Tools · Cheminformatics & Structure

Conformer Ensemble Generator

Generate an RDKit 3D conformer ensemble per molecule (energy window / RMSD prune)

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Prices, workflows, and method papers Open 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.

Conformer Ensemble Generator `conformer-ensemble`

Job type: conformer-ensemble
Hardware: cpu (default)
Typical runtime: 5 min on CPU

Payload

Payload fields
Field	Type	Description
`input_data[]`required	`(string \| object)[]`	Limits: `min items 1, max items 1000`
`input_format`required	`string`	One of: `"smiles", "molblock", "sdf"`
`num_confs`	`integer`	Default: `50`Limits: `≥ 1, ≤ 200`
`prune_rmsd_angstrom`	`number`	Default: `0.5`Limits: `≥ 0`
`energy_window_kcal`	`number \| null`	Default: `10`Limits: `≥ 0`
`force_field`	`string`	Default: `"mmff94"`One of: `"mmff94", "mmff94s", "uff"`
`add_hydrogens`	`boolean`	Default: `true`
`random_seed`	`integer`	Default: `42`Limits: `≥ 0`

Example

from cognichem_client import CogniChem

client = CogniChem.from_env()  # reads COGNICHEM_API_KEY
payload = {
    "input_data": ["CCO"],
    "input_format": "smiles",
    "num_confs": 5,
    "prune_rmsd_angstrom": 0.5,
    "energy_window_kcal": 10,
    "force_field": "mmff94",
    "add_hydrogens": True,
    "random_seed": 42,
}

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

job = client.jobs.submit(
    job_name="my-conformer-ensemble-run",
    job_type="conformer-ensemble",
    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-conformer-ensemble-run",
  "job_type": "conformer-ensemble",
  "payload": {
    "input_data": [
      "CCO"
    ],
    "input_format": "smiles",
    "num_confs": 5,
    "prune_rmsd_angstrom": 0.5,
    "energy_window_kcal": 10,
    "force_field": "mmff94",
    "add_hydrogens": true,
    "random_seed": 42
  },
  "resource": "cpu"
}'

{
  "input_data": [
    "CCO"
  ],
  "input_format": "smiles",
  "num_confs": 5,
  "prune_rmsd_angstrom": 0.5,
  "energy_window_kcal": 10,
  "force_field": "mmff94",
  "add_hydrogens": true,
  "random_seed": 42
}

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, MOLBLOCK, SDF

Workflow outputs

ArchiveZIP
MoleculesSDF
TableCSV

Run it from the API

Conformer Ensemble Generator conformer-ensemble

Conformer Ensemble Generator `conformer-ensemble`