Here is a simple patch to IMP.i which adds macros to handle the thisowns and adds a few missed ones.

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/pyext/IMP_macros.i =================================================================== --- kernel/pyext/IMP_macros.i (revision 669) +++ kernel/pyext/IMP_macros.i (working copy) @@ -1,6 +1,38 @@ #define IMPDLLEXPORT #define IMPDLLLOCAL

+%define IMP_OWN_FIRST_CONSTRUCTOR(Ucname) +%pythonprepend Ucname::Ucname %{ + args[0].thisown=0 +%} +%enddef + +%define IMP_OWN_FIRST_SECOND_CONSTRUCTOR(Ucname) +%pythonprepend Ucname::Ucname %{ + args[0].thisown=0 + args[1].thisown=0 +%} +%enddef + +%define IMP_SET_OBJECT(Ucname, methodname) +%pythonprepend Ucname::methodname %{ + args[1].thisown=0 +%} +%enddef + +%define IMP_ADD_OBJECT(Ucname, methodname) +%pythonprepend Ucname::methodname %{ + args[1].thisown=0 +%} +%enddef + +%define IMP_ADD_OBJECTS(Ucname, methodname) +%pythonprepend Ucname::methodname %{ + for p in args[1]: + p.thisown=0 +%} +%enddef + /* Add additional IMP_CONTAINER methods for scripting languages */ %define IMP_CONTAINER_SWIG(type, Ucname, lcname) %extend type { @@ -9,6 +41,8 @@ return ret; } } +IMP_ADD_OBJECT(type, add_##lcname) +IMP_ADD_OBJECTS(type, add_##lcname##s) %enddef

%include "IMP/macros.h" Index: kernel/pyext/IMP.i =================================================================== --- kernel/pyext/IMP.i (revision 669) +++ kernel/pyext/IMP.i (working copy) @@ -27,94 +27,30 @@ %}

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 +80,19 @@

%}

- 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 +113,7 @@ %feature("director") IMP::TripletScore; %feature("director") IMP::Optimizer; %feature("director") IMP::ParticleRefiner; +%feature("director") IMP::Mover;

%include "IMP/Key.h" %include "IMP/Object.h" Index: SConstruct =================================================================== --- SConstruct (revision 669) +++ SConstruct (working copy) @@ -52,7 +52,7 @@ #SConscript('domino/SConscript')

# bin script first requires kernel libraries to be built: -env.Depends(bin, [src, pyext]) +env.Depends(bin, [pyext, src])

# Build the binaries by default: env.Default(bin)