Changelog

v0.5.0

Added:

  • Added API documentation, which can be found at openfe-analysis.openfree.energy (PR #74).

  • Plotting utilities for ligand RMSD, COM drift timeseries, and protein 2D RMSD (PR #106).

  • Symmetry-corrected ligand RMSD via spyrmsd (SymmetryCorrectedLigandRMSD) (PR #92).

Changed:

  • apply_complex_alignment_transformations() now handles multiple ligands, as needed for the SepTop protocol (PR #110).

  • Universe creation and trajectory alignment split into separate functions: create_universe_single_state(), apply_complex_alignment_transformations() (for protein-ligand systems), and apply_ligand_alignment_transformations() (for ligand-only systems) (PR #93).

  • Structural analyses refactored into MDAnalysis AnalysisBase classes (PR #90).

Removed:

  • make_Universe() — replaced by create_universe_single_state() combined with apply_complex_alignment_transformations() or apply_ligand_alignment_transformations() (PR #93).

Fixed:

  • _determine_position_indices() now correctly handles single-frame trajectories (PR #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).

Removed:

  • Removed openfe-analysis CLI (PR #86).

Fixed:

  • Fixed periodic boundary condition bug in multi-chain RMSD analysis (Issue #30).

v0.3.1

Fixed:

  • Fixed n_frames reading in netcdf reader (PR #48).

v0.3.0

Added:

  • Added support for multistate netcdf files generated by openmmtools with variable position and velocity writing rates (PR #40 and #44 .