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Merged
hannahbaumann merged 2 commits into from
Feb 23, 2026
Merged

Update Readme after FEReader change #89

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Update Readme after FEReader change
hannahbaumann Feb 20, 2026
d8fe963
Update README.md
hannahbaumann Feb 23, 2026
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8 changes: 5 additions & 3 deletions README.md
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Expand Up @@ -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`` (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:
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