mmCIF Parser in Python

A lightweight mmCIF (Macromolecular Crystallographic Information File) parser built from scratch in Python, with no external dependencies. Designed as both an educational resource and a practical tool for structural bioinformatics.

See Features.md for a detailed feature list.

---

Features

• No external dependencies (no Biopython required)
• Clean, object-oriented Python code
• Extracts atomic-level information from CIF files
• Supports .cif files from RCSB PDB
• Useful for understanding how structural biology file formats work internally

---

Theoretical Binary Data Structure Model

Objective

Define a low-level binary data structure for storing mmCIF entries and sections efficiently in memory, simulating a compiled or serialized format.

Data Record Structure

Each mmCIF data item (atom site, loop header, value) is represented in the following binary format:

Segment	Description	Example
RECORD_TYPE (1B)	0x01 = header, 0x02 = loop, 0x03 = data value	0x02
RECORD_ID (2B)	Unique ID for the entry (short int)	0x00FA
FIELD_NAME_LENGTH (1B)	Length of the field name	0x07
FIELD_NAME	UTF-8 string of field name	_atom_site
VALUE_LENGTH (1B)	Length of the value	0x05
VALUE	UTF-8 string of the value	C1'

Block Structure

Each mmCIF block is a binary sequence of multiple record units. A block header can optionally store metadata such as loop count, atom count, etc.

Why This Model

• Enables serialization and memory-efficient storage
• Fast search and indexing for compiled applications
• Suitable for integration with compiled languages (C, Rust)
• Can be exported as .bin for direct loading into visualization tools or bioinformatics engines

---

File Structure

mmCIF_Parser_Project/
├── main.py                # Run this to see the parser in action
├── mmcif_parser.py        # Core parsing logic
├── data_structures.py     # Binary data structure model
├── enzyme_parser.py       # Enzyme-specific parsing utilities
├── example.cif            # Sample mmCIF file
├── data/                  # Additional CIF files
└── README.md

Usage

python main.py data/example.cif

Tests

python test_mmcif_parser.py

---

Extended Analyses

Additional analyses demonstrating real-world applications of mmCIF parsing:

• Enzyme Comparison: TPH1 vs PAH
• TPH1 vs PAH Overview

---

License

See LICENSE for details.