Convert Structure Mol Binary Column to SMILE Text Column Using Python Data Function in Spotfire

Keywords: Python, MOL Binary conversion, SMILES, Chemical structures.

Description:
In Signals Spotfire, you may have molecular structure data stored in a binary format (MolBlock), and you want to convert this data into a more usable format like SMILES strings. This KB article demonstrates how to achieve this using Python data functions.

Solution Instructions:

1. Setup Environment:
- Ensure Spotfire is installed and configured with Python Data Functions.
- Install necessary Python packages (`pandas` and `rdkit`).

2. Create Python Data Function:
- Open TIBCO Spotfire and navigate to `Tools` > `Register Python Data Functions`.
- Create a new Python script with the following code:

python Script:

import pandas as pd
from rdkit import Chem

# Function to convert MolBlock to SMILES
def molToSmile(value):
mol = Chem.MolFromMolBlock(value)
return Chem.MolToSmiles(mol)

def convert_mol_to_smiles(data):
input_df = pd.DataFrame(data)
input_df['Smiles'] = input_df['mol'].apply(molToSmile)
output_df = input_df[['Smiles']]
return output_df

3. Save and Provide Inputs/Output Parameters to the Function:
Save the Python script and deploy it as a data function in Spotfire.

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Please find the attached sample dashboard.

Related Articles:
Export Structures as SMILES