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Resolve issue #53 #97

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Merged
PaulaKramer merged 3 commits into from
Jan 27, 2026
Merged

Resolve issue #53 #97

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3a1ef8c
Merge pull request #92 from volkamerlab/dev
PaulaKramer Nov 20, 2025
bb1ee17
removed next() usage
Jan 14, 2026
06d35cd
bug fix
Jan 26, 2026
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20 changes: 12 additions & 8 deletions kinfraglib/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1328,16 +1328,20 @@ def construct_ligand(fragment_ids, bond_ids, fragment_library):
ed_combo = Chem.EditableMol(combo)
replaced_dummies = []

atoms = combo.GetAtoms()

for bond in bond_ids:

dummy_1 = next(
atom for atom in combo.GetAtoms() if atom.GetProp("fragment_atom_id") == bond[0]
)
dummy_2 = next(
atom for atom in combo.GetAtoms() if atom.GetProp("fragment_atom_id") == bond[1]
)
# should be a one element lists
dummy_1_candidates = [atom for atom in combo.GetAtoms() if atom.GetProp("fragment_atom_id") == bond[0]]
dummy_2_candidates = [atom for atom in combo.GetAtoms() if atom.GetProp("fragment_atom_id") == bond[1]]

if len(dummy_1_candidates) == 0 or len(dummy_2_candidates) == 0:
raise RuntimeError(f'Dummy atoms for bond {bond} not found')
elif len(dummy_1_candidates) > 1 or len(dummy_2_candidates) > 1:
raise RuntimeError(f'This should not happen: Dummy atoms found for bond {bond} are unambigious')

dummy_1 = dummy_1_candidates[0]
dummy_2 = dummy_2_candidates[0]

atom_1 = dummy_1.GetNeighbors()[0]
atom_2 = dummy_2.GetNeighbors()[0]

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