tooluniverse-chemical-sourcing

# 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. De