Your First Validation

Let's validate your first molecule using ChemAudit. We'll walk through validating Aspirin using both the web interface and the API.

Using the Web Interface

Step 1: Open ChemAudit

Navigate to the web interface:

• Development: http://localhost:3002
• Production: http://localhost

Step 2: Enter a Molecule

On the Single Validation page, enter this SMILES string for Aspirin:

CC(=O)Oc1ccccc1C(=O)O

ChemAudit auto-detects the input format (SMILES, InChI, or MOL block), so you can paste any supported format.

Step 3: Run Validation

Click the Validate button. Within seconds, you'll see comprehensive results across multiple tabs:

• Validation: Structural checks and overall score
• Alerts: Structural alert screening (PAINS, BRENK, etc.)
• Scoring: ML-readiness, drug-likeness, ADMET, and more
• Scoring Profiles: Consensus drug-likeness, lead/fragment-likeness, bioavailability radar
• Standardization: ChEMBL-compatible structure cleanup with provenance
• Database Lookup: Cross-references to PubChem, ChEMBL, COCONUT

Step 4: Interpret Results

Look for these key indicators:

Validation Score: A number from 0-100 indicating overall structure quality.

Score Range	Quality	Recommendation
90-100	Excellent	Ready for use
70-89	Good	Minor issues, review recommended
50-69	Fair	Needs attention
0-49	Poor	Significant issues

Check Results: Each validation check shows pass/fail status with severity:

Severity	Meaning
Critical	Must be fixed - structure is invalid
Warning	Should be reviewed - may affect results
Info	Informational - no action required

Using the API

Basic Validation Request

curl -X POST http://localhost:8001/api/v1/validate \
  -H "Content-Type: application/json" \
  -d '{
    "molecule": "CC(=O)Oc1ccccc1C(=O)O",
    "format": "auto"
  }'

Example Response

{
  "status": "completed",
  "molecule_info": {
    "input_smiles": "CC(=O)Oc1ccccc1C(=O)O",
    "canonical_smiles": "CC(=O)OC1=CC=CC=C1C(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)",
    "inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
    "molecular_formula": "C9H8O4",
    "molecular_weight": 180.16,
    "num_atoms": 13
  },
  "overall_score": 95,
  "issues": [],
  "all_checks": [
    {
      "check_name": "valence_check",
      "passed": true,
      "severity": "critical",
      "message": "All atoms have valid valence",
      "affected_atoms": [],
      "details": {}
    }
  ],
  "execution_time_ms": 12,
  "cached": false
}

Using Python

import requests

response = requests.post(
    "http://localhost:8001/api/v1/validate",
    json={
        "molecule": "CC(=O)Oc1ccccc1C(=O)O",
        "format": "auto"
    }
)

result = response.json()
print(f"Score: {result['overall_score']}")
print(f"Issues: {len(result['issues'])}")
print(f"Formula: {result['molecule_info']['molecular_formula']}")

Understanding Validation Checks

ChemAudit runs multiple validation checks grouped by category:

Critical Checks

These must pass for the structure to be valid:

Check	What It Validates
Valence	All atoms have correct number of bonds
Kekulization	Aromatic rings can be kekulized
Sanitization	Molecule passes RDKit sanitization

Warning Checks

These indicate potential issues:

Check	What It Detects
Undefined Stereo	Stereocenters without R/S specification
Stereo Consistency	Conflicting stereochemistry specifications

Info Checks

Informational only, no action required:

Check	What It Reports
SMILES Length	Unusually long SMILES strings
InChI Generation	Whether InChI can be generated

Sample Molecules to Try

Name	SMILES	Description
Aspirin	CC(=O)Oc1ccccc1C(=O)O	Common pain reliever
Caffeine	Cn1cnc2c1c(=O)n(c(=O)n2C)C	Stimulant
Ibuprofen	CC(C)Cc1ccc(cc1)C(C)C(=O)O	Anti-inflammatory
Penicillin G	CC1(C)SC2C(NC(=O)Cc3ccccc3)C(=O)N2C1C(=O)O	Antibiotic
Morphine	CN1CCC23C4C1CC5=C2C(=C(C=C5)O)OC3C(C=C4)O	Analgesic

Try Invalid Structures

To see how ChemAudit handles errors, try validating an invalid SMILES like C1CCC1 (unclosed ring) or CC(C)(C)(C)C (too many substituents).

Next Steps

Now that you've completed your first validation, explore more features:

• Single Molecule Validation - Detailed guide to all validation features
• Batch Processing - Process thousands of molecules at once
• Structural Alerts - Screen for problematic substructures
• Scoring - Comprehensive molecular scoring
• API Reference - Full API documentation