CCD Package

The CCD (Chemical Component Dictionary) package provides functionality for working with RCSB Chemical Component Dictionary data, including automatic download and parsing of BinaryCIF files containing atom and bond information for standard residues.

Module Overview

• CCD Analyzer
  • Classes
  • Examples
  • Data Format
  • Performance Notes
• Constants Generator
  • Classes
  • Functions
  • Generated Constants Format
  • Bond Information Structure
  • Standard Residues Included
  • Usage Example
  • Performance Benefits
• Generate CCD Constants
  • Script Usage
  • Default Output
  • Generated File Contents
  • Standard Residues Processed
  • Workflow
  • Example Output
  • Error Handling
  • Regeneration Guidelines
  • Integration with HBAT
  • Manual Verification

Key Components

The CCD package enables HBAT to access accurate chemical information about standard residues from the RCSB PDB Chemical Component Dictionary. This includes:

• Atom connectivity and bond information

• Bond orders (single, double, aromatic)

• Automatic download and caching of CCD data files

• Efficient in-memory lookup structures

• Constants generation for optimized runtime performance

CCDDataManager (ccd_analyzer.py)

Main class for managing CCD data, including automatic download, caching, and lookup functionality.

ConstantsGenerator (constants_generator.py)

Generates Python constants files from CCD data for standard residues.

Generate CCD Constants Script (generate_ccd_constants.py)

Command-line script to regenerate residue bond constants from CCD data.

Usage Example

from hbat.ccd.ccd_analyzer import CCDDataManager

# Initialize the CCD data manager
ccd_manager = CCDDataManager()

# Ensure CCD files are downloaded
if ccd_manager.ensure_files_exist():
    # Get atom information for alanine
    ala_atoms = ccd_manager.get_component_atoms("ALA")

    # Get bond information for alanine
    ala_bonds = ccd_manager.get_component_bonds("ALA")

    # Get specific atom by ID
    ca_atom = ccd_manager.get_atom_by_id("ALA", "CA")

    # Get bonds involving a specific atom
    ca_bonds = ccd_manager.get_bonds_involving_atom("ALA", "CA")

Data Storage

CCD data files are automatically downloaded and stored in:

• Default location: ~/.hbat/ccd-data/

• Files: cca.bcif (atoms) and ccb.bcif (bonds)

• Source: https://models.rcsb.org/

The data is cached locally for offline use and only downloaded when not present.