tooluniverse-chemical-compound-retrieval

Included with Lifetime

$97 forever

Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling. Use for resolving compound names to SMILES/InChI/CID/ChEMBL IDs, fetching molecular properties, distinguishing isomers/stereo forms, and cross-validating identity across databases. Always use English compound names; flags ambiguous queries (e.g., Vitamin D has multiple forms).

General

What this skill does


# Chemical Compound Information Retrieval

Retrieve comprehensive chemical compound data with proper disambiguation and cross-database validation.

**LOOK UP DON'T GUESS**: Never assume a CID, ChEMBL ID, or molecular property value. Always retrieve from PubChem/ChEMBL.

**English-first**: Always use English compound names in tool calls. Respond in user's language.

## Domain Reasoning: Disambiguation

"Aspirin" = one compound. "Vitamin D" = multiple forms (D2/D3/active metabolite). For generic class names (steroids, vitamins, acids), present candidates and confirm before proceeding.

---

## Workflow

```
Phase 0: Clarify (only if highly ambiguous -- skip for unambiguous names or specific IDs)
Phase 1: Disambiguate → resolve PubChem CID + ChEMBL ID
Phase 2: Retrieve data (silent)
Phase 3: Report compound profile
```

### Phase 1: Disambiguation

```python
# By name
result = tu.tools.PubChem_get_CID_by_compound_name(compound_name=name)
# By SMILES
result = tu.tools.PubChem_get_CID_by_SMILES(smiles=smiles)
# Cross-reference
chembl_result = tu.tools.ChEMBL_search_molecules(query=name, limit=5)
```

Verify: CID + ChEMBL ID + canonical SMILES + stereochemistry + salt forms.

### Phase 2: Data Retrieval

**PubChem**: `PubChem_get_compound_properties_by_CID`, `PubChemBioAssay_get_assay_summary`, `PubChemTox_get_acute_effects`, `PubChem_get_compound_2D_image_by_CID`

**ChEMBL**: `ChEMBL_get_compound_record_activities`, `ChEMBL_get_molecule_targets`, `ChEMBL_get_assay_activities`

**Optional**: `PubChem_get_associated_patents_by_CID`, `PubChem_search_compounds_by_similarity`

### Phase 3: Report

Compound Profile with: Identity (CID, ChEMBL ID, IUPAC, SMILES), Chemical Properties (MW, LogP, HBD, HBA, PSA, Lipinski), Bioactivity (targets, IC50/Ki), Drug Info (if approved), Data Sources.

---

## Fallback Chains

| Primary | Fallback |
|---------|----------|
| PubChem name lookup | ChEMBL search → SMILES → PubChem_get_CID_by_SMILES |
| ChEMBL bioactivity | PubChem bioassay summary |
| Drug label | Note "unavailable" |

---

## Evidence Grading

| Grade | Criteria |
|-------|----------|
| **Confirmed** | CID + ChEMBL cross-match, InChI/SMILES agree |
| **Probable** | CID found, partial ChEMBL match |
| **Uncertain** | Single database only, or multiple CIDs |
| **Unverified** | No cross-reference, single-source |

**Bioactivity**: ChEMBL > PubChem BioAssay for curated data. IC50/Ki < 100nM = potent, 100nM-1uM = moderate, >10uM = weak. Lipinski violations reduce oral bioavailability but don't disqualify.

---

## SMILES Verification

Always verify novel SMILES: `python3 src/tooluniverse/tools/smiles_verifier.py --smiles "SMILES_STRING"`. Invalid SMILES produce wrong results or cryptic errors.

---

## Tool Reference

**PubChem**: `PubChem_get_CID_by_compound_name`, `PubChem_get_CID_by_SMILES`, `PubChem_get_compound_properties_by_CID`, `PubChem_get_compound_2D_image_by_CID`, `PubChemBioAssay_get_assay_summary`, `PubChemTox_get_acute_effects`, `PubChem_get_associated_patents_by_CID`, `PubChem_search_compounds_by_similarity`, `PubChem_search_compounds_by_substructure`

**ChEMBL**: `ChEMBL_search_drugs`, `ChEMBL_get_molecule`, `ChEMBL_get_activity`, `ChEMBL_get_target`, `ChEMBL_search_targets`, `ChEMBL_search_assays`

Files: 3

Size: 9.3 KB

Complexity: 23/100

Category: General

Source: https://github.com/mims-harvard/tooluniverse/tree/main/plugin/skills/tooluniverse-chemical-compound-retrieval

Related in General

modeling-omnistudio-epc-catalog

Included

Salesforce Industries CME EPC product-modeling skill for Product2-based catalog creation. Use when creating EPC products, configuring product attributes, building offer bundles with Product Child Items, or reviewing EPC DataPack JSON metadata for product catalog changes. TRIGGER when: user creates or updates Product2 EPC records, AttributeAssignment payloads, AttributeMetadata/AttributeDefaultValues, Offer bundles, or ProductChildItem relationships. DO NOT TRIGGER when: designing OmniScripts/FlexCards/Integration Procedures (use building-omnistudio-omniscript, building-omnistudio-flexcard, or building-omnistudio-integration-procedure), implementing Apex business logic (use generating-apex), or troubleshooting deployment pipelines (use deploying-metadata).

Generalscripts

relationship-science-coach

Included

Use this skill for direct, practical adult relationship coaching: couples conflict, repair, trust, marriage, dating, flirting, attachment patterns, emotional connection, sex, desire differences, eroticism, kink negotiation, affection, love languages, breakups, and long-term passion. Draw on Gottman, EFT and Hold Me Tight, attachment science, modern sex research, Perel, Nagoski, Kerner, Schnarch, Love and Stosny, and flexible love-language tools. Be concrete and low-hedge. Redirect only for imminent danger, abuse, coercive control, minors, non-consent, self-harm, stalking, or medical/legal/psychiatric decisions.

Generalscripts

building-sf-integrations

Included

Salesforce integration architecture and runtime plumbing with 120-point scoring. Use this skill to set up Named Credentials, External Credentials, External Services, REST/SOAP callout patterns, Platform Events, and Change Data Capture. TRIGGER when: user sets up Named Credentials, External Services, REST/SOAP callouts, Platform Events, CDC, or touches .namedCredential-meta.xml files. DO NOT TRIGGER when: Connected App/OAuth config (use configuring-connected-apps), Apex-only logic (use generating-apex), or data import/export (use handling-sf-data).

Generalscripts

venue-templates

Included

Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). This skill should be used when preparing manuscripts for journal submission, conference papers, research posters, or grant proposals and need venue-specific formatting requirements and templates.

Generalscripts

let-fate-decide

Included

Draws the 12 Houses of the Zodiac Tarot spread to inject entropy into planning when prompts are vague, ambiguous, or casually delegated. Interprets the spread to guide next steps. Use when the user says 'let fate decide', 'YOLO', 'whatever', 'idk', or other nonchalant phrases, makes Yu-Gi-Oh references, or when you are about to arbitrarily pick between multiple reasonable approaches. Prefer over ask-questions-if-underspecified when the user's tone is casual or playful rather than precision-seeking.

Generalscripts

net-ops

Included

Cross-platform network troubleshooting (Windows, macOS, Linux) via local or remote shell. Use for: DNS broken, can't resolve hostnames, nslookup/dig works but apps fail, NRPT, WFP, scutil, /etc/resolver, systemd-resolved, /etc/resolv.conf, NetworkManager, VPN DNS leak residue (ProtonVPN/Mullvad/WireGuard/AnyConnect), AV/firewall blocking DNS or DoH, Tailscale DNS interaction, intermittent connectivity, remote diagnostics over SSH.

Generalscripts