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fix: log compound names when alignment is not found (issue 1495) #651

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merged 1 commit into from
Sep 4, 2024
Merged

fix: log compound names when alignment is not found (issue 1495) #651

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13 changes: 12 additions & 1 deletion viewer/cset_upload.py
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Original file line number Diff line number Diff line change
Expand Up @@ -447,7 +447,18 @@ def set_mol(
# find distances between corresponding atoms of the
# two conformers. if any one exceeds the _DIST_LIMIT,
# consider it to be a new ComputedMolecule
_, _, atom_map = Chem.rdMolAlign.GetBestAlignmentTransform(mol, kmol)
try:
_, _, atom_map = Chem.rdMolAlign.GetBestAlignmentTransform(
mol, kmol
)
except RuntimeError as exc:
msg = (
f'Failed to find alignment between {k.molecule_name} '
+ f'and {mol.GetProp("original ID")}'
)
logger.error(msg)
raise RuntimeError(msg) from exc

molconf = mol.GetConformer()
kmolconf = kmol.GetConformer()
small_enough = True
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