ccd2rdmol 0.2.1

Convert PDB Chemical Component Dictionary (CCD) files to RDKit molecules

ccd2rdmol

A lightweight Python library and CLI tool for converting PDB Chemical Component Dictionary (CCD) files to RDKit molecule objects.

This project is a simplified implementation inspired by pdbeccdutils, focusing solely on CCD to RDKit conversion with 3D conformer support.

Features

• Fast CIF parsing using gemmi
• Conversion to RDKit molecule objects
• Support for both Ideal and Model 3D conformers
• Automatic metal bond to dative bond conversion
• Stereochemistry assignment from 3D coordinates
• CLI tool with rich output

Installation

# Library only
uv add ccd2rdmol

# With CLI support
uv add ccd2rdmol[cli]

Or for development:

git clone https://github.com/N283T/ccd2rdmol.git
cd ccd2rdmol
uv sync  # CLI is included in dev dependencies

Usage

As a Library

from ccd2rdmol import read_ccd_file, read_ccd_block
import gemmi

# Read from file
result = read_ccd_file("ATP.cif")
mol = result.mol

print(f"Atoms: {mol.GetNumAtoms()}")
print(f"Bonds: {mol.GetNumBonds()}")
print(f"Conformers: {mol.GetNumConformers()}")  # 2 (IDEAL + MODEL)
print(f"Sanitized: {result.sanitized}")

# With options
result = read_ccd_file(
    "ATP.cif",
    sanitize_mol=True,      # Sanitize molecule (default: True)
    add_conformers=True,    # Add 3D conformers (default: True)
    remove_hydrogens=True,  # Remove hydrogens (default: True)
)

# From gemmi CIF block
doc = gemmi.cif.read("components.cif")
for block in doc:
    result = read_ccd_block(block)
    print(f"{block.name}: {result.mol.GetNumAtoms()} atoms")

As a CLI

Note: CLI requires extra dependencies. Install with uv add ccd2rdmol[cli]

# Output SMILES to stdout
ccd2rdmol convert ATP.cif

# Write to MOL file
ccd2rdmol convert ATP.cif -o ATP.mol

# Write to SDF format
ccd2rdmol convert ATP.cif -o ATP.sdf

# Keep hydrogen atoms
ccd2rdmol convert ATP.cif --keep-hydrogens

# Show verbose information
ccd2rdmol convert ATP.cif -v

# Show molecule information only
ccd2rdmol info ATP.cif

CLI Options

ccd2rdmol convert [OPTIONS] INPUT_FILE

Arguments:
  INPUT_FILE  Input CCD CIF file path [required]

Options:
  -o, --output PATH       Output file path (.mol, .sdf)
  -f, --format TEXT       Output format (mol, sdf, smiles, inchi)
  --no-sanitize           Skip sanitization step
  --no-conformers         Skip adding 3D conformers
  -H, --keep-hydrogens    Keep hydrogen atoms
  -v, --verbose           Show detailed information
  --help                  Show help message

Development

This project uses poethepoet as a task runner.

# Install dev dependencies
uv sync

# Format code (ruff format)
uv run poe format

# Lint (ruff check)
uv run poe lint

# Lint and auto-fix
uv run poe fix

# Type check (ty)
uv run poe check

# Run tests
uv run poe test

# Multi-version testing with nox (3.10, 3.11, 3.12, 3.13, 3.14)
uv run poe nox

# Run all checks (format, lint, check, test)
uv run poe all

# Clean cache files
uv run poe clean

Acknowledgments

This project is inspired by and built upon concepts from pdbeccdutils by PDBe (Protein Data Bank in Europe). Test data files are derived from the pdbeccdutils test suite.

We thank the PDBe team for their excellent work on chemical component processing tools.

License

MIT License

Test data files in tests/data/ are from pdbeccdutils (Apache-2.0 License).