Fix networks #155
Fix networks #155
Conversation
removing copy past artefact :)
Saving transformations to json
Co-authored-by: Hannah Baumann <[email protected]>
Co-authored-by: Hannah Baumann <[email protected]>
Co-authored-by: Hannah Baumann <[email protected]>
…hmarks2024 into fix_networks
| # build alchemical sub-networks | ||
| g = ligand_network.graph | ||
| all_edges = list(ligand_network.edges) | ||
| sub_network_nodes = list(nx.connected_components(g)) |
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This is failing because it's a multidigraph I think - we can just create a digraph from g and it should work
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Now first creating an undirected graph from g
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| transform_list.append(t_list[0]) | ||
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| return AlchemicalNetwork(transform_list) |
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The AlchemicalNetwork may not have "complete" cycles, i.e. could only have the solvent or complex leg. When generating the LigandNetwork from this, this information gets lost and broken networks are not recognized.
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This was fixed in commit 8f7131f
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If instead the user should remove result .json files from edges where only one leg finished, these two lines can be removed, though at least a warning should be thrown.
| stateB = ChemicalSystem.from_dict(units[0]["inputs"]["stateB"]) | ||
| ligmap = LigandAtomMapping.from_dict(units[0]["inputs"]["ligandmapping"]) | ||
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| if any([isinstance(comp, gufe.ProteinComponent) for comp in stateA.components.values()]): |
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ToDo: Test if this would still work for files that have been cleaned up, i.e. where components have partially been removed.
| # build alchemical sub-networks | ||
| g = ligand_network.graph | ||
| all_edges = list(ligand_network.edges) | ||
| sub_network_nodes = list(nx.connected_components(g)) |
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Now first creating an undirected graph from g
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ToDo:
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ToDo
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| return ru | ||
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| def get_transformation_alternate( |
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From today: we could possibly get solvent/complex from the names.
| for transform in taped_alchemical_network.edges: | ||
| transform.dump(transforms_dir / f"{transform.name}.json") | ||
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| full_ligand_network = get_full_ligand_network(input_ligand_network, res_ligand_network, network_connections) |
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Change this to be only the additional edges.
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Addressed in commit 31c2ac1
Supplements #144
This needs: