Merge pull request #3237 from RosettaCommons/vmullig/add_square_planar_or_square_pyramidal_metals
Vmullig/add square planar or square pyramidal metals
This pull request will allow the `CrosslinkerMover` to place square pyramidal or square planar metals.
- [x] This is branched off of pull request #3222, so that must be merged first.
@srgerb
Tasks:
- [x] Add parameters for nickel.
- [x] Add new helpers.
- [x] Square planar helper.
- [x] Delete std::cout line.
- [x] Square pyramidal helper.
- [x] Delete std::cout line.
- [x] Update them to do something.
- [x] Square planar helper.
- [x] Square pyramidal helper (have it call the square planar helper functions, and inherit from the square planar helper class).
- [x] Link to `CrosslinkerMover`.
- [x] Link to `simple_cycpep_predict`.
- [x] Integration tests:
- [x] Square planar case, asymmetric.
- [x] Square planar case, d2 symmetric.
- [x] Square pyramidal case, asymmetric.
- [x] Shorten this test.
- [x] Square planar case with `simple_cycpep_predict`, with s6 quasi-symmetry. (The two unoccupied positions break symmetry.)
- [x] Check this and add expected results.
- [x] Square pyramidal case with `simple_cycpep_predict`, with s6 quasi-symmetry. (Note that 5th position breaks symmetry.)
- [x] Check this and add expected results.
- [x] Documentation for `CrosslinkerMover`(see https://github.com/RosettaCommons/documentation/pull/22 in the documentation repository).
- [x] Documentation for `simple_cycpep_predict`(see https://github.com/RosettaCommons/documentation/pull/22 in the documentation repository).
- [x] Beauty.