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Fix deprecated from pmg #542

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Merged
minhsueh merged 2 commits into from
Aug 12, 2026
Merged

Fix deprecated from pmg #542

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e9dd6ff
chore: bump release to v2026.7.20
minhsueh Jul 21, 2026
c0b258b
fix pmg deprecated methods
minhsueh Aug 12, 2026
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2 changes: 1 addition & 1 deletion crystal_toolkit/components/localenv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -810,7 +810,7 @@ def get_valences(struct):
[struct[index], *lse.neighbors_sets[index][0].neighb_sites]
)
mol = mol.get_centered_molecule()
mg = MoleculeGraph.with_empty_graph(molecule=mol)
mg = MoleculeGraph.from_empty_graph(molecule=mol)
for i in range(1, len(mol)):
mg.add_edge(0, i)

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8 changes: 4 additions & 4 deletions crystal_toolkit/components/structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -996,19 +996,19 @@ def _preprocess_input_to_graph(
with warnings.catch_warnings():
warnings.simplefilter("ignore")
if isinstance(input, Structure):
graph = StructureGraph.with_local_env_strategy(
graph = StructureGraph.from_local_env_strategy(
input, bonding_strategy
)
else:
graph = MoleculeGraph.with_local_env_strategy(
graph = MoleculeGraph.from_local_env_strategy(
input, bonding_strategy, reorder=False
)
except Exception:
# for some reason computing bonds failed, so let's not have any bonds(!)
if isinstance(input, Structure):
graph = StructureGraph.with_empty_graph(input)
graph = StructureGraph.from_empty_graph(input)
else:
graph = MoleculeGraph.with_empty_graph(input)
graph = MoleculeGraph.from_empty_graph(input)

return graph

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2 changes: 1 addition & 1 deletion crystal_toolkit/renderables/moleculegraph.py
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Expand Up @@ -40,7 +40,7 @@ def get_molecule_graph_scene(
A Molecule Graph scene.
"""
if visualize_bond_orders:
vis_mol_graph = MoleculeGraph.with_local_env_strategy(
vis_mol_graph = MoleculeGraph.from_local_env_strategy(
self.molecule, OpenBabelNN()
)
else:
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