Here is the patch that was discussed a while ago which makes UnaryFunction::evaluate_with_derivative return a std::pair instead of using one pass by reference to return. It also removes the hack in IMP.i to get the return value right.
Index: kernel/include/IMP/UnaryFunction.h =================================================================== --- kernel/include/IMP/UnaryFunction.h (revision 669) +++ kernel/include/IMP/UnaryFunction.h (working copy) @@ -14,9 +14,13 @@ namespace IMP {
+typedef std::pair<Float, Float> FloatPair; + //! Abstract single variable functor class for score functions. /** These functors take a single feature value, and return a corresponding score (and optionally also the first derivative). + + \ingroup kernel */ class IMPDLLEXPORT UnaryFunction : public RefCountedObject { @@ -36,7 +40,7 @@ given feaure. \return Score */ - virtual Float evaluate_with_derivative(Float feature, Float& deriv) const = 0; + virtual FloatPair evaluate_with_derivative(Float feature) const = 0;
virtual void show(std::ostream &out=std::cout) const = 0; }; Index: kernel/include/IMP/optimizers/MonteCarlo.h =================================================================== --- kernel/include/IMP/optimizers/MonteCarlo.h (revision 669) +++ kernel/include/IMP/optimizers/MonteCarlo.h (working copy) @@ -15,8 +15,6 @@ namespace IMP {
-typedef std::vector<Mover*> Movers; - //! A Monte Carlo optimizer. /** The optimizer uses a set of Mover objects to propose steps. Currently each Mover is called at each Monte Carlo iteration. This may change in Index: kernel/include/IMP/optimizers/Mover.h =================================================================== --- kernel/include/IMP/optimizers/Mover.h (revision 669) +++ kernel/include/IMP/optimizers/Mover.h (working copy) @@ -76,6 +76,8 @@
IMP_OUTPUT_OPERATOR(Mover);
+typedef std::vector<Mover*> Movers; + } // namespace IMP
#endif /* __IMP_MOVER_H */ Index: kernel/include/IMP/internal/evaluate_distance_pair_score.h =================================================================== --- kernel/include/IMP/internal/evaluate_distance_pair_score.h (revision 669) +++ kernel/include/IMP/internal/evaluate_distance_pair_score.h (working copy) @@ -9,6 +9,7 @@ #define __IMP_EVALUATE_DISTANCE_PAIR_SCORE_H
#include "../Vector3D.h" +#include <boost/tuple/tuple.hpp>
namespace IMP { @@ -43,7 +44,7 @@ if (da && distance >= MIN_DISTANCE) { Float deriv;
- score = f->evaluate_with_derivative(shifted_distance, deriv); + boost::tie(score, deriv) = f->evaluate_with_derivative(shifted_distance);
Vector3D d= delta/distance *deriv; d0.add_to_coordinates_derivative(d, *da); Index: kernel/include/IMP/unary_functions/ClosedCubicSpline.h =================================================================== --- kernel/include/IMP/unary_functions/ClosedCubicSpline.h (revision 669) +++ kernel/include/IMP/unary_functions/ClosedCubicSpline.h (working copy) @@ -40,12 +40,10 @@
//! Calculate 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. \exception ValueException Feature is out of defined range. \return Score */ - virtual Float evaluate_with_derivative(Float feature, Float& deriv) const; + virtual FloatPair evaluate_with_derivative(Float feature) const;
void show(std::ostream &out=std::cout) const { out << "Closed cubic spline of " << values_.size() << " values from " Index: kernel/include/IMP/unary_functions/Linear.h =================================================================== --- kernel/include/IMP/unary_functions/Linear.h (revision 669) +++ kernel/include/IMP/unary_functions/Linear.h (working copy) @@ -28,9 +28,8 @@ return (feature-offset_)*slope_; }
- virtual Float evaluate_with_derivative(Float feature, Float& deriv) const { - deriv= slope_; - return evaluate(feature); + virtual FloatPair evaluate_with_derivative(Float feature) const { + return std::make_pair(evaluate(feature), slope_); }
void set_slope(Float f) { Index: kernel/include/IMP/unary_functions/WormLikeChain.h =================================================================== --- kernel/include/IMP/unary_functions/WormLikeChain.h (revision 669) +++ kernel/include/IMP/unary_functions/WormLikeChain.h (working copy) @@ -62,10 +62,8 @@
//! Calculate the WormLikeChain energy given the length /** \param[in] l Current length in angstroms - \param[out] deriv force in kcal/angstrom mol - \return Score */ - virtual Float evaluate_with_derivative(Float fl, Float& deriv) const { + virtual FloatPair evaluate_with_derivative(Float fl) const { unit::Angstrom l(fl); if (l < unit::Angstrom(0)) l=unit::Angstrom(0); unit::Piconewton doubled; @@ -81,9 +79,9 @@ // convert from picoNewton unit::YoctoKilocaloriePerAngstrom du= unit::convert_J_to_Cal(doubled);
- deriv = (du*unit::ATOMS_PER_MOL).get_value(); + Float deriv = (du*unit::ATOMS_PER_MOL).get_value(); //std::cout << "Which converts to " << d << std::endl; - return evaluate(fl); + return std::make_pair(evaluate(fl), deriv); }
void show(std::ostream &out=std::cout) const { Index: kernel/include/IMP/unary_functions/Cosine.h =================================================================== --- kernel/include/IMP/unary_functions/Cosine.h (revision 669) +++ kernel/include/IMP/unary_functions/Cosine.h (working copy) @@ -43,11 +43,9 @@
//! Calculate 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 */ - virtual Float evaluate_with_derivative(Float feature, Float& deriv) const; + virtual FloatPair evaluate_with_derivative(Float feature) const;
void show(std::ostream &out=std::cout) const { out << "Cosine function with force " << force_constant_ Index: kernel/include/IMP/unary_functions/Harmonic.h =================================================================== --- kernel/include/IMP/unary_functions/Harmonic.h (revision 669) +++ kernel/include/IMP/unary_functions/Harmonic.h (working copy) @@ -56,20 +56,17 @@ \return Score */ virtual Float evaluate(Float feature) const { - Float d; - return evaluate_with_derivative(feature, d); + return evaluate_with_derivative(feature).first; }
//! 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 */ - virtual Float evaluate_with_derivative(Float feature, Float& deriv) const { + virtual FloatPair evaluate_with_derivative(Float feature) const { Float e = (feature - mean_); - deriv = k_ * e; - return 0.5 * k_ * e * e; + Float deriv = k_ * e; + return std::make_pair(0.5 * k_ * e * e, deriv); }
void show(std::ostream &out=std::cout) const { Index: kernel/include/IMP/unary_functions/HarmonicLowerBound.h =================================================================== --- kernel/include/IMP/unary_functions/HarmonicLowerBound.h (revision 669) +++ kernel/include/IMP/unary_functions/HarmonicLowerBound.h (working copy) @@ -37,16 +37,13 @@ //! 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 */ - virtual Float evaluate_with_derivative(Float feature, Float& deriv) const { + virtual FloatPair evaluate_with_derivative(Float feature) const { if (feature >= Harmonic::get_mean()) { - deriv = 0.0; - return 0.0; + return std::make_pair(0.0f, 0.0f); } else { - return Harmonic::evaluate_with_derivative(feature, deriv); + return Harmonic::evaluate_with_derivative(feature); } }
Index: kernel/include/IMP/unary_functions/OpenCubicSpline.h =================================================================== --- kernel/include/IMP/unary_functions/OpenCubicSpline.h (revision 669) +++ kernel/include/IMP/unary_functions/OpenCubicSpline.h (working copy) @@ -25,7 +25,7 @@ \param[in] minrange Feature value at first spline point \param[in] spacing Distance (in feature space) between points */ - OpenCubicSpline(const std::vector<Float> &values, Float minrange, + OpenCubicSpline(const Floats &values, Float minrange, Float spacing);
virtual ~OpenCubicSpline() {} @@ -39,12 +39,10 @@
//! Calculate 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. \exception ValueException Feature is out of defined range. \return Score */ - virtual Float evaluate_with_derivative(Float feature, Float& deriv) const; + virtual FloatPair evaluate_with_derivative(Float feature) const;
void show(std::ostream &out=std::cout) const { out << "Open cubic spline of " << values_.size() << " values from " Index: kernel/include/IMP/unary_functions/HarmonicUpperBound.h =================================================================== --- kernel/include/IMP/unary_functions/HarmonicUpperBound.h (revision 669) +++ kernel/include/IMP/unary_functions/HarmonicUpperBound.h (working copy) @@ -37,16 +37,13 @@ //! 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 */ - virtual Float evaluate_with_derivative(Float feature, Float& deriv) const { + virtual FloatPair evaluate_with_derivative(Float feature) const { if (feature <= Harmonic::get_mean()) { - deriv = 0.0; - return 0.0; + return std::make_pair(0.0f, 0.0f); } else { - return Harmonic::evaluate_with_derivative(feature, deriv); + return Harmonic::evaluate_with_derivative(feature); } }
Index: kernel/src/singleton_scores/AttributeSingletonScore.cpp =================================================================== --- kernel/src/singleton_scores/AttributeSingletonScore.cpp (revision 669) +++ kernel/src/singleton_scores/AttributeSingletonScore.cpp (working copy) @@ -8,7 +8,7 @@ #include "IMP/singleton_scores/AttributeSingletonScore.h" #include "IMP/UnaryFunction.h" #include "IMP/Particle.h" - +#include <boost/tuple/tuple.hpp> namespace IMP {
@@ -20,8 +20,8 @@ DerivativeAccumulator *da) const { if (da) { - Float d; - float r= f_->evaluate_with_derivative(b->get_value(k_), d); + Float d, r; + boost::tie(d,r) = f_->evaluate_with_derivative(b->get_value(k_)); b->add_to_derivative(k_, d, *da); return r; } else { Index: kernel/src/singleton_scores/TunnelSingletonScore.cpp =================================================================== --- kernel/src/singleton_scores/TunnelSingletonScore.cpp (revision 669) +++ kernel/src/singleton_scores/TunnelSingletonScore.cpp (working copy) @@ -8,7 +8,7 @@
#include "IMP/singleton_scores/TunnelSingletonScore.h" #include "IMP/decorators/XYZDecorator.h" - +#include <boost/tuple/tuple.hpp> namespace IMP {
@@ -58,7 +58,7 @@ // look below if changed Float dist= -std::min(std::min(rd, hdu), hdd) - radius; if (accum) { - score= f_->evaluate_with_derivative(dist, deriv_scalar); + boost::tie(score, deriv_scalar)= f_->evaluate_with_derivative(dist); } else { score= f_->evaluate(dist); } Index: kernel/src/unary_functions/Cosine.cpp =================================================================== --- kernel/src/unary_functions/Cosine.cpp (revision 669) +++ kernel/src/unary_functions/Cosine.cpp (working copy) @@ -18,11 +18,11 @@ - force_constant_ * std::cos(periodicity_ * feature + phase_); }
-Float Cosine::evaluate_with_derivative(Float feature, Float& deriv) const +FloatPair Cosine::evaluate_with_derivative(Float feature) const { - deriv = force_constant_ * periodicity_ - * std::sin(periodicity_ * feature + phase_); - return evaluate(feature); + Float deriv = force_constant_ * periodicity_ + * std::sin(periodicity_ * feature + phase_); + return std::make_pair(evaluate(feature), deriv); }
} // namespace IMP Index: kernel/src/unary_functions/OpenCubicSpline.cpp =================================================================== --- kernel/src/unary_functions/OpenCubicSpline.cpp (revision 669) +++ kernel/src/unary_functions/OpenCubicSpline.cpp (working copy) @@ -66,8 +66,7 @@ * (spacing_ * spacing_) / 6.; }
-Float OpenCubicSpline::evaluate_with_derivative(Float feature, - Float& deriv) const +FloatPair OpenCubicSpline::evaluate_with_derivative(Float feature) const { size_t lowbin = static_cast<size_t>((feature - minrange_) / spacing_); // handle the case where feature ~= maxrange @@ -79,11 +78,11 @@ Float a = 1. - b; float sixthspacing = spacing_ / 6.;
- deriv = (values_[highbin] - values_[lowbin]) / spacing_ - - (3. * a * a - 1.) * sixthspacing * second_derivs_[lowbin] - + (3. * b * b - 1.) * sixthspacing * second_derivs_[highbin]; + Float deriv = (values_[highbin] - values_[lowbin]) / spacing_ + - (3. * a * a - 1.) * sixthspacing * second_derivs_[lowbin] + + (3. * b * b - 1.) * sixthspacing * second_derivs_[highbin];
- return evaluate(feature); + return std::make_pair(evaluate(feature), deriv); }
} // namespace IMP Index: kernel/src/unary_functions/ClosedCubicSpline.cpp =================================================================== --- kernel/src/unary_functions/ClosedCubicSpline.cpp (revision 669) +++ kernel/src/unary_functions/ClosedCubicSpline.cpp (working copy) @@ -82,8 +82,8 @@ * (spacing_ * spacing_) / 6.; }
-Float ClosedCubicSpline::evaluate_with_derivative(Float feature, - Float& deriv) const +FloatPair +ClosedCubicSpline::evaluate_with_derivative(Float feature) const { size_t lowbin = static_cast<size_t>((feature - minrange_) / spacing_); size_t highbin = lowbin + 1; @@ -99,11 +99,11 @@ Float a = 1. - b; float sixthspacing = spacing_ / 6.;
- deriv = (values_[highbin] - values_[lowbin]) / spacing_ + Float deriv = (values_[highbin] - values_[lowbin]) / spacing_ - (3. * a * a - 1.) * sixthspacing * second_derivs_[lowbin] + (3. * b * b - 1.) * sixthspacing * second_derivs_[highbin];
- return evaluate(feature); + return std::make_pair(evaluate(feature), deriv); }
} // namespace IMP Index: kernel/src/restraints/DihedralRestraint.cpp =================================================================== --- kernel/src/restraints/DihedralRestraint.cpp (revision 669) +++ kernel/src/restraints/DihedralRestraint.cpp (working copy) @@ -15,6 +15,8 @@ #include "IMP/restraints/DihedralRestraint.h" #include "IMP/decorators/XYZDecorator.h"
+#include <boost/tuple/tuple.hpp> + namespace IMP {
@@ -80,7 +82,7 @@
if (accum) { Float deriv; - score = score_func_->evaluate_with_derivative(angle, deriv); + boost::tie(score, deriv) = score_func_->evaluate_with_derivative(angle);
// method for derivative calculation from van Schaik et al. // J. Mol. Biol. 234, 751-762 (1993) Index: kernel/src/triplet_scores/AngleTripletScore.cpp =================================================================== --- kernel/src/triplet_scores/AngleTripletScore.cpp (revision 669) +++ kernel/src/triplet_scores/AngleTripletScore.cpp (working copy) @@ -8,7 +8,7 @@ #include "IMP/triplet_scores/AngleTripletScore.h" #include "IMP/decorators/XYZDecorator.h" #include "IMP/UnaryFunction.h" - +#include <boost/tuple/tuple.hpp> namespace IMP {
@@ -46,7 +46,7 @@
if (da) { Float deriv; - score = f_->evaluate_with_derivative(angle, deriv); + boost::tie(score, deriv) = f_->evaluate_with_derivative(angle);
Vector3D unit_rij = rij.get_unit_vector(); Vector3D unit_rkj = rkj.get_unit_vector(); Index: kernel/pyext/IMP.i =================================================================== --- kernel/pyext/IMP.i (revision 669) +++ kernel/pyext/IMP.i (working copy) @@ -14,8 +14,17 @@
/* Return derivatives from unary functions */ %include "typemaps.i" -%apply double &OUTPUT { IMP::Float& deriv };
+namespace IMP { + %typemap(out) std::pair<Float,Float> { + PyObject *tup= PyTuple_New(2); + PyTuple_SetItem(tup, 0, PyFloat_FromDouble($1.first)); + PyTuple_SetItem(tup, 1, PyFloat_FromDouble($1.second)); + $result= tup; + } +} + + %pythoncode %{ def check_particle(p, a): if (not p.get_is_active()): @@ -27,94 +36,30 @@ %}
namespace IMP { - %pythonprepend Model::add_restraint %{ - args[1].thisown=0 - %} - %pythonprepend Model::add_score_state %{ - args[1].thisown=0 - %} - %pythonprepend Optimizer::add_optimizer_state %{ - args[1].thisown=0 - %} - %pythonprepend RestraintSet::add_restraint %{ - args[1].thisown=0 - %} - %pythonprepend NonbondedListScoreState::add_bonded_list %{ - args[1].thisown=0 - %} - %pythonprepend DistanceRestraint::DistanceRestraint %{ - args[0].thisown=0 - %} - %pythonprepend AngleRestraint::AngleRestraint %{ - args[0].thisown=0 - %} - %pythonprepend DihedralRestraint::DihedralRestraint %{ - args[0].thisown=0 - %} - %pythonprepend TorusRestraint::TorusRestraint %{ - args[3].thisown=0 - %} - %pythonprepend NonbondedRestraint::NonbondedRestraint %{ - args[0].thisown=0 - %} - %pythonprepend BondDecoratorRestraint::BondDecoratorRestraint %{ - args[0].thisown=0 - %} - %pythonprepend SingletonListRestraint::SingletonListRestraint %{ - args[0].thisown=0 - %} - %pythonprepend PairListRestraint::PairListRestraint %{ - args[0].thisown=0 - %} - %pythonprepend TripletChainRestraint::TripletChainRestraint %{ - args[0].thisown=0 - %} - %pythonprepend PairChainRestraint::PairChainRestraint %{ - args[0].thisown=0 - %} - %pythonprepend ConnectivityRestraint::ConnectivityRestraint %{ - args[0].thisown=0 - %} - %pythonprepend DistancePairScore::DistancePairScore %{ - args[0].thisown=0 - %} - %pythonprepend TransformedDistancePairScore::TransformedDistancePairScore %{ - args[0].thisown=0 - %} - %pythonprepend BondCoverPairScore::BondCoverPairScore %{ - args[0].thisown=0 - %} - %pythonprepend SphereDistancePairScore::SphereDistancePairScore %{ - args[0].thisown=0 - %} - %pythonprepend RefineOncePairScore::RefineOncePairScore %{ - args[0].thisown=0 - args[1].thisown=0 - %} - %pythonprepend DistanceToSingletonScore::DistanceToSingletonScore %{ - args[0].thisown=0 - %} - %pythonprepend AttributeSingletonScore::AttributeSingletonScore %{ - args[0].thisown=0 - %} - %pythonprepend TunnelSingletonScore::TunnelSingletonScore %{ - args[0].thisown=0 - %} - %pythonprepend AngleTripletScore::AngleTripletScore %{ - args[0].thisown=0 - %} - %pythonprepend MonteCarlo::add_mover %{ - args[1].thisown=0 - %} - %pythonprepend MonteCarlo::set_local_optimizer %{ - args[1].thisown=0 - %} - %pythonprepend VRMLLogOptimizerState::add_particle_refiner %{ - args[1].thisown=0 - %} - %pythonprepend TypedPairScore::set_pair_score %{ - args[1].thisown=0 - %} + // need to special case particle so can't add this to macro + IMP_OWN_FIRST_CONSTRUCTOR(DistanceRestraint) + IMP_OWN_FIRST_CONSTRUCTOR(AngleRestraint) + IMP_OWN_FIRST_CONSTRUCTOR(DihedralRestraint) + IMP_OWN_FIRST_CONSTRUCTOR(TorusRestraint) + IMP_OWN_FIRST_CONSTRUCTOR(NonbondedRestraint) + IMP_OWN_FIRST_CONSTRUCTOR(BondDecoratorRestraint) + IMP_OWN_FIRST_CONSTRUCTOR(SingletonListRestraint) + IMP_OWN_FIRST_CONSTRUCTOR(PairListRestraint) + IMP_OWN_FIRST_CONSTRUCTOR(TripletChainRestraint) + IMP_OWN_FIRST_CONSTRUCTOR(PairChainRestraint) + IMP_OWN_FIRST_CONSTRUCTOR(ConnectivityRestraint) + IMP_OWN_FIRST_CONSTRUCTOR(DistancePairScore) + IMP_OWN_FIRST_CONSTRUCTOR(TransformedDistancePairScore) + IMP_OWN_FIRST_CONSTRUCTOR(BondCoverPairScore) + IMP_OWN_FIRST_CONSTRUCTOR(SphereDistancePairScore) + IMP_OWN_FIRST_SECOND_CONSTRUCTOR(RefineOncePairScore) + IMP_OWN_FIRST_CONSTRUCTOR(DistanceToSingletonScore) + IMP_OWN_FIRST_CONSTRUCTOR(AttributeSingletonScore) + IMP_OWN_FIRST_CONSTRUCTOR(TunnelSingletonScore) + IMP_OWN_FIRST_CONSTRUCTOR(AngleTripletScore) + IMP_SET_OBJECT(MonteCarlo, set_local_optimizer) + IMP_SET_OBJECT(TypedPairScore, set_pair_score) + %pythonprepend Particle::get_value %{ check_particle(args[0], args[1]) %} @@ -144,10 +89,19 @@
%}
- IMP_CONTAINER_SWIG(Model, Particle, particle); + // special case since particles are ref counted + %extend Model { + Particles get_particles() const { + IMP::Particles ret(self->particles_begin(), self->particles_end()); + return ret; + } + } IMP_CONTAINER_SWIG(Model, ScoreState, score_state); IMP_CONTAINER_SWIG(Model, Restraint, restraint); IMP_CONTAINER_SWIG(RestraintSet, Restraint, restraint); + IMP_CONTAINER_SWIG(MonteCarlo, Mover, mover); + IMP_CONTAINER_SWIG(Optimizer, OptimizerState, optimizer_state); + IMP_CONTAINER_SWIG(NonbondedListScoreState, BondedListScoreState, bonded_list); }
%feature("ref") Particle "$this->ref();" @@ -168,6 +122,7 @@ %feature("director") IMP::TripletScore; %feature("director") IMP::Optimizer; %feature("director") IMP::ParticleRefiner; +%feature("director") IMP::Mover;
%include "IMP/Key.h" %include "IMP/Object.h"
Daniel Russel wrote: > Here is the patch that was discussed a while ago which makes > UnaryFunction::evaluate_with_derivative return a std::pair instead of > using one pass by reference to return. It also removes the hack in IMP.i > to get the return value right.
I'm not sure sure why you call it a hack, since it's the regular way to deal with reference return values in SWIG. And that code deals with any errors the Python API (or any other scripting language) may return. But regardless, the code (patch attached) does not work on synth:
% scons test ... RuntimeError: Previously freed object is not valid: 0x89c1224 File "kernel/src/Object.cpp", line 32
unit tests FAILED
Ben
Well, the set of all patches runs passes the tests on flute when run in valgrind (other than the dna read which fails for a virgin svn copy). And all pass (without valgrind) on my mac. I suspect the problem is changes you made to the patches I submitted, but it is also possible that the patches simply expose bugs created by the problems in attribute table that a later patch fixed. Either way, you have a working set of patches.
On Tue, Aug 26, 2008 at 7:55 PM, Ben Webb ben@salilab.org wrote:
> Daniel Russel wrote: > > Here is the patch that was discussed a while ago which makes > > UnaryFunction::evaluate_with_derivative return a std::pair instead of > > using one pass by reference to return. It also removes the hack in IMP.i > > to get the return value right. > > I'm not sure sure why you call it a hack, since it's the regular way to > deal with reference return values in SWIG. And that code deals with any > errors the Python API (or any other scripting language) may return. But > regardless, the code (patch attached) does not work on synth: > > % scons test > ... > RuntimeError: Previously freed object is not valid: 0x89c1224 > File "kernel/src/Object.cpp", line 32 > > unit tests FAILED > > Ben > -- > ben@salilab.org http://salilab.org/~ben/http://salilab.org/%7Eben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > > Index: kernel/include/IMP/UnaryFunction.h > =================================================================== > --- kernel/include/IMP/UnaryFunction.h (revision 669) > +++ kernel/include/IMP/UnaryFunction.h (working copy) > @@ -14,9 +14,13 @@ > namespace IMP > { > > +typedef std::pair<Float, Float> FloatPair; > + > //! Abstract single variable functor class for score functions. > /** These functors take a single feature value, and return a corresponding > score (and optionally also the first derivative). > + > + \ingroup kernel > */ > class IMPDLLEXPORT UnaryFunction : public RefCountedObject > { > @@ -36,7 +40,7 @@ > given feaure. > \return Score > */ > - virtual Float evaluate_with_derivative(Float feature, Float& deriv) > const = 0; > + virtual FloatPair evaluate_with_derivative(Float feature) const = 0; > > virtual void show(std::ostream &out=std::cout) const = 0; > }; > Index: kernel/include/IMP/internal/evaluate_distance_pair_score.h > =================================================================== > --- kernel/include/IMP/internal/evaluate_distance_pair_score.h (revision > 669) > +++ kernel/include/IMP/internal/evaluate_distance_pair_score.h (working > copy) > @@ -9,6 +9,7 @@ > #define __IMP_EVALUATE_DISTANCE_PAIR_SCORE_H > > #include "../Vector3D.h" > +#include <boost/tuple/tuple.hpp> > > namespace IMP > { > @@ -43,7 +44,7 @@ > if (da && distance >= MIN_DISTANCE) { > Float deriv; > > - score = f->evaluate_with_derivative(shifted_distance, deriv); > + boost::tie(score, deriv) = > f->evaluate_with_derivative(shifted_distance); > > Vector3D d= delta/distance *deriv; > d0.add_to_coordinates_derivative(d, *da); > Index: kernel/include/IMP/unary_functions/Linear.h > =================================================================== > --- kernel/include/IMP/unary_functions/Linear.h (revision 669) > +++ kernel/include/IMP/unary_functions/Linear.h (working copy) > @@ -28,9 +28,8 @@ > return (feature-offset_)*slope_; > } > > - virtual Float evaluate_with_derivative(Float feature, Float& deriv) > const { > - deriv= slope_; > - return evaluate(feature); > + virtual FloatPair evaluate_with_derivative(Float feature) const { > + return std::make_pair(evaluate(feature), slope_); > } > > void set_slope(Float f) { > Index: kernel/include/IMP/unary_functions/ClosedCubicSpline.h > =================================================================== > --- kernel/include/IMP/unary_functions/ClosedCubicSpline.h (revision > 669) > +++ kernel/include/IMP/unary_functions/ClosedCubicSpline.h (working > copy) > @@ -40,12 +40,10 @@ > > //! Calculate 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. > \exception ValueException Feature is out of defined range. > \return Score > */ > - virtual Float evaluate_with_derivative(Float feature, Float& deriv) > const; > + virtual FloatPair evaluate_with_derivative(Float feature) const; > > void show(std::ostream &out=std::cout) const { > out << "Closed cubic spline of " << values_.size() << " values from " > Index: kernel/include/IMP/unary_functions/WormLikeChain.h > =================================================================== > --- kernel/include/IMP/unary_functions/WormLikeChain.h (revision 669) > +++ kernel/include/IMP/unary_functions/WormLikeChain.h (working copy) > @@ -62,10 +62,8 @@ > > //! Calculate the WormLikeChain energy given the length > /** \param[in] l Current length in angstroms > - \param[out] deriv force in kcal/angstrom mol > - \return Score > */ > - virtual Float evaluate_with_derivative(Float fl, Float& deriv) const { > + virtual FloatPair evaluate_with_derivative(Float fl) const { > unit::Angstrom l(fl); > if (l < unit::Angstrom(0)) l=unit::Angstrom(0); > unit::Piconewton doubled; > @@ -81,9 +79,9 @@ > // convert from picoNewton > unit::YoctoKilocaloriePerAngstrom du= unit::convert_J_to_Cal(doubled); > > - deriv = (du*unit::ATOMS_PER_MOL).get_value(); > + Float deriv = (du*unit::ATOMS_PER_MOL).get_value(); > //std::cout << "Which converts to " << d << std::endl; > - return evaluate(fl); > + return std::make_pair(evaluate(fl), deriv); > } > > void show(std::ostream &out=std::cout) const { > Index: kernel/include/IMP/unary_functions/Harmonic.h > =================================================================== > --- kernel/include/IMP/unary_functions/Harmonic.h (revision 669) > +++ kernel/include/IMP/unary_functions/Harmonic.h (working copy) > @@ -56,20 +56,17 @@ > \return Score > */ > virtual Float evaluate(Float feature) const { > - Float d; > - return evaluate_with_derivative(feature, d); > + return evaluate_with_derivative(feature).first; > } > > //! 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 > */ > - virtual Float evaluate_with_derivative(Float feature, Float& deriv) > const { > + virtual FloatPair evaluate_with_derivative(Float feature) const { > Float e = (feature - mean_); > - deriv = k_ * e; > - return 0.5 * k_ * e * e; > + Float deriv = k_ * e; > + return std::make_pair(0.5 * k_ * e * e, deriv); > } > > void show(std::ostream &out=std::cout) const { > Index: kernel/include/IMP/unary_functions/Cosine.h > =================================================================== > --- kernel/include/IMP/unary_functions/Cosine.h (revision 669) > +++ kernel/include/IMP/unary_functions/Cosine.h (working copy) > @@ -43,11 +43,9 @@ > > //! Calculate 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 > */ > - virtual Float evaluate_with_derivative(Float feature, Float& deriv) > const; > + virtual FloatPair evaluate_with_derivative(Float feature) const; > > void show(std::ostream &out=std::cout) const { > out << "Cosine function with force " << force_constant_ > Index: kernel/include/IMP/unary_functions/HarmonicLowerBound.h > =================================================================== > --- kernel/include/IMP/unary_functions/HarmonicLowerBound.h (revision > 669) > +++ kernel/include/IMP/unary_functions/HarmonicLowerBound.h (working > copy) > @@ -37,16 +37,13 @@ > //! 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 > */ > - virtual Float evaluate_with_derivative(Float feature, Float& deriv) > const { > + virtual FloatPair evaluate_with_derivative(Float feature) const { > if (feature >= Harmonic::get_mean()) { > - deriv = 0.0; > - return 0.0; > + return std::make_pair(0.0f, 0.0f); > } else { > - return Harmonic::evaluate_with_derivative(feature, deriv); > + return Harmonic::evaluate_with_derivative(feature); > } > } > > Index: kernel/include/IMP/unary_functions/OpenCubicSpline.h > =================================================================== > --- kernel/include/IMP/unary_functions/OpenCubicSpline.h (revision > 669) > +++ kernel/include/IMP/unary_functions/OpenCubicSpline.h (working > copy) > @@ -25,7 +25,7 @@ > \param[in] minrange Feature value at first spline point > \param[in] spacing Distance (in feature space) between points > */ > - OpenCubicSpline(const std::vector<Float> &values, Float minrange, > + OpenCubicSpline(const Floats &values, Float minrange, > Float spacing); > > virtual ~OpenCubicSpline() {} > @@ -39,12 +39,10 @@ > > //! Calculate 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. > \exception ValueException Feature is out of defined range. > \return Score > */ > - virtual Float evaluate_with_derivative(Float feature, Float& deriv) > const; > + virtual FloatPair evaluate_with_derivative(Float feature) const; > > void show(std::ostream &out=std::cout) const { > out << "Open cubic spline of " << values_.size() << " values from " > Index: kernel/include/IMP/unary_functions/HarmonicUpperBound.h > =================================================================== > --- kernel/include/IMP/unary_functions/HarmonicUpperBound.h (revision > 669) > +++ kernel/include/IMP/unary_functions/HarmonicUpperBound.h (working > copy) > @@ -37,16 +37,13 @@ > //! 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 > */ > - virtual Float evaluate_with_derivative(Float feature, Float& deriv) > const { > + virtual FloatPair evaluate_with_derivative(Float feature) const { > if (feature <= Harmonic::get_mean()) { > - deriv = 0.0; > - return 0.0; > + return std::make_pair(0.0f, 0.0f); > } else { > - return Harmonic::evaluate_with_derivative(feature, deriv); > + return Harmonic::evaluate_with_derivative(feature); > } > } > > Index: kernel/src/singleton_scores/AttributeSingletonScore.cpp > =================================================================== > --- kernel/src/singleton_scores/AttributeSingletonScore.cpp (revision > 669) > +++ kernel/src/singleton_scores/AttributeSingletonScore.cpp (working > copy) > @@ -8,7 +8,7 @@ > #include "IMP/singleton_scores/AttributeSingletonScore.h" > #include "IMP/UnaryFunction.h" > #include "IMP/Particle.h" > - > +#include <boost/tuple/tuple.hpp> > namespace IMP > { > > @@ -20,8 +20,8 @@ > DerivativeAccumulator *da) const > { > if (da) { > - Float d; > - float r= f_->evaluate_with_derivative(b->get_value(k_), d); > + Float d, r; > + boost::tie(d,r) = f_->evaluate_with_derivative(b->get_value(k_)); > b->add_to_derivative(k_, d, *da); > return r; > } else { > Index: kernel/src/singleton_scores/TunnelSingletonScore.cpp > =================================================================== > --- kernel/src/singleton_scores/TunnelSingletonScore.cpp (revision > 669) > +++ kernel/src/singleton_scores/TunnelSingletonScore.cpp (working > copy) > @@ -8,7 +8,7 @@ > > #include "IMP/singleton_scores/TunnelSingletonScore.h" > #include "IMP/decorators/XYZDecorator.h" > - > +#include <boost/tuple/tuple.hpp> > namespace IMP > { > > @@ -58,7 +58,7 @@ > // look below if changed > Float dist= -std::min(std::min(rd, hdu), hdd) - radius; > if (accum) { > - score= f_->evaluate_with_derivative(dist, deriv_scalar); > + boost::tie(score, deriv_scalar)= > f_->evaluate_with_derivative(dist); > } else { > score= f_->evaluate(dist); > } > Index: kernel/src/unary_functions/Cosine.cpp > =================================================================== > --- kernel/src/unary_functions/Cosine.cpp (revision 669) > +++ kernel/src/unary_functions/Cosine.cpp (working copy) > @@ -18,11 +18,11 @@ > - force_constant_ * std::cos(periodicity_ * feature + phase_); > } > > -Float Cosine::evaluate_with_derivative(Float feature, Float& deriv) const > +FloatPair Cosine::evaluate_with_derivative(Float feature) const > { > - deriv = force_constant_ * periodicity_ > - * std::sin(periodicity_ * feature + phase_); > - return evaluate(feature); > + Float deriv = force_constant_ * periodicity_ > + * std::sin(periodicity_ * feature + phase_); > + return std::make_pair(evaluate(feature), deriv); > } > > } // namespace IMP > Index: kernel/src/unary_functions/OpenCubicSpline.cpp > =================================================================== > --- kernel/src/unary_functions/OpenCubicSpline.cpp (revision 669) > +++ kernel/src/unary_functions/OpenCubicSpline.cpp (working copy) > @@ -66,8 +66,7 @@ > * (spacing_ * spacing_) / 6.; > } > > -Float OpenCubicSpline::evaluate_with_derivative(Float feature, > - Float& deriv) const > +FloatPair OpenCubicSpline::evaluate_with_derivative(Float feature) const > { > size_t lowbin = static_cast<size_t>((feature - minrange_) / spacing_); > // handle the case where feature ~= maxrange > @@ -79,11 +78,11 @@ > Float a = 1. - b; > float sixthspacing = spacing_ / 6.; > > - deriv = (values_[highbin] - values_[lowbin]) / spacing_ > - - (3. * a * a - 1.) * sixthspacing * second_derivs_[lowbin] > - + (3. * b * b - 1.) * sixthspacing * second_derivs_[highbin]; > + Float deriv = (values_[highbin] - values_[lowbin]) / spacing_ > + - (3. * a * a - 1.) * sixthspacing * second_derivs_[lowbin] > + + (3. * b * b - 1.) * sixthspacing * second_derivs_[highbin]; > > - return evaluate(feature); > + return std::make_pair(evaluate(feature), deriv); > } > > } // namespace IMP > Index: kernel/src/unary_functions/ClosedCubicSpline.cpp > =================================================================== > --- kernel/src/unary_functions/ClosedCubicSpline.cpp (revision 669) > +++ kernel/src/unary_functions/ClosedCubicSpline.cpp (working copy) > @@ -82,8 +82,8 @@ > * (spacing_ * spacing_) / 6.; > } > > -Float ClosedCubicSpline::evaluate_with_derivative(Float feature, > - Float& deriv) const > +FloatPair > +ClosedCubicSpline::evaluate_with_derivative(Float feature) const > { > size_t lowbin = static_cast<size_t>((feature - minrange_) / spacing_); > size_t highbin = lowbin + 1; > @@ -99,11 +99,11 @@ > Float a = 1. - b; > float sixthspacing = spacing_ / 6.; > > - deriv = (values_[highbin] - values_[lowbin]) / spacing_ > + Float deriv = (values_[highbin] - values_[lowbin]) / spacing_ > - (3. * a * a - 1.) * sixthspacing * second_derivs_[lowbin] > + (3. * b * b - 1.) * sixthspacing * second_derivs_[highbin]; > > - return evaluate(feature); > + return std::make_pair(evaluate(feature), deriv); > } > > } // namespace IMP > Index: kernel/src/restraints/DihedralRestraint.cpp > =================================================================== > --- kernel/src/restraints/DihedralRestraint.cpp (revision 669) > +++ kernel/src/restraints/DihedralRestraint.cpp (working copy) > @@ -15,6 +15,8 @@ > #include "IMP/restraints/DihedralRestraint.h" > #include "IMP/decorators/XYZDecorator.h" > > +#include <boost/tuple/tuple.hpp> > + > namespace IMP > { > > @@ -80,7 +82,7 @@ > > if (accum) { > Float deriv; > - score = score_func_->evaluate_with_derivative(angle, deriv); > + boost::tie(score, deriv) = > score_func_->evaluate_with_derivative(angle); > > // method for derivative calculation from van Schaik et al. > // J. Mol. Biol. 234, 751-762 (1993) > Index: kernel/src/triplet_scores/AngleTripletScore.cpp > =================================================================== > --- kernel/src/triplet_scores/AngleTripletScore.cpp (revision 669) > +++ kernel/src/triplet_scores/AngleTripletScore.cpp (working copy) > @@ -8,7 +8,7 @@ > #include "IMP/triplet_scores/AngleTripletScore.h" > #include "IMP/decorators/XYZDecorator.h" > #include "IMP/UnaryFunction.h" > - > +#include <boost/tuple/tuple.hpp> > namespace IMP > { > > @@ -46,7 +46,7 @@ > > if (da) { > Float deriv; > - score = f_->evaluate_with_derivative(angle, deriv); > + boost::tie(score, deriv) = f_->evaluate_with_derivative(angle); > > Vector3D unit_rij = rij.get_unit_vector(); > Vector3D unit_rkj = rkj.get_unit_vector(); > Index: kernel/pyext/IMP.i > =================================================================== > --- kernel/pyext/IMP.i (revision 672) > +++ kernel/pyext/IMP.i (working copy) > @@ -14,8 +14,17 @@ > > /* Return derivatives from unary functions */ > %include "typemaps.i" > -%apply double &OUTPUT { IMP::Float& deriv }; > > +namespace IMP { > + %typemap(out) std::pair<Float,Float> { > + PyObject *tup= PyTuple_New(2); > + PyTuple_SetItem(tup, 0, PyFloat_FromDouble($1.first)); > + PyTuple_SetItem(tup, 1, PyFloat_FromDouble($1.second)); > + $result= tup; > + } > +} > + > + > %pythoncode %{ > def check_particle(p, a): > if (not p.get_is_active()): > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >
Daniel Russel wrote: > Well, the set of all patches runs passes the tests on flute when run in > valgrind (other than the dna read which fails for a virgin svn copy). > And all pass (without valgrind) on my mac. I suspect the problem is > changes you made to the patches I submitted, but it is also possible > that the patches simply expose bugs created by the problems in attribute > table that a later patch fixed.
The first was the correct one - I missed the IMP_ADD_OBJECT(s) that you added to IMP_CONTAINER_SWIG. Should be fixed now though.
For the DNA reader, you will need to update Modeller, since that has been updated to work with remediated RNA and DNA.
Ben
On Aug 27, 2008, at 8:30 AM, Ben Webb ben@salilab.org wrote: > > For the DNA reader, you will need to update Modeller, since that has > been updated to work with remediated RNA and DNA. > Thanks
Ben Webb wrote: > Daniel Russel wrote: > >> Well, the set of all patches runs passes the tests on flute when run in >> valgrind (other than the dna read which fails for a virgin svn copy). >> And all pass (without valgrind) on my mac. I suspect the problem is >> changes you made to the patches I submitted, but it is also possible >> that the patches simply expose bugs created by the problems in attribute >> table that a later patch fixed. >> > > The first was the correct one - I missed the IMP_ADD_OBJECT(s) that you > added to IMP_CONTAINER_SWIG. Should be fixed now though. > Such things are really delicate in IMP and there are, I'm sure, still a whole bunch of places where the thisown things are missing. I wish we had a more robust solution. One possibility is that if you can put a hook into swig on each member function which checks if each argument is either an Object or a vector of objects and calls thisown appropriately. I can write C++ code which tests if an object should have thisown called.
On Aug 26, 2008, at 7:55 PM, Ben Webb ben@salilab.org wrote:
> Daniel Russel wrote: >> Here is the patch that was discussed a while ago which makes >> UnaryFunction::evaluate_with_derivative return a std::pair instead of >> using one pass by reference to return. It also removes the hack in >> IMP.i >> to get the return value right. > > I'm not sure sure why you call it a hack, since it's the regular way > to > deal with reference return values in SWIG. The function returns two equivalent return values two different ways, breaks if you happen to call your argument something different and looks completely different in python and c.
> And that code deals with any > errors the Python API (or any other scripting language) may return. > But > regardless, the code (patch attached) does not work on synth: > > % scons test > ... > RuntimeError: Previously freed object is not valid: 0x89c1224 > File "kernel/src/Object.cpp", line 32 > > unit tests FAILED > > Ben > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > Index: kernel/include/IMP/UnaryFunction.h > =================================================================== > --- kernel/include/IMP/UnaryFunction.h (revision 669) > +++ kernel/include/IMP/UnaryFunction.h (working copy) > @@ -14,9 +14,13 @@ > namespace IMP > { > > +typedef std::pair<Float, Float> FloatPair; > + > //! Abstract single variable functor class for score functions. > /** These functors take a single feature value, and return a > corresponding > score (and optionally also the first derivative). > + > + \ingroup kernel > */ > class IMPDLLEXPORT UnaryFunction : public RefCountedObject > { > @@ -36,7 +40,7 @@ > given feaure. > \return Score > */ > - virtual Float evaluate_with_derivative(Float feature, Float& > deriv) const = 0; > + virtual FloatPair evaluate_with_derivative(Float feature) const = > 0; > > virtual void show(std::ostream &out=std::cout) const = 0; > }; > Index: kernel/include/IMP/internal/evaluate_distance_pair_score.h > =================================================================== > --- kernel/include/IMP/internal/evaluate_distance_pair_score.h > (revision 669) > +++ kernel/include/IMP/internal/evaluate_distance_pair_score.h > (working copy) > @@ -9,6 +9,7 @@ > #define __IMP_EVALUATE_DISTANCE_PAIR_SCORE_H > > #include "../Vector3D.h" > +#include <boost/tuple/tuple.hpp> > > namespace IMP > { > @@ -43,7 +44,7 @@ > if (da && distance >= MIN_DISTANCE) { > Float deriv; > > - score = f->evaluate_with_derivative(shifted_distance, deriv); > + boost::tie(score, deriv) = f- > >evaluate_with_derivative(shifted_distance); > > Vector3D d= delta/distance *deriv; > d0.add_to_coordinates_derivative(d, *da); > Index: kernel/include/IMP/unary_functions/Linear.h > =================================================================== > --- kernel/include/IMP/unary_functions/Linear.h (revision 669) > +++ kernel/include/IMP/unary_functions/Linear.h (working copy) > @@ -28,9 +28,8 @@ > return (feature-offset_)*slope_; > } > > - virtual Float evaluate_with_derivative(Float feature, Float& > deriv) const { > - deriv= slope_; > - return evaluate(feature); > + virtual FloatPair evaluate_with_derivative(Float feature) const { > + return std::make_pair(evaluate(feature), slope_); > } > > void set_slope(Float f) { > Index: kernel/include/IMP/unary_functions/ClosedCubicSpline.h > =================================================================== > --- kernel/include/IMP/unary_functions/ClosedCubicSpline.h > (revision 669) > +++ kernel/include/IMP/unary_functions/ClosedCubicSpline.h > (working copy) > @@ -40,12 +40,10 @@ > > //! Calculate 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. > \exception ValueException Feature is out of defined range. > \return Score > */ > - virtual Float evaluate_with_derivative(Float feature, Float& > deriv) const; > + virtual FloatPair evaluate_with_derivative(Float feature) const; > > void show(std::ostream &out=std::cout) const { > out << "Closed cubic spline of " << values_.size() << " values > from " > Index: kernel/include/IMP/unary_functions/WormLikeChain.h > =================================================================== > --- kernel/include/IMP/unary_functions/WormLikeChain.h (revision > 669) > +++ kernel/include/IMP/unary_functions/WormLikeChain.h (working > copy) > @@ -62,10 +62,8 @@ > > //! Calculate the WormLikeChain energy given the length > /** \param[in] l Current length in angstroms > - \param[out] deriv force in kcal/angstrom mol > - \return Score > */ > - virtual Float evaluate_with_derivative(Float fl, Float& deriv) > const { > + virtual FloatPair evaluate_with_derivative(Float fl) const { > unit::Angstrom l(fl); > if (l < unit::Angstrom(0)) l=unit::Angstrom(0); > unit::Piconewton doubled; > @@ -81,9 +79,9 @@ > // convert from picoNewton > unit::YoctoKilocaloriePerAngstrom du= > unit::convert_J_to_Cal(doubled); > > - deriv = (du*unit::ATOMS_PER_MOL).get_value(); > + Float deriv = (du*unit::ATOMS_PER_MOL).get_value(); > //std::cout << "Which converts to " << d << std::endl; > - return evaluate(fl); > + return std::make_pair(evaluate(fl), deriv); > } > > void show(std::ostream &out=std::cout) const { > Index: kernel/include/IMP/unary_functions/Harmonic.h > =================================================================== > --- kernel/include/IMP/unary_functions/Harmonic.h (revision 669) > +++ kernel/include/IMP/unary_functions/Harmonic.h (working copy) > @@ -56,20 +56,17 @@ > \return Score > */ > virtual Float evaluate(Float feature) const { > - Float d; > - return evaluate_with_derivative(feature, d); > + return evaluate_with_derivative(feature).first; > } > > //! 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 > */ > - virtual Float evaluate_with_derivative(Float feature, Float& > deriv) const { > + virtual FloatPair evaluate_with_derivative(Float feature) const { > Float e = (feature - mean_); > - deriv = k_ * e; > - return 0.5 * k_ * e * e; > + Float deriv = k_ * e; > + return std::make_pair(0.5 * k_ * e * e, deriv); > } > > void show(std::ostream &out=std::cout) const { > Index: kernel/include/IMP/unary_functions/Cosine.h > =================================================================== > --- kernel/include/IMP/unary_functions/Cosine.h (revision 669) > +++ kernel/include/IMP/unary_functions/Cosine.h (working copy) > @@ -43,11 +43,9 @@ > > //! Calculate 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 > */ > - virtual Float evaluate_with_derivative(Float feature, Float& > deriv) const; > + virtual FloatPair evaluate_with_derivative(Float feature) const; > > void show(std::ostream &out=std::cout) const { > out << "Cosine function with force " << force_constant_ > Index: kernel/include/IMP/unary_functions/HarmonicLowerBound.h > =================================================================== > --- kernel/include/IMP/unary_functions/HarmonicLowerBound.h > (revision 669) > +++ kernel/include/IMP/unary_functions/HarmonicLowerBound.h > (working copy) > @@ -37,16 +37,13 @@ > //! 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 > */ > - virtual Float evaluate_with_derivative(Float feature, Float& > deriv) const { > + virtual FloatPair evaluate_with_derivative(Float feature) const { > if (feature >= Harmonic::get_mean()) { > - deriv = 0.0; > - return 0.0; > + return std::make_pair(0.0f, 0.0f); > } else { > - return Harmonic::evaluate_with_derivative(feature, deriv); > + return Harmonic::evaluate_with_derivative(feature); > } > } > > Index: kernel/include/IMP/unary_functions/OpenCubicSpline.h > =================================================================== > --- kernel/include/IMP/unary_functions/OpenCubicSpline.h > (revision 669) > +++ kernel/include/IMP/unary_functions/OpenCubicSpline.h (working > copy) > @@ -25,7 +25,7 @@ > \param[in] minrange Feature value at first spline point > \param[in] spacing Distance (in feature space) between points > */ > - OpenCubicSpline(const std::vector<Float> &values, Float minrange, > + OpenCubicSpline(const Floats &values, Float minrange, > Float spacing); > > virtual ~OpenCubicSpline() {} > @@ -39,12 +39,10 @@ > > //! Calculate 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. > \exception ValueException Feature is out of defined range. > \return Score > */ > - virtual Float evaluate_with_derivative(Float feature, Float& > deriv) const; > + virtual FloatPair evaluate_with_derivative(Float feature) const; > > void show(std::ostream &out=std::cout) const { > out << "Open cubic spline of " << values_.size() << " values > from " > Index: kernel/include/IMP/unary_functions/HarmonicUpperBound.h > =================================================================== > --- kernel/include/IMP/unary_functions/HarmonicUpperBound.h > (revision 669) > +++ kernel/include/IMP/unary_functions/HarmonicUpperBound.h > (working copy) > @@ -37,16 +37,13 @@ > //! 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 > */ > - virtual Float evaluate_with_derivative(Float feature, Float& > deriv) const { > + virtual FloatPair evaluate_with_derivative(Float feature) const { > if (feature <= Harmonic::get_mean()) { > - deriv = 0.0; > - return 0.0; > + return std::make_pair(0.0f, 0.0f); > } else { > - return Harmonic::evaluate_with_derivative(feature, deriv); > + return Harmonic::evaluate_with_derivative(feature); > } > } > > Index: kernel/src/singleton_scores/AttributeSingletonScore.cpp > =================================================================== > --- kernel/src/singleton_scores/AttributeSingletonScore.cpp > (revision 669) > +++ kernel/src/singleton_scores/AttributeSingletonScore.cpp > (working copy) > @@ -8,7 +8,7 @@ > #include "IMP/singleton_scores/AttributeSingletonScore.h" > #include "IMP/UnaryFunction.h" > #include "IMP/Particle.h" > - > +#include <boost/tuple/tuple.hpp> > namespace IMP > { > > @@ -20,8 +20,8 @@ > DerivativeAccumulator *da) > const > { > if (da) { > - Float d; > - float r= f_->evaluate_with_derivative(b->get_value(k_), d); > + Float d, r; > + boost::tie(d,r) = f_->evaluate_with_derivative(b->get_value(k_)); > b->add_to_derivative(k_, d, *da); > return r; > } else { > Index: kernel/src/singleton_scores/TunnelSingletonScore.cpp > =================================================================== > --- kernel/src/singleton_scores/TunnelSingletonScore.cpp > (revision 669) > +++ kernel/src/singleton_scores/TunnelSingletonScore.cpp (working > copy) > @@ -8,7 +8,7 @@ > > #include "IMP/singleton_scores/TunnelSingletonScore.h" > #include "IMP/decorators/XYZDecorator.h" > - > +#include <boost/tuple/tuple.hpp> > namespace IMP > { > > @@ -58,7 +58,7 @@ > // look below if changed > Float dist= -std::min(std::min(rd, hdu), hdd) - radius; > if (accum) { > - score= f_->evaluate_with_derivative(dist, deriv_scalar); > + boost::tie(score, deriv_scalar)= f_- > >evaluate_with_derivative(dist); > } else { > score= f_->evaluate(dist); > } > Index: kernel/src/unary_functions/Cosine.cpp > =================================================================== > --- kernel/src/unary_functions/Cosine.cpp (revision 669) > +++ kernel/src/unary_functions/Cosine.cpp (working copy) > @@ -18,11 +18,11 @@ > - force_constant_ * std::cos(periodicity_ * feature + > phase_); > } > > -Float Cosine::evaluate_with_derivative(Float feature, Float& deriv) > const > +FloatPair Cosine::evaluate_with_derivative(Float feature) const > { > - deriv = force_constant_ * periodicity_ > - * std::sin(periodicity_ * feature + phase_); > - return evaluate(feature); > + Float deriv = force_constant_ * periodicity_ > + * std::sin(periodicity_ * feature + phase_); > + return std::make_pair(evaluate(feature), deriv); > } > > } // namespace IMP > Index: kernel/src/unary_functions/OpenCubicSpline.cpp > =================================================================== > --- kernel/src/unary_functions/OpenCubicSpline.cpp (revision 669) > +++ kernel/src/unary_functions/OpenCubicSpline.cpp (working copy) > @@ -66,8 +66,7 @@ > * (spacing_ * spacing_) / 6.; > } > > -Float OpenCubicSpline::evaluate_with_derivative(Float feature, > - Float& deriv) const > +FloatPair OpenCubicSpline::evaluate_with_derivative(Float feature) > const > { > size_t lowbin = static_cast<size_t>((feature - minrange_) / > spacing_); > // handle the case where feature ~= maxrange > @@ -79,11 +78,11 @@ > Float a = 1. - b; > float sixthspacing = spacing_ / 6.; > > - deriv = (values_[highbin] - values_[lowbin]) / spacing_ > - - (3. * a * a - 1.) * sixthspacing * second_derivs_[lowbin] > - + (3. * b * b - 1.) * sixthspacing * > second_derivs_[highbin]; > + Float deriv = (values_[highbin] - values_[lowbin]) / spacing_ > + - (3. * a * a - 1.) * sixthspacing * second_derivs_[lowbin] > + + (3. * b * b - 1.) * sixthspacing * second_derivs_[highbin]; > > - return evaluate(feature); > + return std::make_pair(evaluate(feature), deriv); > } > > } // namespace IMP > Index: kernel/src/unary_functions/ClosedCubicSpline.cpp > =================================================================== > --- kernel/src/unary_functions/ClosedCubicSpline.cpp (revision 669) > +++ kernel/src/unary_functions/ClosedCubicSpline.cpp (working copy) > @@ -82,8 +82,8 @@ > * (spacing_ * spacing_) / 6.; > } > > -Float ClosedCubicSpline::evaluate_with_derivative(Float feature, > - Float& deriv) const > +FloatPair > +ClosedCubicSpline::evaluate_with_derivative(Float feature) const > { > size_t lowbin = static_cast<size_t>((feature - minrange_) / > spacing_); > size_t highbin = lowbin + 1; > @@ -99,11 +99,11 @@ > Float a = 1. - b; > float sixthspacing = spacing_ / 6.; > > - deriv = (values_[highbin] - values_[lowbin]) / spacing_ > + Float deriv = (values_[highbin] - values_[lowbin]) / spacing_ > - (3. * a * a - 1.) * sixthspacing * second_derivs_[lowbin] > + (3. * b * b - 1.) * sixthspacing * > second_derivs_[highbin]; > > - return evaluate(feature); > + return std::make_pair(evaluate(feature), deriv); > } > > } // namespace IMP > Index: kernel/src/restraints/DihedralRestraint.cpp > =================================================================== > --- kernel/src/restraints/DihedralRestraint.cpp (revision 669) > +++ kernel/src/restraints/DihedralRestraint.cpp (working copy) > @@ -15,6 +15,8 @@ > #include "IMP/restraints/DihedralRestraint.h" > #include "IMP/decorators/XYZDecorator.h" > > +#include <boost/tuple/tuple.hpp> > + > namespace IMP > { > > @@ -80,7 +82,7 @@ > > if (accum) { > Float deriv; > - score = score_func_->evaluate_with_derivative(angle, deriv); > + boost::tie(score, deriv) = score_func_- > >evaluate_with_derivative(angle); > > // method for derivative calculation from van Schaik et al. > // J. Mol. Biol. 234, 751-762 (1993) > Index: kernel/src/triplet_scores/AngleTripletScore.cpp > =================================================================== > --- kernel/src/triplet_scores/AngleTripletScore.cpp (revision 669) > +++ kernel/src/triplet_scores/AngleTripletScore.cpp (working copy) > @@ -8,7 +8,7 @@ > #include "IMP/triplet_scores/AngleTripletScore.h" > #include "IMP/decorators/XYZDecorator.h" > #include "IMP/UnaryFunction.h" > - > +#include <boost/tuple/tuple.hpp> > namespace IMP > { > > @@ -46,7 +46,7 @@ > > if (da) { > Float deriv; > - score = f_->evaluate_with_derivative(angle, deriv); > + boost::tie(score, deriv) = f_->evaluate_with_derivative(angle); > > Vector3D unit_rij = rij.get_unit_vector(); > Vector3D unit_rkj = rkj.get_unit_vector(); > Index: kernel/pyext/IMP.i > =================================================================== > --- kernel/pyext/IMP.i (revision 672) > +++ kernel/pyext/IMP.i (working copy) > @@ -14,8 +14,17 @@ > > /* Return derivatives from unary functions */ > %include "typemaps.i" > -%apply double &OUTPUT { IMP::Float& deriv }; > > +namespace IMP { > + %typemap(out) std::pair<Float,Float> { > + PyObject *tup= PyTuple_New(2); > + PyTuple_SetItem(tup, 0, PyFloat_FromDouble($1.first)); > + PyTuple_SetItem(tup, 1, PyFloat_FromDouble($1.second)); > + $result= tup; > + } > +} > + > + > %pythoncode %{ > def check_particle(p, a): > if (not p.get_is_active()): > tions */ > %include "typemaps.i" > -%apply double &OUTPUT { IMP::Float& deriv }; > > +namespace IMP { > + %typemap(out) std::pair<Float,Float> { > + PyObject *tup= PyTuple_New(2); > + PyTuple_SetItem(tup, 0, PyFloat_FromDouble($1.first)); > + PyTuple_SetItem(tup, 1, PyFloat_FromDouble($1.second)); > + $result= tup; > + } > +} > + > + > %pythoncode %{ > def check_particle(p, a): > if (not p.get_is_active()): > t_is_active()): > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
participants (2)
-
Ben Webb -
Daniel Russel