First some minor cleanups - adding operator<< to Vector3D and fixing some header inclusion issues
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cleanup
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Second adding particle removal as previous discussed:- There is a new base class RefCountedObject which is used for Particle and is ref counted. Vector and ObjectContainer ref count ref counted objects that are contained in them
- particles now have a Particle attribute type- the usual caveats about changes to SConscript files being ignore and IMP.i containing some extra changes apply (extra %includes) - if a particle is removed from the model it is made inactive also. We should probably have the particle constructor make the particle inactive until it is added to a model.
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particle_removal
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Bonds use the Particle attribute: - no visible changes
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bonds
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Hierarchy uses the particle attribute - no visible changes
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hierarchy
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The nonbonded list is more dynamic: - it drops inactive particles silently- you can add particles and they are handled correctly, if not terribly efficiently
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nbl
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I can't guarantee that the patches all work independently