Tools · Computational Biology
SURFMAP
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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
| Field | Type | Description |
|---|---|---|
input_moderequired | string | One of: |
tomaprequired | string | One of: |
proj | string | Default: |
rad | number | Default: |
grid_size | integer | Default: |
nosmooth | boolean | Default: |
png | boolean | Default: |
keep | boolean | Default: |
ff | string | Default: |
verbose | integer | Default: |
protein | file_object | Required when input_mode is pdb; must have .pdb extension. |
protein.name | string | Limits: |
protein.filename | string | Limits: |
protein.content_b64 | string | Limits: |
protein.content | any | |
protein.bytes | any | |
matrix | file_object | Required when input_mode is matrix. |
matrix.name | string | Limits: |
matrix.filename | string | Limits: |
matrix.content_b64 | string | Limits: |
matrix.content | any | |
matrix.bytes | any | |
pqr | file_object | |
pqr.name | string | Limits: |
pqr.filename | string | Limits: |
pqr.content_b64 | string | Limits: |
pqr.content | any | |
pqr.bytes | any | |
residue_list | file_object | |
residue_list.name | string | Limits: |
residue_list.filename | string | Limits: |
residue_list.content_b64 | string | Limits: |
residue_list.content | any | |
residue_list.bytes | any | |
elec_max_value | number | |
bfactor_min_value | number | |
bfactor_max_value | number |
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=".")curl -X POST "https://api.cognichem.com/api/v1/jobs/submit" \
-H "X-Api-Key: $COGNICHEM_API_KEY" \
-H "Idempotency-Key: $(uuidgen)" \
-H "Content-Type: application/json" \
-d '{
"job_name": "my-surfmap-run",
"job_type": "surfmap",
"payload": {
"input_mode": "pdb",
"tomap": "stickiness",
"protein": {
"name": "target.pdb",
"content_b64": "<file contents, base64>"
}
},
"resource": "cpu"
}'{
"input_mode": "pdb",
"tomap": "stickiness",
"protein": {
"name": "target.pdb",
"content_b64": "<file contents, base64>"
}
}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