Re: [IMP-dev] [IMP-commits] r1102 - in trunk/kernel: doc/patch include pyext/IMP src test/particles

[Daniel Russel <>]

This patch needs the following added to the appropriate place to not  
break memory management.

+  %pythonprepend Particle::Particle %{
+        if len(args) >0: self.thisown=False
+  %}

Probably got lost somewhere in the patch process.


On Jan 5, 2009, at 11:43 AM, Notification of IMP commits wrote:

> Author: 
> Date: 2009-01-05 11:43:25 -0800 (Mon, 05 Jan 2009)
> New Revision: 1102
>
> Removed:
>   trunk/kernel/doc/patch/particle_model.patch
>   trunk/kernel/doc/patch/particle_model.readme
> Modified:
>   trunk/kernel/include/Particle.h
>   trunk/kernel/pyext/IMP/test.py
>   trunk/kernel/src/Particle.cpp
>   trunk/kernel/test/particles/test_refcount.py
> Log:
> Patch from Daniel, with minor cleanup by me: add a constructor to  
> Particle to
> take a Model, and change a few tests to use this constructor.
>
>
> Modified: trunk/kernel/include/Particle.h
> ===================================================================
> --- trunk/kernel/include/Particle.h	2008-12-31 00:40:19 UTC (rev 1101)
> +++ trunk/kernel/include/Particle.h	2009-01-05 19:43:25 UTC (rev 1102)
> @@ -96,8 +96,9 @@
>
> public:
>
> +  //! Construct a particle and add it to the Model
> +  Particle(Model *m);
>
> -
>   Particle();
>   ~Particle();
>
>
> Modified: trunk/kernel/pyext/IMP/test.py
> ===================================================================
> --- trunk/kernel/pyext/IMP/test.py	2008-12-31 00:40:19 UTC (rev 1101)
> +++ trunk/kernel/pyext/IMP/test.py	2009-01-05 19:43:25 UTC (rev 1102)
> @@ -34,8 +34,7 @@
>     def create_point_particle(self, model, x, y, z):
>         """Make a particle with optimizable x, y and z attributes, and
>            add it to the model."""
> -        p = IMP.Particle()
> -        model.add_particle(p)
> +        p = IMP.Particle(model)
>         p.add_attribute(IMP.FloatKey("x"), x, True)
>         p.add_attribute(IMP.FloatKey("y"), y, True)
>         p.add_attribute(IMP.FloatKey("z"), z, True)
>
> Modified: trunk/kernel/src/Particle.cpp
> ===================================================================
> --- trunk/kernel/src/Particle.cpp	2008-12-31 00:40:19 UTC (rev 1101)
> +++ trunk/kernel/src/Particle.cpp	2009-01-05 19:43:25 UTC (rev 1102)
> @@ -11,6 +11,13 @@
>
> IMP_BEGIN_NAMESPACE
>
> +Particle::Particle(Model *m)
> +{
> +  is_active_ = true;
> +  m->add_particle(this);
> +}
> +
> +
> Particle::Particle()
> {
>   is_active_ = true;
>
> Modified: trunk/kernel/test/particles/test_refcount.py
> ===================================================================
> --- trunk/kernel/test/particles/test_refcount.py	2008-12-31 00:40:19  
> UTC (rev 1101)
> +++ trunk/kernel/test/particles/test_refcount.py	2009-01-05 19:43:25  
> UTC (rev 1102)
> @@ -34,8 +34,7 @@
>         self._check_number(0)
>
>         m= IMP.Model()
> -        p= IMP.Particle()
> -        m.add_particle(p)
> +        p= IMP.Particle(m)
>         self._check_number(1)
>
>         p=1
> @@ -47,8 +46,8 @@
>         """Check that ref counting works with removing particles"""
>         self._check_number(0)
>         m= IMP.Model()
> -        p= IMP.Particle()
> -        pi= m.add_particle(p)
> +        p= IMP.Particle(m)
> +        pi= p.get_index()
>         self._check_number(1)
>         m.remove_particle(pi)
>         self._check_number(1)
> @@ -86,10 +85,10 @@
>         self._check_number(0)
>         m= IMP.Model()
>         print 7
> -        p= IMP.Particle()
> +        p= IMP.Particle(m)
>         print p
>         print 8
> -        pi= m.add_particle(p)
> +        pi= p.get_index()
>         print 9
>         p=None
>         self._check_number(1)
> @@ -141,8 +140,8 @@
>         """Check that removed particles are skipped"""
>         print "skipped"
>         m= IMP.Model()
> -        p= IMP.Particle()
> -        pi= m.add_particle(p)
> +        p= IMP.Particle(m)
> +        pi= p.get_index()
>         ps= m.get_particles()
>         self.assertEqual(len(ps), 1, "Should only be 1 particle")
>         m.remove_particle(pi)
>
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