Merge pull request #3336 from RosettaCommons/JWLabonte/sugars/database
Carbohdyrates: unit test to check stereochem./atom-placement of monosacharide residues in the database
This merge adds a complicated "dynamic" unit test that used a "rubric" file with expected answers to check carbohydrate .params files for ICOOR errors.
The errors it checks for include:
Proper superimposition of virtual atoms with real atoms
Expected stereochemistry of ring atoms (based on a rubric data file, stereochem_test.key)
Expected ring conformer (based on the same rubric file)
Hydrogen placement
The test checks both reducing-end and non-reducing end versions of the residues, by creating disaccharides.
The unit test reveals an assortment of ICOOR errors, as I expected, which I am systematically fixing. Notably, post-merge, hydrogen placement should always be correct — the problem was in the patch files for lower termini — and the RingConformerSet should correctly assign the current RingConformer consistently — the problem was in virtual atom superimposition.
I have also decided to organize the .params files in a deeper subdirectory scheme.
Finally, and perhaps most significantly, I have "idealized" heavy atom ICOOR records to use simpler, average, less precise values. I do not think this will affect scientific performance, though it may affect Cartesian minimization. If it does not, I think this is a better, more standardized way of writing sugar .params files and will simplify the implementation of my long desire to script the generation of hundreds of possible topography files for future design work.
All unit tests pass.
This merge will result in integration test changes for ALL tests involving glycans, as literally every sugar .params file has been modified.