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pull names directly from ligandmapping (#1702)
* pull names directly from ligandmapping * update news entry
This commit is contained in:
Alyssa Travitz
GitHub
@@ -4,7 +4,7 @@
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**Changed:**
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* ``openfe gather`` is now more rigorous in extracting ligand names and run types. These are now determined directly from component attributes, rather than relying on naming conventions. See `PR #1691 <https://github.com/OpenFreeEnergy/openfe/pull/1691>`_ for more details.
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* ``openfe gather`` is now more rigorous in extracting ligand names and run types. These are now determined directly from component attributes, rather than relying on naming conventions. See `PR #1691 <https://github.com/OpenFreeEnergy/openfe/pull/1702>`_ for more details.
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**Deprecated:**
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@@ -221,25 +221,23 @@ def _get_names(result: dict) -> tuple[str, str]:
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# TODO: I don't like this [0][0] indexing, but I can't think of a better way currently
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protocol_data = list(result["protocol_result"]["data"].values())[0][0]
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ligand_A = gufe.SmallMoleculeComponent.from_dict(
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protocol_data["inputs"]["stateA"]["components"]["ligand"]
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)
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ligand_B = gufe.SmallMoleculeComponent.from_dict(
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protocol_data["inputs"]["stateB"]["components"]["ligand"]
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)
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return ligand_A.name, ligand_B.name
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name_A = protocol_data["inputs"]["ligandmapping"]["componentA"]["molprops"]["ofe-name"]
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name_B = protocol_data["inputs"]["ligandmapping"]["componentB"]["molprops"]["ofe-name"]
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return name_A, name_B
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def _get_type(result: dict) -> Literal["vacuum", "solvent", "complex"]:
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"""Determine the simulation type based on the component types."""
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protocol_data = list(result["protocol_result"]["data"].values())[0][0]
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chem_sys_A = gufe.ChemicalSystem.from_dict(protocol_data["inputs"]["stateA"])
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if not chem_sys_A.contains(gufe.SolventComponent):
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component_types = [
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x["__module__"] for x in protocol_data["inputs"]["stateA"]["components"].values()
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]
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if "gufe.components.solventcomponent" not in component_types:
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return "vacuum"
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elif chem_sys_A.contains(gufe.ProteinComponent):
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elif "gufe.components.proteincomponent" in component_types:
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return "complex"
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else:
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return "solvent"
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@@ -207,6 +207,206 @@ def min_result_json():
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"__qualname__": "ChemicalSystem",
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"__module__": "gufe.chemicalsystem",
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},
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"ligandmapping": {
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"componentA": {
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[6, 0, 0, True, 0, 0, {}],
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[6, 0, 0, True, 0, 0, {}],
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[1, 0, 0, False, 0, 0, {}],
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[1, 0, 0, False, 0, 0, {}],
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[17, 0, 0, False, 0, 0, {}],
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[1, 0, 0, False, 0, 0, {}],
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],
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"bonds": [
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[0, 1, 1, 0, {}],
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[1, 6, 12, 0, {}],
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[1, 2, 12, 0, {}],
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[2, 3, 12, 0, {}],
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[2, 31, 1, 0, {}],
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[3, 4, 12, 0, {}],
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[3, 30, 1, 0, {}],
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[4, 5, 12, 0, {}],
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[4, 9, 1, 0, {}],
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[5, 6, 12, 0, {}],
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[5, 8, 1, 0, {}],
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[6, 7, 1, 0, {}],
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[9, 10, 2, 0, {}],
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[9, 11, 1, 0, {}],
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[11, 12, 1, 0, {}],
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[11, 13, 1, 0, {}],
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[13, 18, 12, 0, {}],
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[13, 14, 12, 0, {}],
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[14, 15, 12, 0, {}],
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[14, 29, 1, 0, {}],
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[15, 16, 12, 0, {}],
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[15, 28, 1, 0, {}],
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[17, 18, 12, 0, {}],
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],
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"conformer": [
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{},
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],
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"molprops": {"ofe-name": "lig_ejm_31"},
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"__qualname__": "SmallMoleculeComponent",
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"__module__": "gufe.components.smallmoleculecomponent",
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},
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"componentB": {
|
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"atoms": [
|
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[1, 0, 0, False, 0, 0, {}],
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[6, 0, 0, True, 0, 0, {}],
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[6, 0, 0, True, 0, 0, {}],
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[6, 0, 0, True, 0, 0, {}],
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[6, 0, 0, True, 0, 0, {}],
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[6, 0, 0, True, 0, 0, {}],
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|
||||
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|
||||
{},
|
||||
],
|
||||
"molprops": {"ofe-name": "lig_ejm_42"},
|
||||
"__qualname__": "SmallMoleculeComponent",
|
||||
"__module__": "gufe.components.smallmoleculecomponent",
|
||||
},
|
||||
"componentA_to_componentB": {
|
||||
"0": 0,
|
||||
"1": 1,
|
||||
"2": 2,
|
||||
"3": 3,
|
||||
"4": 4,
|
||||
"5": 5,
|
||||
"6": 6,
|
||||
"7": 7,
|
||||
"8": 8,
|
||||
"9": 9,
|
||||
"10": 10,
|
||||
"11": 11,
|
||||
"12": 12,
|
||||
"13": 13,
|
||||
"14": 14,
|
||||
"15": 15,
|
||||
"16": 16,
|
||||
"17": 17,
|
||||
"18": 18,
|
||||
"19": 19,
|
||||
"20": 20,
|
||||
"21": 21,
|
||||
"22": 22,
|
||||
"23": 23,
|
||||
"24": 24,
|
||||
"25": 26,
|
||||
"27": 25,
|
||||
"28": 31,
|
||||
"29": 32,
|
||||
"30": 33,
|
||||
"31": 34,
|
||||
},
|
||||
"annotations": '{"score": 0.09516258196404048}',
|
||||
"__qualname__": "LigandAtomMapping",
|
||||
"__module__": "gufe.mapping.ligandatommapping",
|
||||
},
|
||||
},
|
||||
}
|
||||
]
|
||||
|
||||
Reference in New Issue
Block a user