add dssp analysis (PR #4304)

- Fixes #1612
- add `MDAnalysis.analysis.dssp` module with the `DSSP` class for secondary structure analysis, using code implemented in pydssp package available for secondary structure annotation; source *pydssp* v.0.9.0 (https://github.com/ShintaroMinami/PyDSSP) by Shintaro Minami, distributed under MIT license.
- include modified pydssp_numpy.py where einops was removed as a dependency and replaced with pure numpy operations
- adds tests from pydssp package and many test files
- add additional tests 
- add docs
- update CHANGELOG
- Add entry for pydssp in LICENSE

---------

Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
Co-authored-by: Yuxuan Zhuang <yuzhuang@stanford.edu>

LICENSE

@@ -1765,6 +1765,33 @@ PyQCPROT
     OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 
+==========================================================================
+
+DSSP module code for protein secondary structure assignment
+ - analysis/dssp/pydssp_numpy.py
+
+MIT License
+
+Copyright (c) 2022 Shintaro Minami
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
 ==========================================================================
 
 MDAnalysis logo (see doc/sphinx/source/logos)

package/CHANGELOG

@@ -45,6 +45,7 @@ Fixes
  * Fix groups.py doctests using sphinx directives (Issue #3925, PR #4374)
 
 Enhancements
+ * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)
  * Added a tqdm progress bar for `MDAnalysis.analysis.pca.PCA.transform()`
    (PR #4531)
  * Improved performance of PDBWriter (Issue #2785, PR #4472)

package/MDAnalysis/analysis/dssp/__init__.py

@@ -0,0 +1,7 @@
+__all__ = [
+    "DSSP",
+    "assign",
+    "translate",
+]
+
+from .dssp import DSSP, assign, translate