Tools · Cheminformatics & Structure

Ligand Ionization & Tautomer States

Enumerate plausible protonation and tautomer states of small molecules at a target pH with estimated populations

On this page

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.

Ligand Ionization & Tautomer States `ligand-ionize`

Job type: ligand-ionize
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 10000`
`input_format`required	`string`	One of: `"smiles", "sdf", "molblock", "inchi"`
`ph`	`number`	Default: `7.4`Limits: `≥ 0, ≤ 14`
`precision`	`number`	Default: `1`Limits: `≥ 0, ≤ 3`
`tautomer_mode`	`string`	Default: `"none"`One of: `"none", "canonical", "enumerate"`
`max_states_per_parent`	`integer`	Default: `8`Limits: `≥ 1, ≤ 128`
`min_population`	`number`	Default: `0.01`Limits: `≥ 0, ≤ 0.5`

Example

from cognichem_client import CogniChem

client = CogniChem.from_env()  # reads COGNICHEM_API_KEY
payload = {
    "input_data": [
        "CC(=O)O",
        "N[C@@H](Cc1c[nH]cn1)C(=O)O",
        "Nc1ccncc1",
        "Oc1ccccn1",
    ],
    "input_format": "smiles",
    "ph": 7.4,
    "precision": 1,
    "tautomer_mode": "canonical",
    "max_states_per_parent": 8,
    "min_population": 0.01,
}

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

job = client.jobs.submit(
    job_name="my-ligand-ionize-run",
    job_type="ligand-ionize",
    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-ligand-ionize-run",
  "job_type": "ligand-ionize",
  "payload": {
    "input_data": [
      "CC(=O)O",
      "N[C@@H](Cc1c[nH]cn1)C(=O)O",
      "Nc1ccncc1",
      "Oc1ccccn1"
    ],
    "input_format": "smiles",
    "ph": 7.4,
    "precision": 1,
    "tautomer_mode": "canonical",
    "max_states_per_parent": 8,
    "min_population": 0.01
  },
  "resource": "cpu"
}'

{
  "input_data": [
    "CC(=O)O",
    "N[C@@H](Cc1c[nH]cn1)C(=O)O",
    "Nc1ccncc1",
    "Oc1ccccn1"
  ],
  "input_format": "smiles",
  "ph": 7.4,
  "precision": 1,
  "tautomer_mode": "canonical",
  "max_states_per_parent": 8,
  "min_population": 0.01
}

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

Run it from the API

Ligand Ionization & Tautomer States ligand-ionize

Ligand Ionization & Tautomer States `ligand-ionize`