[IMP-dev] Various minor patches

[Daniel Russel <>]

In brief, NonbondedListScoreState is now an abstract class and the  
corresponding class is AllNonbondedListScoreScoreState. I don't like  
the name, so if you have a better one, please suggest it. I needed to  
have a base class for the lists so that I can implemented one which  
handles particles with varying radii nicely.

In more depth:
1) Better string handling in the exception base class

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2) added bounds check on vector access

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3) Refactored the non-bonded list code. There is a new internal class  
which implements a voxel grid for particles. There is also a base  
class for non-bonded lists which AllNonbondedList and  
BipartiteNonbondedList both inherit from. I also got rid of the subdir  
for the bonded lists and fixed various documentation. SConscipt files  
and IMP.h changes are not submitted.

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