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@dehaenw
Created October 5, 2023 12:16
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Never go from inchi back to mol!!
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{
"cells": [
{
"cell_type": "markdown",
"id": "6bf9e994-59c0-4c86-bdd8-02d29d0eec17",
"metadata": {},
"source": [
"# Never go from inchi to mol\n",
"It's not intended to use in this way. The tautomer canonicalization algorithm, which is very useful for matching molecules, also leads to tautomeric states that are far from the major ones, notably including amides being shown as the imidic acid form."
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "8352e8ca-9a5f-462a-b16a-75af77326c32",
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7ff7b6d25d90>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"image/png": "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",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7ff7b6d25b60>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"from rdkit import Chem\n",
"from rdkit.Chem import inchi\n",
"mol=Chem.MolFromSmiles(\"CC(=O)NCC\")\n",
"display(mol)\n",
"roundtrip_mol=inchi.MolFromInchi(inchi.MolToInchi(mol))\n",
"display(roundtrip_mol)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.12"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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