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    Tools · Cheminformatics & Structure

    Molecule Standardizer

    Salt-strip, neutralize, tautomer, and stereo cleanup to parent structures
    On this page

    Prices, workflows, and method papersOpen in the app

    Run it from the API

    Submit with Submit a job and the job_type below. Price it first with Estimate job reservation cost: submitting reserves that amount from your wallet, and the charge settles at the actual runtime.

    Molecule Standardizer molecule-standardize

    Job type
    molecule-standardize
    Hardware
    cpu (default)
    Typical runtime
    5 min on CPU

    Payload

    Payload fields
    FieldTypeDescription
    input_data[]required(string | object)[]

    Limits: min items 1, max items 50000

    input_formatrequiredstring

    One of: "smiles", "sdf", "molblock", "inchi"

    largest_fragmentboolean

    Default: true

    unchargeboolean

    Default: true

    canonical_tautomerboolean

    Default: true

    cleanup_stereoboolean

    Default: true

    Example

    from cognichem_client import CogniChem

client = CogniChem.from_env()  # reads COGNICHEM_API_KEY
payload = {
    "input_data": ["CC(=O)[O-].[Na+]", "Oc1ccccc1"],
    "input_format": "smiles",
    "largest_fragment": True,
    "uncharge": True,
    "canonical_tautomer": True,
    "cleanup_stereo": True,
}

estimate = client.jobs.estimate(job_type="molecule-standardize", payload=payload, resource="cpu")
print(f"Reserves ${estimate.cost:.2f}")

job = client.jobs.submit(
    job_name="my-molecule-standardize-run",
    job_type="molecule-standardize",
    payload=payload,
    resource="cpu",
)
status = client.jobs.wait(job.process_id)
if status.status == "completed":
    client.jobs.result(job.process_id, save_path=".")

    Sample data from the job catalog; long values are shortened here. Each job_name must be unique among your jobs.

    Workflow inputs

    • Molecules (list)SMILES, SDF, MOLBLOCK, INCHI

    Workflow outputs

    • ArchiveZIP
    • TableCSV
    • MoleculesSMILES