Fix atom labeling so they can be named in constraints #226
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Atom labels were not unique which prevented their use for constraints
wukevin
requested changes
Dec 9, 2024
chai_lab/data/sources/rdkit.py
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| for atom in mol_with_hs.GetAtoms(): | ||
| atom.SetProp("name", atom.GetSymbol()) | ||
| for i, atom in enumerate(mol_with_hs.GetAtoms()): | ||
| atom.SetProp("name", atom.GetSymbol()+str(i+1)) |
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This a great addition, but I think we can modify this slightly to better conform to prior naming conventions. In particular, instead of numbering every atom in strictly ascending order, let's instead number every atom with as the i-th element.
Something like:
element_counter = 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]))
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Sorry I made a bit of a mess of it but I think it should pass now.
per element based numbering
fix import
|
Due to persistent errors in this PR, I've implemented the logic here in a separate PR; we'll close this one out when that merges. |
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Description
Old behavior named ligand atoms by element. Added 1-indexed index to element symbol.
Motivation
Atoms require a unique label so they can be specified in constraints.