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    Tools · Computational Biology

    SURFMAP

    2D projections of protein surface features from PDB structures or SURFMAP matrix files
    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.

    SURFMAP surfmap

    Job type
    surfmap
    Hardware
    cpu (default)
    Typical runtime
    5 min on CPU

    Payload

    Payload fields
    FieldTypeDescription
    input_moderequiredstring

    One of: "pdb", "matrix"

    tomaprequiredstring

    One of: "all", "stickiness", "kyte_doolittle", "wimley_white", "circular_variance", "circular_variance_atom", "electrostatics", "bfactor", "binding_sites"

    projstring

    Default: "flamsteed"One of: "flamsteed", "mollweide", "lambert"

    radnumber

    Default: 3Limits: ≥ 0.5, ≤ 10

    grid_sizeinteger

    Default: 5Limits: ≥ 1, ≤ 20

    nosmoothboolean

    Default: false

    pngboolean

    Default: true

    keepboolean

    Default: false

    ffstring

    Default: "CHARMM"One of: "AMBER", "CHARMM", "PARSE", "TYL06", "PEOEPB", "SWANSON"

    verboseinteger

    Default: 1One of: 0, 1, 2

    proteinfile_object
    protein.namestring

    Limits: min length 1

    protein.filenamestring

    Limits: min length 1

    protein.content_b64string

    Limits: min length 1

    protein.contentany
    protein.bytesany
    matrixfile_object
    matrix.namestring

    Limits: min length 1

    matrix.filenamestring

    Limits: min length 1

    matrix.content_b64string

    Limits: min length 1

    matrix.contentany
    matrix.bytesany
    pqrfile_object
    pqr.namestring

    Limits: min length 1

    pqr.filenamestring

    Limits: min length 1

    pqr.content_b64string

    Limits: min length 1

    pqr.contentany
    pqr.bytesany
    residue_listfile_object
    residue_list.namestring

    Limits: min length 1

    residue_list.filenamestring

    Limits: min length 1

    residue_list.content_b64string

    Limits: min length 1

    residue_list.contentany
    residue_list.bytesany
    elec_max_valuenumber
    bfactor_min_valuenumber
    bfactor_max_valuenumber

    File fields take {"name": "x.pdb", "content_b64": "…"} or a stored artifact, {"$artifact": {"id": "art-…", "port": "…"}}. Files are up to 25 MiB each.

    Example

    from cognichem_client import CogniChem
    
    client = CogniChem.from_env()  # reads COGNICHEM_API_KEY
    payload = {
        "input_mode": "pdb",
        "tomap": "stickiness",
        "protein": {"name": "target.pdb", "content_b64": "<file contents, base64>"},
    }
    
    estimate = client.jobs.estimate(job_type="surfmap", payload=payload, resource="cpu")
    print(f"Reserves ${estimate.cost:.2f}")
    
    job = client.jobs.submit(
        job_name="my-surfmap-run",
        job_type="surfmap",
        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

    • Protein structure · optionalPDB

    Workflow outputs

    • ArchiveZIP