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Minor edit to atom_name_to_molsetup_index; Support input in both ways: --macromol (ProDy) and --pdb (RDKit) #172

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Minor edit to atom_name_to_molsetup_index; Support input in both ways: --macromol (ProDy) and --pdb (RDKit) #172

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11 changes: 5 additions & 6 deletions meeko/reactive.py
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Original file line number Diff line number Diff line change
Expand Up @@ -115,17 +115,16 @@ def get_basetype_and_order(self, atype):


def atom_name_to_molsetup_index(chorizo_residue, atom_name):
indices = []
for atom in chorizo_residue.raw_rdkit_mol.GetAtoms():
name = atom.GetPDBResidueInfo().GetName().strip()
if name == atom_name:
indices.append(atom.GetIdx())

# get matched indices from parameterized chorizo_residue
indices = [index for index, name in enumerate(chorizo_residue.atom_names) if name == atom_name]

if len(indices) > 1:
raise RuntimeError(f"multiple atoms matched query atom name {atom_name}")
if len(indices) == 0:
return None

index = indices[0]
index = chorizo_residue.mapidx_from_raw[index]
inv = {j: i for i, j in chorizo_residue.molsetup_mapidx.items()}
index = inv[index]
return index
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