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hannahbaumann
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| # adaptive transformation settings are only supported for RelativeHybridTopologyProtocol currently | ||
| protocol_settings = RelativeHybridTopologyProtocol.default_settings() | ||
| protocol_settings.forcefield_settings.small_molecule_forcefield = FORCEFIELD | ||
| protocol_settings.protocol_repeats = 1 |
| transformation = openfe.Transformation( | ||
| stateA=system_a, | ||
| stateB=system_b, | ||
| mapping=None, |
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We don't need the mapping for this protocol, but could we include it with the system_group and system_name, like we do in _example_plan_rbfe.py, so we can track which systems the edge corresponds to?
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I think I'm not quite sure what you mean here, could you maybe clarify?
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We'll keep the mapping for now, opening an issue in gufe to allow adding annotations to Transformations, will revisit after gufe decision.
| componentA=ligands_by_name[edge.componentA.name], | ||
| componentB=ligands_by_name[edge.componentB.name], | ||
| componentA_to_componentB=edge.componentA_to_componentB, | ||
| annotations=edge.annotations, |
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If we can keep the mapping lets track the system_group and system_name in the annotations field for the new edge.
| transformation = openfe.Transformation( | ||
| stateA=system_a, | ||
| stateB=system_b, | ||
| mapping=None, |
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| mapping=None, | |
| mapping=new_edge, |
@jthorton is this what you meant here? This is what the plan rbfe script does.
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