Process PDB

This tool processes a PDB file to ensure that certain records (HEADER, CRYST1, MODEL, ENDMDL, and END) are present and correctly ordered. It modifies the input PDB file in-place.

Features

• Adds a HEADER record if missing.
• Adds a CRYST1 record before the first MODEL record if missing.
• Ensures a MODEL record precedes ATOM records.
• Ensures ENDMDL and END records are present and in the correct order.

Requirements

• A C compiler supporting the specified optimization flags.
• The project uses -O3 -flto -march=native for improved performance.

Building

Run make in the project directory:

make

This will produce an executable named process_pdb.

makefile Flags

• -O3: High-level optimization for speed.
• -flto: Link-time optimization.
• -march=native: Optimizes the code for your CPU’s features.

Usage

./process_pdb path_to_pdb_file

The tool will process the specified PDB file in place, ensuring all required records are present and properly ordered.

Project Structure

DSSP-Pre/
├── makefile
├── README.md
├── include/
│   └── process_pdb.h
└── src/
    └── process_pdb.c

• makefile: Builds the process_pdb executable.
• README.md: Instructions and usage details.
• include/process_pdb.h: Declarations of functions and constants.
• src/process_pdb.c: Implementation of the logic to process the PDB file.

Notes

• It’s recommended to keep a backup of your original PDB file before running the tool, as it overwrites the input file.
• Adjust compilation flags in the makefile if you need different optimization settings or broader compatibility.

To-Do

• Add support for bulk processing of multiple PDB files.