Constants Generator

Constants Generator#

This module provides functionality to generate Python constants files from CCD data for standard residues. It extracts bond information from the Chemical Component Dictionary and creates optimized data structures for runtime use.

Classes#

Functions#

Generated Constants Format#

The generated constants file contains:

# Auto-generated from CCD data
# Generated on: YYYY-MM-DD HH:MM:SS

from typing import Dict, List, Any

RESIDUE_BONDS: Dict[str, Dict[str, Any]] = {
    "ALA": {
        "bonds": [
            {"atom1": "N", "atom2": "CA", "order": "SING", "aromatic": False},
            {"atom1": "CA", "atom2": "C", "order": "SING", "aromatic": False},
            {"atom1": "C", "atom2": "O", "order": "DOUB", "aromatic": False},
            # ... more bonds
        ],
        "bond_count": 10,
        "aromatic_bonds": 0,
        "bond_orders": {"SING": 9, "DOUB": 1}
    },
    # ... more residues
}

Bond Information Structure#

Each residue entry contains:

  • bonds: List of bond dictionaries with:

    • atom1: First atom name

    • atom2: Second atom name

    • order: Bond order (“SING”, “DOUB”, “TRIP”, “AROM”)

    • aromatic: Boolean indicating aromaticity

  • bond_count: Total number of bonds

  • aromatic_bonds: Count of aromatic bonds

  • bond_orders: Dictionary of bond order counts

Standard Residues Included#

The generator extracts bond data for all standard amino acids and nucleotides:

Amino Acids: ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL

Nucleotides: A, C, G, U, DA, DC, DG, DT

Usage Example#

from hbat.ccd.constants_generator import ConstantsGenerator
from hbat.ccd.ccd_analyzer import CCDDataManager

# Initialize generator
ccd_manager = CCDDataManager()
generator = ConstantsGenerator(ccd_manager)

# Extract bonds for specific residues
residue_list = ["ALA", "GLY", "VAL"]
bonds_data = generator.extract_residue_bonds(residue_list)

# Generate full constants file
generator.generate_constants_file("my_constants.py")

# Or write specific data
generator.write_constants_file(bonds_data, "partial_constants.py")

Performance Benefits#

Pre-generating constants provides:

  • Instant access to bond information without parsing CCD files

  • No runtime dependency on CCD data files

  • Reduced memory usage compared to loading full CCD dataset

  • Type-safe access to bond information

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