Chrisjurich/reactive docking pr2

[chrisjurich]

This is a major update to the reactive docking API as well as internals in the structure.structure_constraint and structure.structure_region sub-modules. Brief descriptions are below:

• structure.structure_constraint allows for the definition of generic StructureConstraint classes that define a variety of geometric constraints between residues and atoms. Basic infrastructure for constraint I/O was implemented

• structure.structure_region allows for the creation of subregions in the Pose. It is mostly used for QM clustering. While variation of this have existed before, they relied on pymol and were prone to failure. The new version uses internal functions and does not require pymol or the corresponding interface.

[shaoqx]

I pushed several commits to the branch for fixing some bug and unit tests. Sorry for doing it before having your consent, i can revert it if you dont like them.

[shaoqx]

Merging. Making unresolved discussions issues,