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Document SMILES string escaping in the input JSON

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Augustin Zidek
2024-12-18 12:02:36 +00:00
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@ -332,10 +332,44 @@ The fields specify the following:
standard CCD codes, or custom codes pointing to the
[user-provided CCD](#user-provided-ccd).
* `smiles: str`: An optional string defining the ligand using a SMILES string.
The SMILES string must be correctly JSON-escaped.
Each ligand may be specified using CCD codes or SMILES but not both, i.e. for a
given ligand, the `ccdCodes` and `smiles` fields are mutually exclusive.
#### SMILES string JSON escaping
The SMILES string must be correctly JSON-escaped, in particular the backslash
character must be escaped as two backslashes, otherwise the JSON parser will
fail with a `JSONDecodeError`. For instance, the following SMILES string
`CCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\CO` has to be specified as:
```json
{
"ligand": {
"id": "A",
"smiles": "CCC[C@@H](O)CC\\C=C\\C=C\\C#CC#C\\C=C\\CO"
}
}
```
You can JSON-escape the SMILES string using the
[`jq`](https://github.com/jqlang/jq) command-line tool which should be easily
installable on most Linux systems:
```bash
jq -R . <<< 'CCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\CO' # Replace with your SMILES.
```
Alternatively, you can use this Python code:
```python
import json
smiles = r'CCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\CO' # Replace with your SMILES.
print(json.dumps(smiles))
```
### Ions
Ions are treated as ligands, e.g. a magnesium ion would simply be a ligand with