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_example_plan_rbfe.py incompatible with openfe 1.13 #153
Description
Describe the bug
AttributeError: 'LigandAtomMapping' object has no attribute 'heavy_atom_componentA_to_componentB' in openfe 1.13 (actually using '1.12.1.dev36+g18208178d' in lieu of a release.)
To Reproduce
Install main branch of openfe as of this date and run _example_plan_rbfe.py
Software versions
- Which operating system and version did you use? MacOS 15.1
- Which method did you use to install this package? Micromamba
- Copy/paste the output of
conda list(or the equivalent for your package manager):- python 3.12.14
- openfe '1.12.1.dev36+g18208178d'
- gufe 1.12.0
Output
2026-09-30 11:44:13 - openfe_benchmarks.data._benchmark_systems - INFO - Loaded system 'hne' from system group 'mcs_docking_set' with:
5 ligand file(s), and 5 cofactor file(s).
Found protein file: True.
Found 1 ligand network files with keys: industry_benchmarks_network
2026-09-30 11:44:14,123 __main__ INFO: Validating transformations for system mcs_docking_set hne
Traceback (most recent call last):
File "/Users/jenniferclark/bin/openfe-benchmarks/openfe_benchmarks/scripts/_example_plan_rbfe.py", line 403, in <module>
main()
File "/Users/jenniferclark/bin/openfe-benchmarks/openfe_benchmarks/scripts/_example_plan_rbfe.py", line 212, in main
edge.create()
File "/Users/jenniferclark/mamba/envs/openfe-113/lib/python3.12/site-packages/gufe/transformations/transformation.py", line 273, in create
return self.protocol.create(
^^^^^^^^^^^^^^^^^^^^^
File "/Users/jenniferclark/mamba/envs/openfe-113/lib/python3.12/site-packages/gufe/protocols/protocol.py", line 263, in create
protocol_units=self._create(
^^^^^^^^^^^^^
File "/Users/jenniferclark/bin/openfe/src/openfe/protocols/openmm_rfe/hybridtop_protocols.py", line 698, in _create
self.validate(stateA=stateA, stateB=stateB, mapping=mapping, extends=extends)
File "/Users/jenniferclark/mamba/envs/openfe-113/lib/python3.12/site-packages/gufe/protocols/protocol.py", line 377, in validate
self._validate(stateA=stateA, stateB=stateB, mapping=mapping, extends=extends)
File "/Users/jenniferclark/bin/openfe/src/openfe/protocols/openmm_rfe/hybridtop_protocols.py", line 623, in _validate
self._validate_mapping(mapping, alchem_comps)
File "/Users/jenniferclark/bin/openfe/src/openfe/protocols/openmm_rfe/hybridtop_protocols.py", line 307, in _validate_mapping
RelativeHybridTopologyProtocol._check_minimum_number_of_mapped_atoms(mapping=m)
File "/Users/jenniferclark/bin/openfe/src/openfe/protocols/openmm_rfe/hybridtop_protocols.py", line 383, in _check_minimum_number_of_mapped_atoms
mapped_heavy_atoms = mapping.heavy_atom_componentA_to_componentB
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'LigandAtomMapping' object has no attribute 'heavy_atom_componentA_to_componentB'
Expected behavior
No error
AI disclosure
None
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jthorton commentedon Oct 7, 2026
This should be fixed by using
gufe>=1.13which will be pinned in the next openfe release.jaclark5 commentedon Oct 7, 2026
I updated to gufe=1.13.1, installed exorcist, and you are correct the current openfe main as of October 7 2026 (soon to be openfe=1.13) only errors like #151
Note: I needed to test this on the branch #150 to run since pontibus is not compatible with OpenFE >1.12