Index: kernel/test/states/test_nonbonded_list.py
===================================================================
--- kernel/test/states/test_nonbonded_list.py (revision 467)
+++ kernel/test/states/test_nonbonded_list.py (working copy)
@@ -119,6 +119,8 @@
self.assertEqual(score, 25, "Wrong score")
def test_spheres2(self):
"""Test the nonbonded list of spheres (num pairs)"""
+ # This uses the internal checks of the nonbonded list to
+ # verify correctness
m= IMP.Model()
rk= IMP.FloatKey("radius")
for i in range(0,100):
Index: kernel/test/unary_functions/test_harmonic.py
===================================================================
--- kernel/test/unary_functions/test_harmonic.py (revision 467)
+++ kernel/test/unary_functions/test_harmonic.py (working copy)
@@ -9,11 +9,11 @@
"""Test Harmonic accessors"""
func = IMP.Harmonic(10.0, 1.0)
self.assertEqual(func.get_mean(), 10.0)
- self.assertEqual(func.get_sd(), 1.0)
+ self.assertEqual(func.get_k(), 1.0)
func.set_mean(5.0)
- func.set_sd(2.0)
+ func.set_k(2.0)
self.assertEqual(func.get_mean(), 5.0)
- self.assertEqual(func.get_sd(), 2.0)
+ self.assertEqual(func.get_k(), 2.0)
def test_show(self):
"""Check Harmonic::show() method"""
Index: kernel/test/restraints/test_dihedral.py
===================================================================
--- kernel/test/restraints/test_dihedral.py (revision 467)
+++ kernel/test/restraints/test_dihedral.py (working copy)
@@ -18,16 +18,17 @@
particles.append(IMP.utils.XYZParticle(model, 0.0, 0.0, 0.0))
particles.append(IMP.utils.XYZParticle(model, math.cos(system_angle),
math.sin(system_angle), 0.0))
- r = IMP.DistanceRestraint(IMP.Harmonic(1.0, 0.1),
+ k = IMP.Harmonic.k_from_standard_deviation(.1)
+ r = IMP.DistanceRestraint(IMP.Harmonic(1.0, k),
particles[0], particles[1])
model.add_restraint(r)
- r = IMP.DistanceRestraint(IMP.Harmonic(1.0, 0.1),
+ r = IMP.DistanceRestraint(IMP.Harmonic(1.0, k),
particles[1], particles[2])
model.add_restraint(r)
- r = IMP.DistanceRestraint(IMP.Harmonic(1.0, 0.1),
+ r = IMP.DistanceRestraint(IMP.Harmonic(1.0, k),
particles[2], particles[3])
model.add_restraint(r)
- rsr = IMP.DihedralRestraint(IMP.Harmonic(scored_angle, 0.1),
+ rsr = IMP.DihedralRestraint(IMP.Harmonic(scored_angle, k),
particles[0], particles[1], particles[2],
particles[3])
model.add_restraint(rsr)
Index: kernel/test/restraints/test_angle.py
===================================================================
--- kernel/test/restraints/test_angle.py (revision 467)
+++ kernel/test/restraints/test_angle.py (working copy)
@@ -17,11 +17,12 @@
particles.append(IMP.utils.XYZParticle(model, 0.0, 0.0, 0.0))
particles.append(IMP.utils.XYZParticle(model, -math.cos(system_angle),
math.sin(system_angle), 0.0))
- r = IMP.DistanceRestraint(IMP.Harmonic(1.0, 0.1),particles[0], particles[1])
+ k = IMP.Harmonic.k_from_standard_deviation(0.1)
+ r = IMP.DistanceRestraint(IMP.Harmonic(1.0, k),particles[0], particles[1])
model.add_restraint(r)
- r = IMP.DistanceRestraint(IMP.Harmonic(1.0, 0.1), particles[1], particles[2])
+ r = IMP.DistanceRestraint(IMP.Harmonic(1.0, k), particles[1], particles[2])
model.add_restraint(r)
- rsr = IMP.AngleRestraint(IMP.Harmonic(scored_angle, 0.1),
+ rsr = IMP.AngleRestraint(IMP.Harmonic(scored_angle, k),
particles[0], particles[1], particles[2])
model.add_restraint(rsr)
return model, rsr
@@ -36,7 +37,7 @@
self.assert_(model.evaluate(False) < 1e-6)
# When the angle is different, score should be far from zero:
model, rsr = self._setup_particles(angles[i], angles[-i-1])
- self.assert_(model.evaluate(False) > 10.0)
+ self.assert_(model.evaluate(False) > 2.0)
# Optimizing should reduce the score to zero:
opt = IMP.ConjugateGradients()
opt.set_model(model)
Index: kernel/include/IMP/unary_functions/Harmonic.h
===================================================================
--- kernel/include/IMP/unary_functions/Harmonic.h (revision 467)
+++ kernel/include/IMP/unary_functions/Harmonic.h (working copy)
@@ -23,7 +23,7 @@
class IMPDLLEXPORT Harmonic : public UnaryFunction
{
public:
- Harmonic(Float mean, Float sd) : mean_(mean), sd_(sd) {}
+ Harmonic(Float mean, Float k) : mean_(mean), k_(k) {}
virtual ~Harmonic() {}
@@ -32,9 +32,9 @@
return mean_;
}
- //! \return the standard deviation of this function
- Float get_sd() const {
- return sd_;
+ //! \return the spring constant
+ Float get_k() const {
+ return k_;
}
//! Set the mean of this function
@@ -42,16 +42,19 @@
mean_ = mean;
}
- //! Set the standard deviation of this function
- void set_sd(Float sd) {
- sd_ = sd;
+ //! Set the spring constant
+ void set_k(Float k) {
+ k_ = k;
}
//! Calculate harmonic score with respect to the given feature.
/** \param[in] feature Value of feature being tested.
\return Score
*/
- virtual Float operator()(Float feature);
+ virtual Float operator()(Float feature) {
+ Float d;
+ return operator()(feature, d);
+ }
//! Calculate harmonic score and derivative with respect to the given feature.
/** \param[in] feature Value of feature being tested.
@@ -59,15 +62,28 @@
the feature value.
\return Score
*/
- virtual Float operator()(Float feature, Float& deriv);
+ virtual Float operator()(Float feature, Float& deriv) {
+ Float e = (feature - mean_);
+ deriv = k_*e / 2.0;
+ return k_*e * e;
+ }
void show(std::ostream &out=std::cout) const {
- out << "Harmonic: " << mean_ << " and " << sd_ << std::endl;
+ out << "Harmonic: " << mean_ << " and " << k_ << std::endl;
}
-protected:
+ //! Return the k to use for a given modeller standard deviation
+ /** See the Modeller paper for an explaination.
+ Convert standard deviation to force constant, by dividing it
+ by sqrt(RT/2) where T=297.15K and energy units are kcal/mol.
+ */
+ static Float k_from_standard_deviation(Float sd, Float t=297.15) {
+ return (8.3145*0.0002388459*t/2) / square(sd);
+ }
+
+private:
Float mean_;
- Float sd_;
+ Float k_;
};
} // namespace IMP
Index: kernel/include/IMP/unary_functions/HarmonicLowerBound.h
===================================================================
--- kernel/include/IMP/unary_functions/HarmonicLowerBound.h (revision 467)
+++ kernel/include/IMP/unary_functions/HarmonicLowerBound.h (working copy)
@@ -18,7 +18,7 @@
class IMPDLLEXPORT HarmonicLowerBound : public Harmonic
{
public:
- HarmonicLowerBound(Float mean, Float sd) : Harmonic(mean, sd) {}
+ HarmonicLowerBound(Float mean, Float k) : Harmonic(mean, k) {}
virtual ~HarmonicLowerBound() {}
//! Calculate lower-bound harmonic score with respect to the given feature.
@@ -26,7 +26,13 @@
\param[in] feature Value of feature being tested.
\return Score
*/
- virtual Float operator()(Float feature);
+ virtual Float operator()(Float feature) {
+ if (feature >= Harmonic::get_mean()) {
+ return 0.0;
+ } else {
+ return Harmonic::operator()(feature);
+ }
+ }
//! Calculate lower-bound harmonic score and derivative for a feature.
/** If the feature is greater than or equal to the mean, the score is zero.
@@ -35,10 +41,18 @@
the feature value.
\return Score
*/
- virtual Float operator()(Float feature, Float& deriv);
+ virtual Float operator()(Float feature, Float& deriv) {
+ if (feature >= Harmonic::get_mean()) {
+ deriv = 0.0;
+ return 0.0;
+ } else {
+ return Harmonic::operator()(feature, deriv);
+ }
+ }
void show(std::ostream &out=std::cout) const {
- out << "HarmonicLB: " << mean_ << " and " << sd_ << std::endl;
+ out << "HarmonicLB: " << Harmonic::get_mean()
+ << " and " << Harmonic::get_k() << std::endl;
}
};
Index: kernel/include/IMP/unary_functions/SConscript
===================================================================
--- kernel/include/IMP/unary_functions/SConscript (revision 467)
+++ kernel/include/IMP/unary_functions/SConscript (working copy)
@@ -1,10 +1,13 @@
+Import('env')
import os.path
-Import('env')
-
-files = ['Harmonic.h', 'HarmonicLowerBound.h', 'HarmonicUpperBound.h',
- 'OpenCubicSpline.h', 'ClosedCubicSpline.h', 'Cosine.h', 'Linear.h']
-
-# Install the include files:
-includedir = os.path.join(env['includedir'], 'IMP', 'unary_functions')
+files=[]
+files.append( 'ClosedCubicSpline.h' )
+files.append( 'Cosine.h' )
+files.append( 'Harmonic.h' )
+files.append( 'HarmonicLowerBound.h' )
+files.append( 'HarmonicUpperBound.h' )
+files.append( 'Linear.h' )
+files.append( 'OpenCubicSpline.h' )
+includedir = os.path.join(env['includedir'], 'IMP', 'unary_functions' )
inst = env.Install(includedir, files)
env.Alias('install', inst)
Index: kernel/include/IMP/unary_functions/HarmonicUpperBound.h
===================================================================
--- kernel/include/IMP/unary_functions/HarmonicUpperBound.h (revision 467)
+++ kernel/include/IMP/unary_functions/HarmonicUpperBound.h (working copy)
@@ -26,7 +26,13 @@
\param[in] feature Value of feature being tested.
\return Score
*/
- virtual Float operator()(Float feature);
+ virtual Float operator()(Float feature) {
+ if (feature <= Harmonic::get_mean()) {
+ return 0.0;
+ } else {
+ return Harmonic::operator()(feature);
+ }
+ }
//! Calculate upper-bound harmonic score and derivative for a feature.
/** If the feature is less than or equal to the mean, the score is zero.
@@ -35,10 +41,18 @@
the feature value.
\return Score
*/
- virtual Float operator()(Float feature, Float& deriv);
+ virtual Float operator()(Float feature, Float& deriv) {
+ if (feature <= Harmonic::get_mean()) {
+ deriv = 0.0;
+ return 0.0;
+ } else {
+ return Harmonic::operator()(feature, deriv);
+ }
+ }
void show(std::ostream &out=std::cout) const {
- out << "HarmonicLUB: " << mean_ << " and " << sd_ << std::endl;
+ out << "HarmonicLUB: " << Harmonic::get_mean()
+ << " and " << Harmonic::get_k() << std::endl;
}
};
Index: kernel/src/unary_functions/Harmonic.cpp
===================================================================
--- kernel/src/unary_functions/Harmonic.cpp (revision 467)
+++ kernel/src/unary_functions/Harmonic.cpp (working copy)
@@ -1,44 +0,0 @@
-/**
- * \file Harmonic.cpp \brief Harmonic function.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#include "IMP/unary_functions/Harmonic.h"
-#include "IMP/log.h"
-
-namespace IMP
-{
-
-//! Calculate harmonic score with respect to the given feature.
-/** \param[in] feature Value of feature being tested.
- \return Score
- */
-Float Harmonic::operator()(Float feature)
-{
- Float dummy;
-
- return operator()(feature, dummy);
-}
-
-//! Calculate harmonic score and derivative with respect to the given feature.
-/** \param[in] feature Value of feature being tested.
- \param[out] deriv Partial derivative of the score with respect to
- the feature value.
- \return Score
- */
-Float Harmonic::operator()(Float feature, Float& deriv)
-{
- Float e;
- Float sd;
-
- // convert standard deviation to force constant, by dividing by sqrt(RT/2)
- // where T=297.15K and energy units are kcal/mol
- sd = sd_ / 0.54318464;
- e = (feature - mean_) / sd;
- deriv = e / sd * 2.0;
- return e * e;
-}
-
-} // namespace IMP
Index: kernel/src/unary_functions/HarmonicLowerBound.cpp
===================================================================
--- kernel/src/unary_functions/HarmonicLowerBound.cpp (revision 467)
+++ kernel/src/unary_functions/HarmonicLowerBound.cpp (working copy)
@@ -1,46 +0,0 @@
-/**
- * \file HarmonicLowerBound.cpp \brief Harmonic lower bound function.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#include "IMP/unary_functions/HarmonicLowerBound.h"
-#include "IMP/log.h"
-
-namespace IMP
-{
-
-//! Calculate lower-bound harmonic score with respect to the given feature.
-/** If the feature is greater than or equal to the mean, the score is zero.
- \param[in] feature Value of feature being tested.
- \return Score
- */
-Float HarmonicLowerBound::operator()(Float feature)
-{
- if (feature >= mean_) {
- return 0.0;
- } else {
- return Harmonic::operator()(feature);
- }
-}
-
-
-//! Calculate lower-bound harmonic score and derivative for a feature.
-/** If the feature is greater than or equal to the mean, the score is zero.
- \param[in] feature Value of feature being tested.
- \param[out] deriv Partial derivative of the score with respect to
- the feature value.
- \return Score
- */
-Float HarmonicLowerBound::operator()(Float feature, Float& deriv)
-{
- if (feature >= mean_) {
- deriv = 0.0;
- return 0.0;
- } else {
- return Harmonic::operator()(feature, deriv);
- }
-}
-
-} // namespace IMP
Index: kernel/src/unary_functions/HarmonicUpperBound.cpp
===================================================================
--- kernel/src/unary_functions/HarmonicUpperBound.cpp (revision 467)
+++ kernel/src/unary_functions/HarmonicUpperBound.cpp (working copy)
@@ -1,46 +0,0 @@
-/**
- * \file HarmonicUpperBound.cpp \brief Harmonic upper bound function.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#include "IMP/unary_functions/HarmonicUpperBound.h"
-#include "IMP/log.h"
-
-namespace IMP
-{
-
-//! Calculate upper-bound harmonic score with respect to the given feature.
-/** If the feature is less than or equal to the mean, the score is zero.
- \param[in] feature Value of feature being tested.
- \return Score
- */
-Float HarmonicUpperBound::operator()(Float feature)
-{
- if (feature <= mean_) {
- return 0.0;
- } else {
- return Harmonic::operator()(feature);
- }
-}
-
-
-//! Calculate upper-bound harmonic score and derivative for a feature.
-/** If the feature is less than or equal to the mean, the score is zero.
- \param[in] feature Value of feature being tested.
- \param[out] deriv Partial derivative of the score with respect to
- the feature value.
- \return Score
- */
-Float HarmonicUpperBound::operator()(Float feature, Float& deriv)
-{
- if (feature <= mean_) {
- deriv = 0.0;
- return 0.0;
- } else {
- return Harmonic::operator()(feature, deriv);
- }
-}
-
-} // namespace IMP
Index: kernel/src/unary_functions/SConscript
===================================================================
--- kernel/src/unary_functions/SConscript (revision 467)
+++ kernel/src/unary_functions/SConscript (working copy)
@@ -1,7 +1,6 @@
Import('env')
-
-files = ['Harmonic.cpp', 'HarmonicLowerBound.cpp', 'HarmonicUpperBound.cpp',
- 'OpenCubicSpline.cpp', 'ClosedCubicSpline.cpp', 'Cosine.cpp']
-
-files = [File(x) for x in files]
+files=[]
+files.append(File( 'ClosedCubicSpline.cpp' ))
+files.append(File( 'Cosine.cpp' ))
+files.append(File( 'OpenCubicSpline.cpp' ))
Return('files')