ChemInformant Documentation

Welcome to the official documentation for ChemInformant - a robust data acquisition engine for the PubChem database, engineered for the modern scientific workflow.

Key Features:

• 📊 Analysis-Ready Pandas/SQL Output - Clean DataFrames and direct SQL export, eliminating data wrangling boilerplate

• 🔄 Automated Network Reliability - Built-in persistent caching, smart rate-limiting, and automatic retries

• 🎯 Flexible & Fault-Tolerant Input - Mixed identifiers (names, CIDs, SMILES) with intelligent error handling

• ⚡ Efficient Batch Processing - Retrieve multiple compounds and properties in single API calls with automatic pagination

• 🔧 22 Convenience Functions - Quick access to individual properties like get_weight(), get_formula(), get_cas()

• ⚡ Dual API for Simplicity and Power - Convenience layer backed by powerful get_properties batch engine

• 🛡️ Guaranteed Data Integrity - Pydantic v2 models for rigorous runtime data validation

• 💻 Terminal-Ready CLI Tools - chemfetch and chemdraw for rapid data retrieval and visualization

• 🆕 Modern and Actively Maintained - Contemporary tech stack for long-term reliability

This page serves as the central entry point for all feature modules, guides, and API references.

🧭 User Guide

• Installation
  • Installation via PyPI (Recommended)
  • Installation from Source (For Developers)
• Basic Usage
  • Core Functionality: Bulk Fetching of Multiple Properties
  • Getting All Properties or Including 3D Descriptors
  • Getting Complete Information for a Single Compound
  • Convenient Shortcut Functions
  • Visualizing Compound Structures
• Application in Real-World Scientific Workflows
  • Example 1: Batch Preprocessing and Analysis with RDKit
  • Example 2: Multi-Class Classification with Scikit-learn
  • Example 3: Similarity Networking and Community Detection with NetworkX
• Command-Line Interface (CLI)
  • chemfetch
  • chemdraw
• Caching Guide
  • 1. Why Caching is Essential
  • 2. Quick Start
  • 3. Core Configuration: Understanding setup_cache()
  • 4. Managing Your Cache
  • 5. Advanced Usage: Fine-Grained Path Control with PyStow

🎓 Tutorials

• Interactive Tutorial

🔬 API Reference

• Main API Interface (cheminfo_api)
  • get_properties()
  • get_compound()
  • get_compounds()
  • get_weight()
  • get_formula()
  • get_cas()
  • get_iupac_name()
  • get_canonical_smiles()
  • get_isomeric_smiles()
  • get_inchi()
  • get_inchi_key()
  • get_xlogp()
  • get_tpsa()
  • get_complexity()
  • get_exact_mass()
  • get_monoisotopic_mass()
  • get_h_bond_donor_count()
  • get_h_bond_acceptor_count()
  • get_rotatable_bond_count()
  • get_heavy_atom_count()
  • get_charge()
  • get_atom_stereo_count()
  • get_bond_stereo_count()
  • get_covalent_unit_count()
  • get_synonyms()
  • draw_compound()
• Data Models and Exceptions (models)
  • Compound
  • NotFoundError
  • AmbiguousIdentifierError
• Internal API Helpers (api_helpers)
  • setup_cache()
  • get_session()
  • get_cids_by_name()
  • get_cids_by_smiles()
  • get_batch_properties()
  • get_cas_for_cid()
  • get_synonyms_for_cid()

🛠️ Project Information

• Contributing Guide