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Fall back to JMolNN if open babel is not installed when generating MoleculeMetadata #1150

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Fall back to JMolNN if open babel is not installed when generating MoleculeMetadata #1150

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2c41250
Fall back to `JMolNN` if open babel is not installed
Andrew-S-Rosen Nov 29, 2024
f2b6450
Update utils.py
Andrew-S-Rosen Nov 29, 2024
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19 changes: 14 additions & 5 deletions emmet-core/emmet/core/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
from pydantic import BaseModel
from pymatgen.analysis.elasticity.strain import Deformation
from pymatgen.analysis.graphs import MoleculeGraph
from pymatgen.analysis.local_env import OpenBabelNN, metal_edge_extender
from pymatgen.analysis.local_env import JmolNN, OpenBabelNN, metal_edge_extender
from pymatgen.analysis.molecule_matcher import MoleculeMatcher
from pymatgen.analysis.structure_matcher import (
AbstractComparator,
Expand All @@ -30,6 +30,11 @@
except ImportError:
bson = None # type: ignore

try:
from openbabel import openbabel
except Exception:
openbabel = None # type: ignore

SETTINGS = EmmetSettings()


Expand Down Expand Up @@ -240,8 +245,8 @@ def make_mol_graph(
mol: Molecule, critic_bonds: Optional[List[List[int]]] = None
) -> MoleculeGraph:
"""
Construct a MoleculeGraph using OpenBabelNN with metal_edge_extender and
(optionally) Critic2 bonding information.
Construct a MoleculeGraph using OpenBabelNN (or JMolNN if open babel not
installed) with metal_edge_extender and (optionally) Critic2 bonding information.

This bonding scheme was used to define bonding for the Lithium-Ion Battery
Electrolyte (LIBE) dataset (DOI: 10.1038/s41597-021-00986-9)
Expand All @@ -252,7 +257,11 @@ def make_mol_graph(

:return: mol_graph, a MoleculeGraph
"""
mol_graph = MoleculeGraph.with_local_env_strategy(mol, OpenBabelNN())
if openbabel:
env_strategy = OpenBabelNN()
else:
env_strategy = JMolNN()
mol_graph = MoleculeGraph.with_local_env_strategy(mol, env_strategy)
mol_graph = metal_edge_extender(mol_graph)
if critic_bonds:
mg_edges = mol_graph.graph.edges()
Expand All @@ -268,7 +277,7 @@ def make_mol_graph(
def get_graph_hash(mol: Molecule, node_attr: Optional[str] = None):
"""
Return the Weisfeiler Lehman (WL) graph hash of the MoleculeGraph described
by this molecule, using the OpenBabelNN strategy with extension for
by this molecule, using the make_mol_graph env strategy with extension for
metal coordinate bonds

:param mol: Molecule
Expand Down
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