Patoz

Protein Data Bank (pdb) file parser

⚠️ WIP This is a work in progress. Expect breaking changes frequently. Right now use at your own risk

📦 Cargo.toml

patoz = {git = "https//github.com/orhanbalci/patoz"}

🔧 Examples

use std::{
    fs::File,
    io::{BufReader, Read},
    path::PathBuf,
};

use patoz::parse;

fn main() {
    let mut current_file_path = PathBuf::from(file!());
    current_file_path.pop();
    current_file_path.pop();
    current_file_path.push("1BYI.pdb");
    let content = read_file(&current_file_path);
    if let Ok((_, mut res)) = parse(&content) {
        println!(
            "Classification : {:?}",
            res.header().header().unwrap().classification
        );
        println!("Id Code : {:?}", res.header().header().unwrap().id_code);
        println!("Keywords : {:?}", res.header().keywds().unwrap().keywords);
    }
}

fn read_file(path: &PathBuf) -> String {
    let file = File::open(path).unwrap();
    let mut buf_reader = BufReader::new(file);
    let mut contents = String::new();
    if let Ok(_read_res) = buf_reader.read_to_string(&mut contents) {
        contents
    } else {
        "".to_owned()
    }
}

📊 Status

Record Parser Status

Title Section

• Header
• Obslte
• Title
• Splt
• Caveat
• Compnd
• Source
• Keywds
• Expdta
• Nummdl
• Mdltyp
• Author
• Sprsde
• Revdat
• Jrnl
  • Auth
  • Titl
  • Edit
  • Ref
  • Publ
  • Refn
  • Pmid
  • Doi
• Remarks

Primary Structure Section

• Dbref
• Dbref1
• Seqadv
• Seqres
• Modres

Heterogen Section

• Het
• Formul
• Hetnam
• Hetsyn

Secondary Structure Section

• Helix
• Sheet

Connectivity Annotation Section

• Ssbond
• Link
• Cispep

Miscellaneous Features Section

• Site

Crystallographic and Coordinate Transformation Section

• Cryst1
• MtrixN
• OrigxN
• ScaleN

Coordinate Section

• Model
• Atom
• Anisou
• Ter
• Hetatm
• Endmdl

Connectivity Section

• Conect

Bookkeeping Section

• Master
• End