Molecular I/O - Usage Guide

Overview

Read, write, and convert molecular file formats including SMILES, SDF, MOL2, and PDB. Inspect representation-sensitive details such as salts, charges, and stereochemistry during conversion, then use the molecular-standardization skill when a registration policy is required.

Prerequisites

pip install rdkit
pip install openbabel-wheel  # For additional format support

Quick Start

Tell your AI agent what you want to do: - "Load my compound library from this SDF file" - "Convert these SMILES to an SDF file with 3D coordinates" - "Inspect my molecule database for salts, mixtures, charge states, and missing stereochemistry before conversion" - "Read MOL2 files and convert to SMILES"

Example Prompts

Reading Molecules

"Load all molecules from compounds.sdf and show me how many were successfully parsed."

"Read SMILES from this CSV file where the SMILES column is named 'structure'."

Writing Molecules

"Save my filtered compounds to an SDF file with properties included."

"Export canonical SMILES for my molecule list."

Checks Before Standardization

"Parse these molecules and report salts, mixtures, charge states, and stereochemistry issues that need a documented standardization policy."

"Convert this compound library without silently changing charge, stereochemistry, or tautomer state, then identify records that need the molecular-standardization workflow."

What the Agent Will Do

1. Parse molecular files using RDKit or Open Babel
2. Handle parsing errors gracefully
3. Preserve representation-sensitive details during conversion and route registration-grade standardization to the dedicated skill
4. Convert between formats as needed
5. Preserve molecular properties during conversion

Tips

• Use the maintained rdkit.Chem.MolStandardize.rdMolStandardize module for custom standardization; standalone MolVS is a legacy package
• For Open Babel 3.x, use from openbabel import pybel not import pybel
• Standardization order is policy-specific; use the molecular-standardization skill and document whether tautomer canonicalization occurs before or after parent selection
• Use rdMolDraw2D when direct control over molecular drawing is needed; Draw.MolToImage remains a supported convenience API
• Always check for None when loading molecules (invalid structures return None)

Related Skills

• molecular-descriptors - Calculate properties after loading
• similarity-searching - Compare loaded molecules
• virtual-screening - Prepare ligands for docking