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Lower case symbols in SMILES for bracket atoms in aromatic rings #3697

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pschwllr opened this issue Jan 6, 2021 · 0 comments · May be fixed by #7428
Open

Lower case symbols in SMILES for bracket atoms in aromatic rings #3697

pschwllr opened this issue Jan 6, 2021 · 0 comments · May be fixed by #7428
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@pschwllr
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pschwllr commented Jan 6, 2021

Tested with rdkit versions (2020.09 and 2020.03), python 3.7

Minimal example:

from rdkit import Chem
smi = '[Al+]1cccccccccc1'
mol = Chem.MolFromSmiles(smi)
print(Chem.MolToSmiles(mol))
# prints 'c1ccccc[al+]cccc1'

[Al+] turned into [al+] when converted to a SMILES and is not readable anymore.

It seems that atoms in an aromatic ring get a lower case symbol independent of their type.

Example PubChem entry with this problem (https://pubchem.ncbi.nlm.nih.gov/compound/71310059)

smi = 'C1=CC=C(C=C1)OC2=CC3=C4NC(=C3C=C2)NC5=C6C=C(C=CC6=C7N5[Al+]N8C(=C9C=CC(=CC9=C8NC1=C2C=CC(=CC2=C(N1)N7)OC1=CC=CC=C1)OC1=CC=CC=C1)N4)OC1=CC=CC=C1.[Cl-]'
mol = Chem.MolFromSmiles(smi)
print(Chem.MolToSmiles(mol))
#prints '[Cl-].c1ccc(Oc2ccc3c4[nH]c([nH]c5c6ccc(Oc7ccccc7)cc6c6[nH]c7[nH]c([nH]c8c9ccc(Oc%10ccccc%10)cc9c([nH]4)n8[al+]n56)c4cc(Oc5ccccc5)ccc74)c3c2)cc1'
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fix: Add aromatic aluminium token iwyoo/rdkit
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