Why did you skip the MonteCarlo and NonbondedList parts?
Notification of IMP commits wrote: > Author: ben@SALILAB.ORG > Date: 2008-08-26 16:59:29 -0700 (Tue, 26 Aug 2008) > New Revision: 672 > > Modified: > trunk/kernel/pyext/IMP.i > trunk/kernel/pyext/IMP_macros.i > trunk/kernel/test/optimizers/test_md_optimizer.py > Log: > Patch from Daniel, with minor changes and testcases by me: > - Add macros to handle the thisown stuff in IMP.i (and add a few missed ones). > - Enable Optimizer::get_optimizer_states() in Python code. > > > Modified: trunk/kernel/pyext/IMP.i > =================================================================== > --- trunk/kernel/pyext/IMP.i 2008-08-26 23:40:30 UTC (rev 671) > +++ trunk/kernel/pyext/IMP.i 2008-08-26 23:59:29 UTC (rev 672) > @@ -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 +80,17 @@ > > %} > > - 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(Optimizer, OptimizerState, optimizer_state); > } > > %feature("ref") Particle "$this->ref();" > > Modified: trunk/kernel/pyext/IMP_macros.i > =================================================================== > --- trunk/kernel/pyext/IMP_macros.i 2008-08-26 23:40:30 UTC (rev 671) > +++ trunk/kernel/pyext/IMP_macros.i 2008-08-26 23:59:29 UTC (rev 672) > @@ -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" > > Modified: trunk/kernel/test/optimizers/test_md_optimizer.py > =================================================================== > --- trunk/kernel/test/optimizers/test_md_optimizer.py 2008-08-26 23:40:30 UTC (rev 671) > +++ trunk/kernel/test/optimizers/test_md_optimizer.py 2008-08-26 23:59:29 UTC (rev 672) > @@ -159,6 +159,18 @@ > ekinetic2 = self.md.get_kinetic_energy() > self.assertNotEqual(ekinetic, ekinetic2) > > + def test_get_optimizer_states(self): > + """Test get_optimizer_states() method""" > + wrtraj = WriteTrajState([]) > + scaler = IMP.VelocityScalingOptimizerState( > + IMP.Particles(self.particles), 298.0, 10) > + self.md.add_optimizer_state(wrtraj) > + self.md.add_optimizer_state(scaler) > + m = self.md.get_optimizer_states() > + self.assertEqual(len(m), 2) > + for a in m: > + self.assert_(isinstance(a, IMP.OptimizerState)) > + > def test_rescaling(self): > """Test thermostatting by velocity rescaling""" > for i in range(100): > > _______________________________________________ > IMP-commits mailing list > IMP-commits@salilab.org > https://salilab.org/mailman/listinfo/imp-commits >