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Fix atom labeling so they can be named in constraints #226

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Fix atom labeling so they can be named in constraints #226

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95d0a21
Unique Atoms Labels
fabgonzal Dec 9, 2024
b187cf5
Update rdkit.py
fabgonzal Dec 9, 2024
d4acae5
Update rdkit.py
fabgonzal Dec 10, 2024
8df8318
Update rdkit.py
fabgonzal Dec 10, 2024
2d2ada6
Update rdkit.py
fabgonzal Dec 10, 2024
736c0b3
Update rdkit.py
fabgonzal Dec 10, 2024
7e279fd
Update rdkit.py
fabgonzal Dec 10, 2024
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10 changes: 8 additions & 2 deletions chai_lab/data/sources/rdkit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
# See the LICENSE file for details.

import logging
from collections import defaultdict
from pathlib import Path

import antipickle
Expand Down Expand Up @@ -157,8 +158,13 @@ def generate(self, smiles: str) -> ConformerData:

AllChem.EmbedMultipleConfs(mol_with_hs, numConfs=1, params=params)
AllChem.RemoveHs(mol_with_hs)
for atom in mol_with_hs.GetAtoms():
atom.SetProp("name", atom.GetSymbol())

element_counter: dict = defaultdict(int)
for i, atom in enumerate(mol_with_hs.GetAtoms()):
elem = atom.GetSymbol()
element_counter[elem] += 1
atom.SetProp("name", elem + str(element_counter[elem]))

retval = self._load_ref_conformer_from_rdkit(mol_with_hs)
retval.atom_names = [a.upper() for a in retval.atom_names]
return retval
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