Chemistry Validate

POST/science/v1/chemistry/validate

What it does

Send any chemical notation — SMILES, InChI, or MDL Molfile (V2000/V3000) — and get back a complete validation report in milliseconds. Powered by RDKit, the industry-standard cheminformatics toolkit.

What you get back

Output	Tier	What it gives you
Canonical SMILES	Free	Normalized, deterministic SMILES string — safe for dedup, indexing, and downstream pipelines.
InChI	Free	IUPAC International Chemical Identifier for cross-database lookup.
Molecular descriptors	Free	Formula, exact weight, atom/bond counts, TPSA, cLogP, rotatable bonds, aromaticity, stereochemistry.
Lipinski Ro5	Free	Drug-likeness check — pass/fail on all four Lipinski rules with actual values.
InChI Key	Premium	27-character hash for exact structure matching and registry dedup.
Molblock	Premium	Full MDL Molblock with 2D coordinates — ready for structure export and visualization.

Invalid molecules are not errors

If the input is chemically invalid, the API still returns a successful response with data.valid: false. You get a structured reason explaining why it failed, plus fix recommendations. This makes it safe to use in form validation, user input pipelines, and batch processing without error handling for expected invalid inputs.

Why use it?

Clean your data before it breaks downstream. Garbage SMILES in a database causes silent failures in docking, retrosynthesis, and ML pipelines. Validate early, fix cheap.
Canonical = deterministic. The same molecule written 10 different ways produces the same canonical SMILES every time. Use it as a primary key, dedup identifier, or cache key.
Real-time form validation. Build input fields that validate chemistry notation as users type — with human-readable error messages, not stack traces.
Drug-likeness screening. Lipinski Rule of Five check built in. Filter compound libraries before expensive experiments.
Actionable fix suggestions. Invalid SMILES? The API analyzes common mistakes (unbalanced parentheses, valence errors, unclosed rings) and tells you exactly what to fix.
No RDKit installation required. Skip the painful C++ build, Python bindings, and WASM setup. One HTTP call, any language.

Examples

Validate Aspirin (SMILES)

curl -X POST https://api.creatornode.io/science/v1/chemistry/validate \
  -H "Content-Type: application/json" \
  -H "X-API-Key: YOUR_KEY" \
  -d '{
    "input": "CC(=O)OC1=CC=CC=C1C(=O)O"
  }'

Response — valid molecule

{
  "success": true,
  "data": {
    "valid": true,
    "format": "smiles",
    "input": "CC(=O)OC1=CC=CC=C1C(=O)O",
    "canonicalSmiles": "CC(=O)Oc1ccccc1C(=O)O",
    "inchi": "InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)",
    "metadata": {
      "molecularFormula": "C9H8O4",
      "exactMolecularWeight": 180.042,
      "numAtoms": 21, "numBonds": 21,
      "numRings": 1, "numHeavyAtoms": 13,
      "numHBA": 4, "numHBD": 1,
      "TPSA": 63.6, "cLogP": 1.31,
      "numRotatableBonds": 3,
      "numAromaticRings": 1, "hasStereo": false
    },
    "drugLikeness": {
      "lipinskiRo5": true, "violations": 0,
      "rules": [
        { "rule": "MW ≤ 500", "passed": true, "value": 180.04 },
        { "rule": "cLogP ≤ 5", "passed": true, "value": 1.31 },
        { "rule": "HBD ≤ 5", "passed": true, "value": 1 },
        { "rule": "HBA ≤ 10", "passed": true, "value": 4 }
      ]
    }
  },
  "meta": {
    "requestId": "abc-123",
    "processingTimeMs": 12,
    "rdkitVersion": "2025.3.4"
  }
}

Response — invalid molecule

{
  "success": true,
  "data": {
    "valid": false,
    "format": "smiles",
    "input": "CC(=O",
    "error": {
      "message": "SMILES Parse Error: unclosed ring or branch"
    }
  },
  "recommendations": [
    {
      "type": "fix",
      "title": "Input fix",
      "message": "Unbalanced parentheses: 1 opening '(' without matching ')'.",
      "priority": "high"
    }
  ]
}

InChI input with premium outputs

{
  "input": "InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)",
  "format": "inchi",
  "options": {
    "inchiKey": true,
    "molblock": true
  }
}

On free tier, inchiKey and molblock are silently ignored — upgrade to Premium to include them in the response.

Supported input formats

Format	Example	When to use
SMILES	`CC(=O)Oc1ccccc1C(=O)O`	Most common. Compact, human-readable line notation.
InChI	`InChI=1S/C9H8O4/...`	Cross-database lookup. Standard identifier from IUPAC.
Molfile	(multi-line V2000/V3000)	Structure files from ChemDraw, Marvin, or database exports.

💡 Auto-detection: You don't need to specify format. The API detects it from the input: InChI strings start with InChI=, Molfiles contain V2000/V3000, everything else is treated as SMILES.

Options reference

Option	Type	Default	What it does
`canonicalSmiles`	boolean	`true`	Include canonical (normalized) SMILES in output.
`inchi`	boolean	`true`	Include InChI string in output.
`inchiKey`	boolean	`false`	Include InChI Key (27-char hash). Premium only.
`molblock`	boolean	`false`	Include MDL Molblock with 2D coords. Premium only.
`descriptors`	boolean	`true`	Include molecular descriptors (weight, TPSA, cLogP, etc.).
`sanitize`	boolean	`true`	Run RDKit sanitization (valence check). Set to `false` for molecules with non-standard valence.

Tips & tricks

💡 Tip: For the full request/response schema, OpenAPI spec, and the interactive demo endpoint, see the API Reference.

Let format auto-detection work for you. The format field defaults to "auto" and correctly identifies SMILES, InChI, and Molfile. Only set it explicitly if you know the format and want to skip detection.
Use canonical SMILES as your primary key. Multiple SMILES strings can represent the same molecule. Canonical SMILES eliminates duplicates — store it, index it, compare it.
Valence errors? Try sanitize: false. Some molecules (vancomycin fragments, metal complexes) have atoms that violate standard valence rules. Setting "options": { "sanitize": false } lets RDKit parse them anyway and produce a canonical SMILES. The API will suggest this automatically when it detects a valence error.
Batch with confidence. The API returns valid: false as a normal response, not an error. You can process hundreds of molecules in a loop without try/catch — just check data.valid.
Read the fix recommendations. When validation fails, the recommendations array contains specific, actionable fixes — unbalanced parentheses, unclosed rings, valence issues — not generic error messages.
Lipinski filtering at scale. Use drugLikeness.lipinskiRo5 to filter compound libraries. Molecules with more than 1 violation are unlikely to be orally bioavailable.
Input limits are in bytes, not characters. UTF-8 encoding means special characters in Molfiles use more than 1 byte. Free tier: 200 bytes, Premium: 4,000 bytes.

Cost & Limits

Feature	Detail
Credit cost	1 credit per request
Input formats	SMILES, InChI, MDL Molfile (V2000/V3000)
Free outputs	canonicalSmiles, inchi, metadata, drugLikeness
Premium outputs	inchiKey, molblock
Engine	RDKit

Tier Limits

Limit	Free	Premium
Max input size	200 bytes	4 000 bytes
InChI Key	No	Yes
Molblock export	No	Yes

Other Endpoints

POST/science/v1/chemistry/compare

Chemistry Compare

Compare two molecules — structural similarity, fingerprint matching, property diff.