data = [] for mol in suppl: if mol is not None: # Extract properties (the data fields from the SDF) props = mol.GetPropsAsDict() # Optionally add SMILES string for structure props['SMILES'] = Chem.MolToSmiles(mol) data.append(props) df = pd.DataFrame(data) df.to_csv('compounds.csv', index=False)
For a quick, no-code solution, Elena opened her terminal.
Elena smiled. “Three ways. Let’s start with the command line.” how to convert sdf file to csv
Within an hour, Elena handed Leo the final compounds.csv . He opened it in Excel: columns neatly aligned, hundreds of compounds ready for analysis.
“First, we need two libraries: rdkit for chemistry and pandas for tables.” data = [] for mol in suppl: if
Just as they finished, the CSV looked strange. Some rows had missing values.
“For the non-programmers on our team,” Elena continued, “we use KNIME. Drag an ‘SDF Reader’ node, connect it to a ‘CSV Writer’ node, and configure which columns to keep. It’s visual—like drawing a flowchart.” Let’s start with the command line
“Ah,” Elena pointed. “Classic SDF problem. Not every molecule has the same set of properties. Pandas handles that by filling blanks with NaN . Open Babel will leave empty cells. The lesson: after conversion.”