[Cdk-patches] patches to update atom/bond permutation classes

[Rajarshi G. <rg...@in...>]

Refactored to use Iterable<IAtomContainer> and also updated to  
consistently use interfaces. The second patch updates code that used  
the permutation classes to use the Iterable interface.

Based on 1.2.x

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Rajarshi Guha  <rg...@in...>
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