for the restraint.
- */
-void DistanceRestraint::set_up(Model* , Particle* p1, Particle* p2,
- ScoreFunc* score_func)
-{
- // LogMsg(VERBOSE, "Set up distance restraint.");
add_particle(p1);
add_particle(p2);
@@ -100,7 +80,10 @@
score = (*score_func_)(distance);
}
- IMP_LOG(VERBOSE, "distance: " << distance << " score: " << score);
+ IMP_LOG(VERBOSE, "For " << get_particle(0)->get_index()
+ << " and " << get_particle(1)->get_index()
+ << " distance: " << distance
+ << " score: " << score << std::endl);
return score;
}
@@ -122,6 +105,7 @@
out << " and " << get_particle(1)->get_index();
out << " ";
score_func_->show(out);
+ out << std::endl;
}
} // namespace IMP
Index: src/restraints/PairConnectivityRestraint.cpp
===================================================================
--- src/restraints/PairConnectivityRestraint.cpp (revision 651)
+++ src/restraints/PairConnectivityRestraint.cpp (working copy)
@@ -53,8 +53,7 @@
} else {
IMP_LOG(VERBOSE, "Adding possible restraint: " << i << " " << j);
ScoreFunc *sf = score_func_params->create_score_func();
- rs_iter->rsr_ = new DistanceRestraint(model,
- get_particle(i),
+ rs_iter->rsr_ = new DistanceRestraint(get_particle(i),
get_particle(j),
sf);
@@ -118,8 +117,7 @@
} else {
IMP_LOG(VERBOSE, "Adding possible restraint: " << i << " " << j);
ScoreFunc *sf = score_func_params->create_score_func();
- rs_iter->rsr_ = new DistanceRestraint(model,
- get_particle(i),
+ rs_iter->rsr_ = new DistanceRestraint(get_particle(i),
get_particle(j),
sf);
Index: src/restraints/SphericalRestraint.cpp
===================================================================
--- src/restraints/SphericalRestraint.cpp (revision 651)
+++ src/restraints/SphericalRestraint.cpp (working copy)
@@ -22,7 +22,7 @@
-SphericalRestraint::SphericalRestraint(Model*, Particle* p,
+SphericalRestraint::SphericalRestraint(Particle* p,
Float x, Float y, Float z,
ScoreFunc* score_func)
{
@@ -79,10 +79,13 @@
out << "Spherical restraint (inactive):" << std::endl;
}
- out << "version: " << version() << " ";
- out << "last_modified_by: " << last_modified_by() << 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: src/restraints/ConnectivityRestraint.cpp
===================================================================
--- src/restraints/ConnectivityRestraint.cpp (revision 651)
+++ src/restraints/ConnectivityRestraint.cpp (working copy)
@@ -51,8 +51,7 @@
// create the restraint
ScoreFunc *sf = score_func_params->create_score_func();
- rs_iter->rsr_ = new DistanceRestraint(model,
- get_particle(i),
+ rs_iter->rsr_ = new DistanceRestraint(get_particle(i),
get_particle(j),
sf);
++rs_iter;
@@ -109,8 +108,7 @@
// create the restraint
ScoreFunc *sf = score_func_params->create_score_func();
- rs_iter->rsr_ = new DistanceRestraint(model,
- get_particle(i),
+ rs_iter->rsr_ = new DistanceRestraint(get_particle(i),
get_particle(j),
sf);
++rs_iter;
Index: src/restraints/ExclusionVolumeRestraint.cpp
===================================================================
--- src/restraints/ExclusionVolumeRestraint.cpp (revision 651)
+++ src/restraints/ExclusionVolumeRestraint.cpp (working copy)
@@ -74,8 +74,7 @@
// create the restraint
ScoreFunc *sf = score_func_params->create_score_func();
- dist_rsrs_.push_back(new DistanceRestraint(model,
- get_particle(i),
+ dist_rsrs_.push_back(new DistanceRestraint(get_particle(i),
get_particle(j),
sf));
}
@@ -128,8 +127,7 @@
// create the restraint
ScoreFunc *sf = score_func_params->create_score_func();
- dist_rsrs_.push_back(new DistanceRestraint(model,
- get_particle(i),
+ dist_rsrs_.push_back(new DistanceRestraint(get_particle(i),
get_particle(j),
sf));
idx++;
Index: test/coordinate/test_coordinate.py
===================================================================
--- test/coordinate/test_coordinate.py (revision 651)
+++ test/coordinate/test_coordinate.py (working copy)
@@ -25,8 +25,7 @@
def _do_test(self, center, sf):
"""All coordinate values should be greater than the set minimum"""
- r= IMP.SphericalRestraint(self.model,
- self.model.get_particle(self.pi),
+ r= IMP.SphericalRestraint(self.model.get_particle(self.pi),
center[0], center[1], center[2],
sf)
ri=self.model.add_restraint(r)
Index: test/distance/test_distance.py
===================================================================
--- test/distance/test_distance.py (revision 651)
+++ test/distance/test_distance.py (working copy)
@@ -35,7 +35,7 @@
for sf in (IMP.HarmonicUpperBound(mean, 0.1),
IMP.HarmonicLowerBound(mean, 0.1),
IMP.Harmonic(mean, 0.1)):
- r = IMP.DistanceRestraint(self.imp_model, p1, p2, sf)
+ r = IMP.DistanceRestraint(p1, p2, sf)
self.rsrs.append(r)
def _make_restraints(self):
@@ -53,27 +53,27 @@
# all should be 0.0
for fs in (IMP.HarmonicUpperBound(3.0, 0.1),
IMP.HarmonicLowerBound(3.0, 0.1), IMP.Harmonic(3.0, 0.1)):
- r = IMP.DistanceRestraint(self.imp_model, self.particles[1],
+ r = IMP.DistanceRestraint(self.particles[1],
self.particles[0], fs)
self.rsrs.append(r)
# exceed lower bound
for fs in (IMP.HarmonicUpperBound(5.0, 0.1),
IMP.HarmonicLowerBound(5.0, 0.1), IMP.Harmonic(5.0, 0.1)):
- r = IMP.DistanceRestraint(self.imp_model, self.particles[1],
+ r = IMP.DistanceRestraint(self.particles[1],
self.particles[2], fs)
self.rsrs.append(r)
# exceed upper bound
for fs in (IMP.HarmonicUpperBound(4.0, 0.1),
IMP.HarmonicLowerBound(4.0, 0.1), IMP.Harmonic(4.0, 0.1)):
- r = IMP.DistanceRestraint(self.imp_model, self.particles[0],
+ r = IMP.DistanceRestraint(self.particles[0],
self.particles[2], fs)
self.rsrs.append(r)
def test_show(self):
"""Test Restraint::show() method"""
- r = IMP.DistanceRestraint(self.imp_model, self.particles[1],
+ r = IMP.DistanceRestraint(self.particles[1],
self.particles[0], IMP.Harmonic(0.0, 0.1))
r.show()
Index: test/misc/test_restraint_sets.py
===================================================================
--- test/misc/test_restraint_sets.py (revision 651)
+++ test/misc/test_restraint_sets.py (working copy)
@@ -17,7 +17,7 @@
20.0, 74.0, -80.0))
# separate particles by 5.0:
- self.distrsr = IMP.DistanceRestraint(self.model, self.particles[0],
+ self.distrsr = IMP.DistanceRestraint(self.particles[0],
self.particles[1],
IMP.Harmonic(5.0, 0.1))
Index: test/modeller/test_exclusion_volumes.py
===================================================================
--- test/modeller/test_exclusion_volumes.py (revision 651)
+++ test/modeller/test_exclusion_volumes.py (working copy)
@@ -126,14 +126,14 @@
p2 = self.particles[i+1]
mean = p1.get_value(radius) + p2.get_value(radius)
sf = IMP.HarmonicUpperBound(mean, 0.1)
- rsrs.append(IMP.DistanceRestraint(self.imp_model, p1, p2, sf))
+ rsrs.append(IMP.DistanceRestraint(p1, p2, sf))
for i in range(5, 11):
p1 = self.particles[i]
p2 = self.particles[i+1]
mean = p1.get_value(radius) + p2.get_value(radius)
sf = IMP.HarmonicUpperBound(mean, 0.1)
- rsrs.append(IMP.DistanceRestraint(self.imp_model, p1, p2, sf))
+ rsrs.append(IMP.DistanceRestraint(p1, p2, sf))
# create the exclusion volume for each protein
score_func_params_lb = IMP.BasicScoreFuncParams("harmonic_lower_bound", 0.0, 0.1)
@@ -192,14 +192,14 @@
p2 = self.particles[i+1]
mean = p1.get_value(radius) + p2.get_value(radius)
sf = IMP.HarmonicUpperBound(mean, 0.1)
- rsrs.append(IMP.DistanceRestraint(self.imp_model, p1, p2, sf))
+ rsrs.append(IMP.DistanceRestraint(p1, p2, sf))
for i in range(5, 11):
p1 = self.particles[i]
p2 = self.particles[i+1]
mean = p1.get_value(radius) + p2.get_value(radius)
sf = IMP.HarmonicUpperBound(mean, 0.1)
- rsrs.append(IMP.DistanceRestraint(self.imp_model, p1, p2, sf))
+ rsrs.append(IMP.DistanceRestraint(p1, p2, sf))
# create the exclusion volume for each protein
score_func_params_lb = IMP.BasicScoreFuncParams("harmonic_lower_bound", 0.0, 0.1)
Index: test/sd_optimizer/test_sd_optimizer.py
===================================================================
--- test/sd_optimizer/test_sd_optimizer.py (revision 651)
+++ test/sd_optimizer/test_sd_optimizer.py (working copy)
@@ -36,7 +36,7 @@
p2 = self.particles[pairs[1]]
mean = p1.get_value(radkey) + p2.get_value(radkey)
sf = IMP.Harmonic(mean, 0.1)
- rsr = IMP.DistanceRestraint(self.imp_model, p1, p2, sf)
+ rsr = IMP.DistanceRestraint(p1, p2, sf)
self.rsrs.append(rsr)
# add restraints
Index: pyext/IMP/utils.py
===================================================================
--- pyext/IMP/utils.py (revision 651)
+++ pyext/IMP/utils.py (working copy)
@@ -88,7 +88,7 @@
mean = particles[i].get_value(radius_name) \
+ particles[j].get_value(radius_name)
sf = IMP.HarmonicLowerBound(mean, sd)
- rsrs.append(IMP.DistanceRestraint(model, particles[i], particles[j],
+ rsrs.append(IMP.DistanceRestraint(particles[i], particles[j],
sf))
Index: pyext/IMP/xml_loader.py
===================================================================
--- pyext/IMP/xml_loader.py (revision 651)
+++ pyext/IMP/xml_loader.py (working copy)
@@ -198,7 +198,7 @@
score_func_params = get_basic_score_func_params(score_func_str, distance, sd)
sf = score_func_params.create_score_func()
- model.restraints.append(IMP.DistanceRestraint(model, p1, p2, sf))
+ model.restraints.append(IMP.DistanceRestraint(p1, p2, sf))
model.restraint_sets[rs_idx].add_restraint(model.restraints[len(model.restraints)-1])
Index: pyext/IMP.i
===================================================================
--- pyext/IMP.i (revision 651)
+++ pyext/IMP.i (working copy)
@@ -25,10 +25,10 @@
args[1].thisown=0
%}
%pythonprepend DistanceRestraint::DistanceRestraint %{
- args[3].thisown=0
+ args[2].thisown=0
%}
%pythonprepend SphericalRestraint::SphericalRestraint %{
- args[5].thisown=0
+ args[4].thisown=0
%}
}