=========
Changelog
=========

.. current developments

v0.5.0
====================

**Added:**

* Added API documentation, which can be found at openfe-analysis.openfree.energy (`PR #74 <https://github.com/OpenFreeEnergy/openfe_analysis/pull/74>`_).
* Plotting utilities for ligand RMSD, COM drift timeseries, and protein 2D RMSD (`PR #106 <https://github.com/OpenFreeEnergy/openfe_analysis/pull/106>`_).
* Symmetry-corrected ligand RMSD via spyrmsd (:class:`SymmetryCorrectedLigandRMSD`) (`PR #92 <https://github.com/OpenFreeEnergy/openfe_analysis/pull/92>`_).

**Changed:**

* :func:`apply_complex_alignment_transformations` now handles multiple ligands, as needed for the SepTop protocol (`PR #110 <https://github.com/OpenFreeEnergy/openfe_analysis/pull/110>`_).
* Universe creation and trajectory alignment split into separate functions:
  :func:`create_universe_single_state`, :func:`apply_complex_alignment_transformations`
  (for protein-ligand systems), and :func:`apply_ligand_alignment_transformations`
  (for ligand-only systems) (`PR #93 <https://github.com/OpenFreeEnergy/openfe_analysis/pull/93>`_).
* Structural analyses refactored into MDAnalysis ``AnalysisBase`` classes (`PR #90 <https://github.com/OpenFreeEnergy/openfe_analysis/pull/90>`_).

**Removed:**

* :func:`make_Universe` — replaced by :func:`create_universe_single_state` combined
  with :func:`apply_complex_alignment_transformations` or
  :func:`apply_ligand_alignment_transformations` (`PR #93 <https://github.com/OpenFreeEnergy/openfe_analysis/pull/93>`_).

**Fixed:**

* :func:`_determine_position_indices` now correctly handles single-frame trajectories (`PR #107 <https://github.com/OpenFreeEnergy/openfe_analysis/pull/107>`_).



v0.4.0
====================

**Changed:**

* Changed ``openfe_analysis.FEReader`` to use parameters ``index`` and ``index_method`` instead of ``state_id`` and ``replica_id`` (`PR #77 <https://github.com/OpenFreeEnergy/openfe_analysis/pull/77>`_).

**Removed:**

* Removed ``openfe-analysis`` CLI (`PR #86 <https://github.com/OpenFreeEnergy/openfe_analysis/pull/86>`_).

**Fixed:**

* Fixed periodic boundary condition bug in multi-chain RMSD analysis (`Issue #30 <https://github.com/OpenFreeEnergy/openfe_analysis/issues/30>`_).



v0.3.1
====================

**Fixed:**

* Fixed ``n_frames`` reading in netcdf reader (`PR #48 <https://github.com/OpenFreeEnergy/openfe_analysis/pull/48>`_).



v0.3.0
======

**Added:**

* Added support for multistate netcdf files generated by openmmtools with variable position and velocity writing rates (`PR #40 <https://github.com/OpenFreeEnergy/openfe_analysis/pull/40>`_ and `#44 <https://github.com/OpenFreeEnergy/openfe_analysis/pull/44>`_ .