openfe_analysis.utils.apply_transformations

Functions

apply_complex_alignment_transformations(...)

Apply a standard set of PBC-handling and alignment transformations required for RMSD-based analyses and other structural analyses that assume a pre-processed trajectory.

apply_ligand_alignment_transformations(...)

Apply PBC-handling and alignment transformations for ligand-only systems.
openfe_analysis.utils.apply_transformations.apply_complex_alignment_transformations(universe: MDAnalysis.Universe, protein: MDAnalysis.AtomGroup, ligands: list[MDAnalysis.AtomGroup] | None = None) → None

Apply a standard set of PBC-handling and alignment transformations required for RMSD-based analyses and other structural analyses that assume a pre-processed trajectory.

Parameters:

  • universe (mda.Universe) – The Universe the transformations are applied to. Modified in-place.

  • protein (mda.AtomGroup) – The AtomGroup of the protein

  • ligands (list[mda.AtomGroup] | None) – List of ligand AtomGroups. Each is unwrapped and shifted to the closest image of the protein independently. If None or empty, only the protein is used.

Raises:

ValueError – If protein is None or contains no atoms.

Notes

The following transformations are applied in order:

  • Unwraps protein and all ligands to be made whole

  • Shifts protein chains and each ligand independently to the image closest to the first protein chain (ClosestImageShift)

  • Aligns the entire system to minimize the protein RMSD (Aligner)

openfe_analysis.utils.apply_transformations.apply_ligand_alignment_transformations(universe: MDAnalysis.Universe, ligand: MDAnalysis.AtomGroup) → None

Apply PBC-handling and alignment transformations for ligand-only systems.

Parameters:

  • universe (mda.Universe) – The Universe the transformations are applied to. Modified in-place.

  • ligand (mda.AtomGroup) – Ligand atoms to apply transformations to.

Raises:

ValueError – If ligand is None or contains no atoms.

Notes

The following transformations are applied in order:

  • Prevents the ligand from jumping between periodic images (NoJump)

  • Aligns the ligand to minimize its RMSD (Aligner)