OpenFreeEnergy / OpenFreeEnergy/openfe

support rdkit 2026.03.4

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#2,069 2 comments 0 reactions 1 assignee View on GitHub

@IAlibay is already working on this.

Since Jul 27, 2026.

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Description

We see the following failures on equality checks when using rdkit 2026.

My naive guess is that it's due to changes in what attributes are included in rdkit representation:

https://github.com/rdkit/rdkit/releases#release-Release_2026_03_4

related to https://github.com/OpenFreeEnergy/openfe/issues/2067

FAILED src/openfe/tests/protocols/openmm_rfe/test_hybrid_top_protocol.py::test_setup_dry_sim_default_vacuum[repex] - assert <mdtraj.Topology with 1 chains, 1 residues, 16 atoms, 16 bonds at 0x33d372510> == <mdtraj.Topology with 1 chains, 1 residues, 16 atoms, 16 bonds at 0x33ef88c30>
 +  where <mdtraj.Topology with 1 chains, 1 residues, 16 atoms, 16 bonds at 0x33ef88c30> = <openfe.protocols.openmm_rfe._rfe_utils.relative.HybridTopologyFactory object at 0x309a2fcb0>.hybrid_topology
FAILED src/openfe/tests/protocols/openmm_rfe/test_hybrid_top_protocol.py::test_setup_dry_sim_default_vacuum[sams] - assert <mdtraj.Topology with 1 chains, 1 residues, 16 atoms, 16 bonds at 0x13b7c8c00> == <mdtraj.Topology with 1 chains, 1 residues, 16 atoms, 16 bonds at 0x33d502e50>
 +  where <mdtraj.Topology with 1 chains, 1 residues, 16 atoms, 16 bonds at 0x33d502e50> = <openfe.protocols.openmm_rfe._rfe_utils.relative.HybridTopologyFactory object at 0x33fb24050>.hybrid_topology
FAILED src/openfe/tests/protocols/openmm_rfe/test_hybrid_top_protocol.py::test_setup_dry_sim_default_vacuum[independent] - assert <mdtraj.Topology with 1 chains, 1 residues, 16 atoms, 16 bonds at 0x33f13d2b0> == <mdtraj.Topology with 1 chains, 1 residues, 16 atoms, 16 bonds at 0x33d267110>
 +  where <mdtraj.Topology with 1 chains, 1 residues, 16 atoms, 16 bonds at 0x33d267110> = <openfe.protocols.openmm_rfe._rfe_utils.relative.HybridTopologyFactory object at 0x33fb24f50>.hybrid_topology
FAILED src/openfe/tests/protocols/openmm_rfe/test_hybrid_top_protocol.py::test_setup_dry_sim_default_vacuum[InDePeNdENT] - assert <mdtraj.Topology with 1 chains, 1 residues, 16 atoms, 16 bonds at 0x33f1cd7b0> == <mdtraj.Topology with 1 chains, 1 residues, 16 atoms, 16 bonds at 0x33f8f2060>
 +  where <mdtraj.Topology with 1 chains, 1 residues, 16 atoms, 16 bonds at 0x33f8f2060> = <openfe.protocols.openmm_rfe._rfe_utils.relative.HybridTopologyFactory object at 0x348528e10>.hybrid_topology

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