[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [IMP-dev] [IMP-commits] r672 - in trunk/kernel: pyext test/optimizers

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