Tools · Cheminformatics & Structure

RMSD Calculator

Calculate the root-mean-square deviation (RMSD) of molecules

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.

RMSD Calculator `molecule-rmsd-matrix`

Job type: molecule-rmsd-matrix
Hardware: cpu (default)
Typical runtime: 30 min on CPU

Payload

Payload fields
Field	Type	Description
`input_data[]`required	`string[]`	Limits: `min items 1, max items 225`
`input_format`required	`string`	One of: `"fasta", "helm", "mol2block", "molblock", "mrvblock", "pdbblock", "scsrblock", "selfies", "sequence", "smarts", "smiles", "tplblock", "xyzblock", "inchi"`
`rotation_method`	`string`	Default: `"kabsch"`One of: `"kabsch", "quaternion"`
`reorder_method`	`string`	Default: `"inertia-hungarian"`One of: `"inertia-hungarian", "qml"`
`add_hydrogens`	`boolean`	Default: `false`
`remove_hydrogens`	`boolean`	Default: `false`

Example

from cognichem_client import CogniChem

client = CogniChem.from_env()  # reads COGNICHEM_API_KEY
payload = {
    "input_data": ["CCO", "CCC"],
    "input_format": "smiles",
    "rotation_method": "kabsch",
    "reorder_method": "inertia-hungarian",
    "add_hydrogens": False,
    "remove_hydrogens": False,
}

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

job = client.jobs.submit(
    job_name="my-molecule-rmsd-matrix-run",
    job_type="molecule-rmsd-matrix",
    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-molecule-rmsd-matrix-run",
  "job_type": "molecule-rmsd-matrix",
  "payload": {
    "input_data": [
      "CCO",
      "CCC"
    ],
    "input_format": "smiles",
    "rotation_method": "kabsch",
    "reorder_method": "inertia-hungarian",
    "add_hydrogens": false,
    "remove_hydrogens": false
  },
  "resource": "cpu"
}'

{
  "input_data": [
    "CCO",
    "CCC"
  ],
  "input_format": "smiles",
  "rotation_method": "kabsch",
  "reorder_method": "inertia-hungarian",
  "add_hydrogens": false,
  "remove_hydrogens": false
}

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

Workflow outputs

ArchiveZIP
TableCSV

Run it from the API

RMSD Calculator molecule-rmsd-matrix

RMSD Calculator `molecule-rmsd-matrix`