chemaudit-molecule-validation

name	chemaudit-molecule-validation
description	Validate and score chemical structures using ChemAudit's 16 deep validation checks, 1,500+ structural alerts, and multi-rule drug-likeness scoring. Use when user says "validate this molecule", "check this SMILES", "is this compound valid", "ML-readiness score", "drug-likeness", "deep validation", "quality score", "PAINS check", or asks about stereochemistry, valence, tautomers, or structural issues. Supports SMILES, InChI, MOL blocks, IUPAC names (OPSIN + PubChem), and database identifiers (ChEMBL ID, CAS, PubChem CID, InChIKey) via the /resolve endpoint.
license	MIT
allowed-tools	Bash(curl:*) Bash(python:*) Bash(chemaudit:*)
compatibility	Requires a running ChemAudit instance (docker compose up) or use the CLI with --local flag for offline mode. Python 3.11+.
metadata	{"author":"Kohulan Rajan","version":"1.0.0","mcp-server":"chemaudit","category":"cheminformatics","tags":["chemistry","validation","drug-discovery","SMILES","molecular-properties"]}

ChemAudit Molecule Validation

Overview

Single-molecule validation with three complementary layers:

1. Validation (/validate) — 16 deep cheminformatics checks, 0-100 score.
2. Scoring (/score) — drug-likeness (Lipinski, QED, Veber, Ghose, Egan, Muegge, Ro3), ADMET, ML-readiness, NP-likeness, safety filters.
3. Alerts (/alerts, /alerts/screen) — PAINS, Brenk, NIH, ZINC, Kazius, NIBR, plus 7 ChEMBL pharma filter sets.

Score interpretation: ≥70 pass, 40–69 warn, <40 fail.

Access modes

• API: HTTP calls to a running ChemAudit instance (default http://localhost:8000).
• CLI: chemaudit validate|score|standardize|profile with --local for offline mode.
• MCP: chemaudit MCP server exposes all tagged endpoints at /mcp.

Input formats auto-detected: SMILES, InChI, MOL block, IUPAC name (OPSIN then PubChem fallback). Identifier resolution (ChEMBL ID, CAS, PubChem CID, ChEBI, UNII, DrugBank, etc.) goes through /api/v1/resolve first.

Workflow

1. Quick validation (default 16 checks + scoring)

curl -sS -X POST http://localhost:8000/api/v1/validate \
  -H 'Content-Type: application/json' \
  -d '{"molecule": "CC(=O)Oc1ccccc1C(=O)O", "format": "auto"}'

Response (abridged):

{
  "status": "completed",
  "molecule_info": {
    "canonical_smiles": "CC(=O)OC1=CC=CC=C1C(=O)O",
    "inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
    "molecular_formula": "C9H8O4",
    "molecular_weight": 180.16,
    "num_stereocenters": 0,
    "has_stereochemistry": false
  },
  "overall_score": 95,
  "issues": [],
  "all_checks": [...],
  "execution_time_ms": 42,
  "cached": false
}

2. Targeted deep checks

Pass specific check names instead of "all" (the default). Full list in references/validation-checks.md:

curl -sS -X POST http://localhost:8000/api/v1/validate \
  -H 'Content-Type: application/json' \
  -d '{
    "molecule": "CC(C)(C)C1=CC=C(C=C1)[N+](=O)[O-]",
    "checks": ["stereoisomer_enumeration", "tautomer_detection",
               "hypervalent_atoms", "radical_detection", "charged_species"]
  }'

Each failing check returns severity (info/warning/error), message, affected_atoms, and a details dict.

3. Drug-likeness and ADMET scoring

curl -sS -X POST http://localhost:8000/api/v1/score \
  -H 'Content-Type: application/json' \
  -d '{
    "molecule": "CC(=O)Oc1ccccc1C(=O)O",
    "include": ["druglikeness", "admet", "np_likeness", "ml_readiness",
                "safety_filters", "consensus", "bioavailability_radar",
                "boiled_egg"]
  }'

Druglikeness returns Lipinski (0–4 violations), QED (0–1), Veber, Ro3, Ghose, Egan, Muegge. ADMET returns SAscore, ESOL solubility, Fsp3, CNS MPO, Pfizer 3/75, GSK 4/400, Golden Triangle. ML-readiness returns 0–100 with 4-dimension breakdown.

4. Scoring profile presets (8 built-in)

Profiles live in the database and are seeded at startup. Retrieve or use by ID:

curl -sS http://localhost:8000/api/v1/profiles

The 8 presets are: Drug-like (Lipinski), Lead-like, Fragment-like (Rule of 3), CNS-penetrant, Ghose (Amgen), Veber (GSK), PPI-like, NP-like. Presets are immutable — duplicate before editing.

5. Structural alerts

Targeted screen against a chosen set of catalogs:

curl -sS -X POST http://localhost:8000/api/v1/alerts \
  -H 'Content-Type: application/json' \
  -d '{
    "molecule": "CC(=O)Oc1ccccc1C(=O)O",
    "catalogs": ["PAINS", "BRENK", "NIH", "ZINC"]
  }'

Unified one-shot screen across all catalogs (PAINS A/B/C, BRENK, NIH, ZINC, Kazius, NIBR, 7 ChEMBL pharma filters, 21 custom SMARTS) with deduplicated concern groups:

curl -sS -X POST http://localhost:8000/api/v1/alerts/screen \
  -H 'Content-Type: application/json' \
  -d '{"molecule": "CCOC(=O)N=Nc1ccccc1"}'

List available catalogs:

curl -sS http://localhost:8000/api/v1/alerts/catalogs

Critical caveat: alerts are investigation flags, not rejections. 87 FDA-approved drugs contain PAINS patterns.

6. Compound profiling (PFI, #stars, bioavailability, SA comparison)

curl -sS -X POST http://localhost:8000/api/v1/profiler/full \
  -H 'Content-Type: application/json' \
  -d '{"smiles": "CC(=O)Oc1ccccc1C(=O)O"}'

Returns PFI, Abbott #stars, consensus LogP, skin permeation, CNS MPO, SA comparison (SA Score + SCScore + SYBA when installed). 3D shape descriptors are lazy — call /profiler/shape-3d separately.

7. CLI usage

chemaudit validate --smiles "CC(=O)Oc1ccccc1C(=O)O"
chemaudit validate --smiles "CCO" --local                # offline
chemaudit validate --file compounds.csv --format json
echo "CCO" | chemaudit validate                           # stdin
chemaudit score --smiles "CCO" --local
chemaudit profile --smiles "CCO"

--local bypasses the HTTP server and calls service functions directly.

8. Identifier resolution (CAS, ChEMBL ID, PubChem CID, names)

Before validating a compound given as a non-structural identifier, resolve it first:

curl -sS -X POST http://localhost:8000/api/v1/resolve \
  -H 'Content-Type: application/json' \
  -d '{"identifier": "50-78-2", "identifier_type": "auto"}'

Supported types: auto, smiles, inchi, inchikey, pubchem_cid, chembl_id, cas, drugbank_id, chebi_id, unii, wikipedia, name. Response includes canonical_smiles, cross_references (CIDs, ChEMBL, DrugBank, UNII, CAS), and resolution_chain provenance.

Examples

Example 1 — "Validate this SMILES and tell me if it's ML-ready"

1. POST /api/v1/validate with {"molecule": "<smi>"} → check overall_score, list issues.
2. POST /api/v1/score with {"molecule": "<smi>", "include": ["ml_readiness", "druglikeness"]} → read ml_readiness.score (0–100) and interpretation.
3. Summarise: parseable, passes Lipinski with X violations, ML-readiness = Y/100 with breakdown across 4 dimensions.

Example 2 — "Run deep validation and explain all issues"

1. POST /api/v1/validate with {"molecule": "<smi>", "checks": ["all"]}.
2. Filter all_checks where passed=false, group by severity.
3. For each issue, explain the check_name using references/validation-checks.md, show affected_atoms and the details dict.

Example 3 — "Score against Lipinski, Ghose, and CNS-penetrant profiles"

1. GET /api/v1/profiles → find IDs for Drug-like (Lipinski), Ghose (Amgen), CNS-penetrant.
2. POST /api/v1/score with {"molecule": "<smi>", "include": ["druglikeness"]} gets Lipinski and Ghose directly.
3. For CNS-penetrant, use /profiler/full → read cns_mpo.score and cns_mpo.cns_penetrant boolean.

Rate limits

Anonymous (no API key):

• 10/min: /validate, /checks, /score, /score/compare, /alerts, /alerts/catalogs, /alerts/quick-check, /alerts/screen, /standardize.
• 30/min: /validate/async, /validate/similarity, /standardize/options, /profiler/full, /profiler/efficiency, /profiler/mpo.
• 20/min: /profiler/sa-comparison.
• 10/min: /profiler/shape-3d.

API key via X-API-Key header raises the tier (300/min on most endpoints).

Troubleshooting

400 "Failed to parse molecule"

The detail dict includes errors[], warnings[], and format_detected. Common fixes:

• Unbalanced ring closures — use POST /api/v1/diagnostics/smiles for position-specific fix suggestions.
• IUPAC name with unusual punctuation — pass "format": "iupac" explicitly to force OPSIN/PubChem.
• MOL block — ensure M END terminator is present and on its own line.

400 "Invalid characters in molecule string"

The validator blocks `< > & ; | $ ``. Strip these client-side before calling.

Input auto-classified as IUPAC when it's a valid SMILES

Short valid SMILES like CO, O, CCO are ambiguous. Pass "input_type": "smiles" or "format": "smiles" to skip name resolution.

504 on /validate/async

The high-priority Celery worker is unavailable. Either use the sync /validate endpoint or check that the high_priority queue worker is running (docker compose logs worker-priority).

429 rate limit

Use X-API-Key header for the 300/min tier, or stagger requests client-side. Batch endpoints (/batch/upload) have their own limits — see the chemaudit-batch-validation skill.

InChIKey-based caching

/validate caches by (inchikey, checks); repeated calls return cached: true with the same score. To bypass, add a meaningless suffix to checks or flush Redis.

Further reading

• references/validation-checks.md — catalog of all 16 deep validation checks with severity, rationale, and fix recipes.
• chemaudit-batch-validation — upload CSV/SDF for bulk validation with analytics.
• chemaudit-diagnostics — when you need to know why a SMILES fails, not just that it did.
• chemaudit-standardization — before validating heterogeneous datasets, standardize first.