Proteuspy

Fixed

- a few small issues with testing under Linux
- Makefile tweaks

Added

- disulfide_schematic.py which has two functions for creating schematic
drawings of Disulfides in various styles:
- ``create_disulfide_schematics()``
- ``create_disulfide_schematic_from_model()``
- test function in the tests/ directory
- script endpoint: proteusPy.create_disulfide_schematics

Fixed

- Finished refactoring for ``DisulfideIO.py``
- Corrected parameter order in ``DisulfideBase.DisulfideList.display_overlay()``
- Corrected the ``.screenshot()`` function to work correctly on Windows.
- Corrected Makefile installation target to install from the wheel, not repo

Added

- ``DisulfideList.Average_Sg_Distance`` property
- Disulfide List info added to the ``rcsb_viewer.py`` info pane

Fixed

- ``rcsb_viewer.py`` - refactored for new ``DisulfideVisualization`` classes.
- Pushed to both DockerHub and GitHub repositories.
-

Added

- Stronger type checking across many functions
- Additional error checking for slicing lists
- Several new Unittests

Changed

- Refactored both ``Disufulfide`` and ``DisulfideList`` and moved plotting and statistics into new classes ``DisulfideVisualization`` and ``DisulfideStats``.
- Simplification and unification of accessing Disulfides via class strings
- Generalized Disulfide class creation, can create up to 26-fold classes now.

Fixed

- DisulfideList.AverageConformation now uses a circular mean function to correctly handle the nature of -180 - 180 degree dihedral angle averaging.

Added

- Disulfide.spin() - Spin the disulfide about the Y axis.
- Test_DisplaySS.py - Unittest improvements.

Changed

- Completely rewrote ``DisulfideClass_Constructor`` methods that generate the binary and octant class strings for simplicity.
- The new ``DisulfideClass_Constructor.get_segment()`` is a more general version of ``DisulfideClass_Constructor.get_eighth_quadrant()``.

Added

- static method ``DisufideClass_Constructor.class_string_from_dihedral()`` - return the binary or octant class string for a single or array of dihedrals.
- properties ``Disulfide.binary_class_string`` and ``Disulfide.octant_class_string``
- ``DisulfideLoader.sslist_from_class()`` - now uses the index value for a specific disulfide that matches the classID from the TorsionDF dataframe. This allows for direct access to the DisulfideList containing the Disulfides via ``loader[index]``, which is significantly faster than looking up via ``loader[disulfide_name]``.

Changed

- vectorized binary and octant class string construction
- added binary and octant class strings to the master ``loader.TorsionDF`` DataFrame.
- Rewrote ``programs/DisulfideClass_Extractor.py`` to use the index-based address scheme described above. This resulted in about a 20x speedup in the program!