From b597c5c3c54380bede1c75d56fecf3193a539a42 Mon Sep 17 00:00:00 2001 From: hannahbaumann Date: Fri, 20 Feb 2026 09:51:39 +0100 Subject: [PATCH 1/2] Update Readme after FEReader change --- README.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index f182bf6..fb68a35 100644 --- a/README.md +++ b/README.md @@ -14,9 +14,11 @@ This package provides a MDAnalysis Reader to start to explore your trajectory da import MDAnalysis as mda from openfe_analysis import FEReader -# a "simulation.nc" file contains multiple replicas, so we must choose which of these we load -# provide either a state (following a single lambda state) or replica (following a particular replica) id (typically 0-10) -u = mda.Universe('hybrid_system.pdb', 'simulation.nc', format=FEReader, state_id=0) +# A "simulation.nc" file contains multiple replicas, so we must choose which of these we load. +# Provide an index for the state or replica to extract. +# The `index_method` then determines whether `index` refers to a Hamiltonian state (following a single lambda state) +# or a replica state (following a particular replica). +u = mda.Universe('hybrid_system.pdb', 'simulation.nc', format=FEReader, index=0, index_method='state') ``` For example to convert your trajectory to a different format for visualisation: From d8fe9639dd9147cccf6aace56c4948d9c7a78994 Mon Sep 17 00:00:00 2001 From: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> Date: Mon, 23 Feb 2026 11:51:49 +0100 Subject: [PATCH 2/2] Update README.md Co-authored-by: Josh Horton --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index fb68a35..b2c4be4 100644 --- a/README.md +++ b/README.md @@ -16,8 +16,8 @@ from openfe_analysis import FEReader # A "simulation.nc" file contains multiple replicas, so we must choose which of these we load. # Provide an index for the state or replica to extract. -# The `index_method` then determines whether `index` refers to a Hamiltonian state (following a single lambda state) -# or a replica state (following a particular replica). +# The `index_method` then determines whether `index` refers to a Hamiltonian ``state`` (following a single lambda state) +# or a ``replica`` (following a particular replica). u = mda.Universe('hybrid_system.pdb', 'simulation.nc', format=FEReader, index=0, index_method='state') ```