Re: [IMP-dev] unaryfunction returns

-- 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()):