Ring Conformers: Two large improvements to the ring conformer system
NEWS: This push introduces 2 major changes:
1st, RingConformerSet and related code has been moved out of carbohydrate
namespaces into more general ones.
2nd, tau angles are now stored in RingConformers.
Now, if anyone wishes to use the RingConformationMover, they only need to
define 2 less than the number of atoms in the ring nu angles and add the
property CYCLIC to the .params file for a ResidueType.
I have added an NCAA, cyclohexylglycine, to the rings integration test to
demonstrate this.
The addition of tau angles (internal bond angles) is because more highly
strained rings have bond angle distortions. Now, when a ring is set to a
strained conformer, the bond angles are also set to ideal values so that
the ring "stays together".
Currently, I only have the system fully working for 6-membered rings, but
5-membered rings should follow shortly, once I calculate/figure out ideal
taus for them.
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Unit test status: Pass
Integration test status: ~150
This is because I introduced one more ResidueType into the Set.
carbohydrates and rings will also change