Chemistry Query Agent v1.4.1

Overview

Full-stack chemistry toolkit combining PubChem data retrieval with RDKit molecule processing, visualization, analysis, retrosynthesis, and synthesis planning. All outputs are structured JSON for easy downstream chaining. Generates PNG/SVG images on demand.

Key capabilities:

• - PubChem compound lookup (info, structure, synthesis refs, similarity search)
• RDKit molecular properties (MW, logP, TPSA, HBD/HBA, rotatable bonds, aromatic rings)
• 2D molecule visualization (PNG/SVG)
• BRICS retrosynthesis with recursive depth control
• Multi-step synthesis route planning
• Forward reaction simulation with SMARTS templates
• Morgan fingerprints and similarity/substructure search
• 21 named reaction templates (Suzuki, Heck, Grignard, Wittig, Diels-Alder, etc.)

Quick Start

CODEBLOCK0

Scripts

scripts/query_pubchem.py

PubChem REST API queries with automatic name→CID resolution and timeout handling.

CODEBLOCK1

• - info: Formula, MW, IUPAC name, InChIKey (JSON)
• structure: SMILES, InChI, image URL, or full JSON
• synthesis: Synonyms/references for a compound
• similar: Similar compounds by 2D fingerprint (top 20)

scripts/rdkit_mol.py

RDKit cheminformatics engine. Resolves names via PubChem automatically.

CODEBLOCK2

Action	Description	Key Args
props	MW, logP, TPSA, HBD, HBA, rotB, aromRings	INLINECODE2
draw

2D PNG/SVG (300×300) | --smiles --output file.png --format png\|svg |
| retro | BRICS recursive retrosynthesis | --target <SMILES\|name> --depth N |
| plan | Multi-step retro route | --target <SMILES\|name> --steps N |
| react | Forward reaction via SMARTS | --reactants "smi1 smi2" --smarts "<SMARTS>" |
| fingerprint | Morgan fingerprint bitvector | --smiles --radius 2 |
| similarity | Tanimoto similarity scoring | --query_smiles --target_smiles "smi1,smi2" |
| substruct | Substructure matching | --query_smiles --target_smiles "smi1,smi2" |
| xyz | 3D coordinates (MMFF optimized) | --smiles |

scripts/chain_entry.py

Standard agent chain interface. Accepts {"smiles": "...", "context": "..."} or {"name": "...", "context": "..."}. Returns unified JSON with props, visualization, and retrosynthesis.

CODEBLOCK3

Output schema:
CODEBLOCK4

scripts/templates.json

21 named reaction templates with SMARTS, expected yields, conditions, and references. Includes: Suzuki, Heck, Buchwald-Hartwig, Grignard, Wittig, Diels-Alder, Click, Sonogashira, Negishi, and more.

Chaining

1. 1. Name → Full Profile: chain_entry.py with {"name": "ibuprofen"} → props + draw + retro
2. Chemistry → Pharmacology: Output feeds directly into INLINECODE17
3. Retro + Viz: Get precursors, then draw each one
4. Suzuki Test: INLINECODE18

Tested With

All features verified end-to-end with RDKit 2024.03+:

Molecule	SMILES	Tests Passed
Caffeine	INLINECODE19	info, structure, props, draw, retro, plan, chain
Aspirin

CC(=O)Oc1ccccc1C(=O)O | info, structure, props, draw, retro, plan, chain |
| Sotorasib | PubChem name lookup | info, structure, props, draw, retro, chain |
| Ibuprofen | PubChem name lookup | info, structure, props, chain |
| Invalid SMILES | XXXINVALID | Graceful JSON error |
| Empty input | {} | Graceful JSON error |

Resources

• - references/api_endpoints.md — PubChem API endpoint reference and rate limits
• INLINECODE24 — Legacy reaction module
• INLINECODE25, scripts/pubmed_search.py, scripts/admet_predict.py — Additional query modules

scripts/advanced_chem.py

Advanced cheminformatics engine with 6 Tier 1 capabilities.

CODEBLOCK5

Action	Description	Key Args
standardize	Salt stripping, charge normalization, tautomer enumeration	INLINECODE29
descriptors

217+ molecular descriptors (RDKit full set), QED, SA Score, Lipinski/Veber rules | --smiles --descriptor_set all\|druglike\|physical\|topological |
| scaffold | Murcko scaffold extraction, generic scaffolds, diversity analysis, R-group decomposition | --smiles or --target_smiles "smi1,smi2,..." --rgroup_core <SMARTS> |
| mcs | Maximum Common Substructure across 2+ molecules | --target_smiles "smi1,smi2,..." |
| mmpa | Matched Molecular Pair Analysis — find single-point transformations | --target_smiles "smi1,smi2,..." |
| chemspace | Chemical space visualization (PCA/t-SNE/UMAP scatter plot PNG) | --target_smiles "smi1,smi2,..." --method pca\|tsne\|umap --output plot.png |

Examples:
CODEBLOCK6

Changelog

v2.0.0 (2026-02-28)

• - NEW: advanced_chem.py with 6 Tier 1 cheminformatics capabilities

- Molecular Standardization & Tautomer Enumeration (salt stripping, charge normalization, canonical tautomers)
- Extended Descriptors (217+ RDKit descriptors, QED, SA Score, Lipinski, Veber)
- Scaffold Analysis (Murcko, generic scaffolds, diversity ratio, R-group decomposition)
- Maximum Common Substructure (rdFMCS with coverage per molecule)
- Matched Molecular Pair Analysis (rdMMPA fragmentation, transformation detection)
- Chemical Space Visualization (PCA/t-SNE/UMAP with matplotlib scatter plots)

• - Dependencies: scikit-learn, matplotlib (added)

v1.4.1 (2026-02-25)

• - Security hardening: input sanitization for all subprocess calls (SMILES, compound names, output paths)
• Added _sanitize_input() — length limits, null-byte rejection for all user inputs
• Added _sanitize_output_path() — prevents path traversal, restricts extensions, blocks arbitrary file writes
• Added shell metacharacter rejection in INLINECODE40
• Added SMILES validation via RDKit in chem_ui.py before subprocess calls
• Added compound input validation in query_pubchem.py (length/null-byte checks)
• Added timeout to resolve_target() PubChem subprocess call
• Addresses VirusTotal "suspicious" classification for argument injection vectors

v1.4.0 (2026-02-14)

• - Fixed PubChem SMILES/InChI endpoint (property/CanonicalSMILES/TXT)
• Fixed chainentry.py HTML entity corruption
• Fixed bricsretro to handle BRICSDecompose string output correctly
• Added request timeouts (15s) to all PubChem calls
• Graceful error handling for invalid SMILES and empty input
• Updated chain output version and schema
• Comprehensive end-to-end testing

v1.3.0

• - RDKit props NoneType fixes, invalid SMILES graceful errors
• React fix: ReactionFromSmarts import
• Name resolution via PubChem for all RDKit actions

v1.2.0

• - BRICS retrosynthesis + 21 reaction templates library
• Multi-step synthesis planning