SMILES/SDF Parsing

Summary

Parse molecular structure representations in SMILES or SDF format and load them into an RDKit molecule object for downstream cheminformatic analysis. This is a foundational step for any workflow that accepts chemical structure input and needs to operate on molecular graphs.

When to use

You have a natural product molecule or compound library provided as SMILES strings, InChI strings, or SDF files, and you need to convert them into an in-memory molecular representation (RDKit Mol object) suitable for fingerprinting, property prediction, or other cheminformatic operations.

When NOT to use

• Input is already an RDKit Mol object or other in-memory molecular representation.
• You are working with protein sequences or genomic data rather than small-molecule chemistry.
• The molecular structure is malformed or incomplete and cannot be unambiguously interpreted as a valid chemical graph.

Inputs

• SMILES string
• InChI string
• SDF file
• Molecule structure in chemical format

Outputs

• RDKit Mol object
• Molecule supplier iterator (for SDF input)

How to apply

Use RDKit's Chem module to parse the input: call Chem.MolFromSmiles() for SMILES strings or Chem.MolFromInchi() for InChI strings to produce a Mol object. For SDF files, use Chem.SDMolSupplier() to iterate over all molecules in the file. Validate that the returned Mol object is not None before proceeding; a None return indicates the parser could not interpret the structure and the input should be checked for formatting errors or chemical validity.

Related tools

• RDKit (Parses SMILES, InChI, and SDF strings/files into Mol objects for cheminformatic operations) — https://www.rdkit.org
• biosynfoni (Accepts RDKit Mol objects parsed from SMILES/SDF and computes biosynformatic fingerprints) — https://github.com/lucinamay/biosynfoni

Examples

from rdkit import Chem
smi = 'CCO'
mol = Chem.MolFromSmiles(smi)
print(mol.GetNumAtoms())

Evaluation signals

• Returned RDKit Mol object is not None and has a valid atomic connectivity graph.
• Mol object has correct atom count, bond types, and stereochemistry matching the input structure.
• When iterated over an SDF file, all molecules are successfully parsed without errors.
• Round-trip conversion (SMILES → Mol → SMILES) produces chemically equivalent structures.
• No warnings or exceptions are raised during parsing of chemically valid input.

Limitations

• Parser will return None if the input SMILES or InChI string is malformed or represents an invalid chemical structure.
• SDF files may contain metadata or properties that are not automatically extracted into the Mol object; use GetProp() or other RDKit accessors to retrieve them.
• Some stereochemical and charge specifications may be ambiguous in SMILES and require explicit annotation or validation against expected chemical rules.
• Large SDF files may require streaming (SDMolSupplier with lazy loading) to avoid memory exhaustion.

Evidence

• [readme] Convert a SMILES string to a fingerprint: from biosynfoni import Biosynfoni from rdkit import Chem smi = <SMILES> mol = Chem.MolFromSmiles(smi): "mol = Chem.MolFromSmiles(smi)"
• [readme] Create a fingerprint from a SMILES string: biosynfoni <SMILES> Create a fingerprint from an InChI string: biosynfoni <InChI> Write the fingerprints of all molecules in an SDF file to a CSV file: biosynfoni <molecule_supplier.sdf>: "Create a fingerprint from a SMILES string: biosynfoni <SMILES> Create a fingerprint from an InChI string: biosynfoni <InChI> Write the fingerprints of all molecules in an SDF file to a CSV file:"
• [other] Load a natural-product molecule structure from SMILES or SDF input using the biosynfoni API.: "Load a natural-product molecule structure from SMILES or SDF input using the biosynfoni API"