tooluniverse-chemical-sourcing

What this skill does

# Chemical Compound Sourcing & Procurement

Pipeline for identifying, sourcing, and purchasing chemical compounds from commercial vendors. Resolves compound identity through PubChem/ChEMBL, searches multiple vendor databases (ZINC, Enamine, eMolecules, Mcule), compares pricing and availability, and identifies purchasable analogs when exact compounds are unavailable.

**Guiding principles**:
1. **Identity first** -- confirm the compound's structure (SMILES, InChI) before searching vendors; names can be ambiguous
2. **Multi-vendor comparison** -- always check multiple sources; pricing and stock vary significantly
3. **Analog fallback** -- if the exact compound is unavailable, search for close analogs
4. **Purity and quantity awareness** -- note catalog purity grades and minimum order quantities
5. **Structure over name** -- vendor searches by SMILES/InChI are more reliable than name searches
6. **English-first queries** -- use English compound names in tool calls

## LOOK UP, DON'T GUESS
When uncertain about any scientific fact, SEARCH databases first rather than reasoning from memory. A database-verified answer is always more reliable than a guess.

---

## COMPUTE, DON'T DESCRIBE
When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.

## When to Use

Typical triggers:
- "Where can I buy [compound]?"
- "Find commercial sources for [SMILES]"
- "Compare prices for [compound] across vendors"
- "Is [compound] commercially available?"
- "Find purchasable analogs of [compound]"
- "I need [quantity] of [compound] -- who sells it?"
- "Search ZINC/Enamine for [compound]"

**Not this skill**: For ADMET/toxicity assessment, use `tooluniverse-admet-prediction`. For drug-target interaction analysis, use `tooluniverse-drug-target-validation`.

---

## Core Databases

| Database | Scope | Best For |
|----------|-------|----------|
| **ZINC** | 230M+ purchasable compounds; aggregates vendors | Broadest coverage; substructure/similarity search; free |
| **Enamine** | ~4M in-stock, 30B+ REAL (make-on-demand) | Large in-stock library; fast delivery; building blocks |
| **eMolecules** | Multi-vendor aggregator; 8M+ compounds | Cross-vendor comparison; pricing transparency |
| **Mcule** | 40M+ compounds; one-stop purchasing | Integrated ordering; quote generation |
| **PubChem** | 110M+ compounds; identity resolution | Authoritative compound identification; CID lookup |
| **ChEMBL** | 2.4M+ bioactive molecules | Bioactivity context for sourced compounds |

---

## Workflow Overview

```
Phase 0: Compound Identity Resolution
  Name/SMILES/CAS -> PubChem CID -> canonical SMILES
    |
Phase 1: Vendor Search
  Query ZINC, Enamine, eMolecules, Mcule
    |
Phase 2: Price & Availability Comparison
  Catalog numbers, pricing, stock status, purity
    |
Phase 3: Analog Search (if needed)
  Similarity search for purchasable alternatives
    |
Phase 4: Bioactivity Context (optional)
  ChEMBL activity data for sourced compounds
    |
Phase 5: Order Summary
  Consolidated vendor comparison table
```

---

## Phase Details

### Phase 0: Compound Identity Resolution

**Objective**: Establish unambiguous compound identity before vendor searches.

**Tools**:
- `PubChem_get_CID_by_compound_name` -- resolve name to CID
  - Input: `name` (compound name)
  - Output: `{IdentifierList: {CID: [...]}}`
- `PubChem_get_compound_properties_by_CID` -- get SMILES, MW, formula
  - Input: `cid` (PubChem CID), `properties` (comma-separated list)
  - Output: `{CID, MolecularWeight, ConnectivitySMILES, IUPACName}`
- `ChEMBL_get_molecule` -- get ChEMBL compound details
  - Input: `molecule_chembl_id` (ChEMBL ID) or search by name
  - Output: SMILES, molecular properties, synonyms

**Workflow**:
1. If user provides a name: resolve to PubChem CID, then get SMILES
2. If user provides SMILES: use directly (optionally verify via PubChem)
3. If user provides CAS number: search PubChem by name (CAS numbers work as search terms)
4. Record: canonical SMILES, molecular weight, molecular formula, IUPAC name

**Important**: PubChem `ConnectivitySMILES` (not `CanonicalSMILES`) is the correct property name. Always confirm the SMILES matches the intended compound before proceeding.

### Phase 1: Vendor Search

**Objective**: Search all available vendor databases for the target compound.

**Tools**:
- `ZINC_search_compounds` -- search ZINC by name or SMILES
  - Input: `query` (name or SMILES), optional `catalog`, `limit`
  - Output: ZINC IDs, vendor info, purchasability status
- `ZINC_get_compound` -- get detailed compound info from ZINC
  - Input: `zinc_id` (ZINC identifier)
  - Output: vendors, catalogs, pricing, SMILES
- `Enamine_search_catalog` -- search Enamine catalog
  - Input: `query` (name or SMILES), optional `catalog_type`, `limit`
  - Output: catalog numbers, availability, pricing
- `Enamine_get_compound` -- get Enamine compound details
  - Input: `compound_id` (Enamine catalog number)
  - Output: structure, pricing, stock status, delivery time
- `eMolecules_search` -- search across multiple vendors
  - Input: `query` (name or SMILES), optional `limit`
  - Output: vendor list, catalog numbers, pricing
- `eMolecules_get_compound` -- get eMolecules compound details
  - Input: `compound_id` (eMolecules ID)
  - Output: vendors, pricing tiers, purity
- `Mcule_get_compound` -- search Mcule database
  - Input: `query` (name or SMILES), optional `limit`
  - Output: Mcule IDs, availability, pricing
- `Mcule_get_compound` -- get Mcule compound details
  - Input: `compound_id` (Mcule ID)
  - Output: pricing, delivery, purity, catalog number

**Workflow**:
1. Search all four vendor databases in parallel using SMILES (preferred) or name
2. For each hit, retrieve detailed compound info (pricing, stock, purity)
3. Deduplicate results by matching SMILES across vendors
4. Flag any structural mismatches (vendor compound differs from target)

**Tip**: SMILES-based searches are more precise than name searches. If name search returns too many results, switch to SMILES.

### Phase 2: Price & Availability Comparison

**Objective**: Create a comparison table across vendors.

Compile from Phase 1 results:

| Field | Description |
|-------|-------------|
| Vendor | Company name |
| Catalog # | Vendor-specific identifier |
| Quantity | Available pack sizes |
| Price | Per unit or per mg |
| Purity | Stated purity grade (>95%, >98%, etc.) |
| Stock | In-stock vs make-on-demand |
| Delivery | Estimated delivery time |

Rank vendors by: (1) in-stock availability, (2) price per mg, (3) purity grade, (4) delivery time.

### Phase 3: Analog Search

**Objective**: When the exact compound is unavailable, find purchasable structural analogs.

Triggered when:
- No vendors carry the target compound
- The compound is prohibitively expensive
- The user explicitly requests analogs

**Approach**:
1. Use ZINC or Enamine similarity search (if supported by the tool's search mode)
2. Search by substructure using the compound's core scaffold SMILES
3. Filter analogs by: Tanimoto similarity >= 0.7, commercial availability, reasonable price
4. Present analogs with structural differences highlighted

### Phase 4: Bioactivity Context (Optional)

**Objective**: Provide biological activity data for context when sourcing compounds for research.

**Tools**:
- `ChEMBL_get_molecule` -- get bioactivity summary
  - Input: compound identifier
  - Output: known targets, activity values, assay data

Useful when:
- User is sourcing compounds for a specific biological assay
- Comparing analogs that might have different activity profiles
- Verifying the compound has published bioactivity data

### Phase 5: Decision & Order Summary

**Vendor selection decision matrix** — don't just list vendors, recommend one:

| Scenario | Bes