https://github.com/orhanbalci/patoz

Protein Data Bank (pdb) file parser
https://github.com/orhanbalci/patoz

bioinformatics nom parser pdb protein-data-bank protein-structure rust

Last synced: 3 months ago
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Protein Data Bank (pdb) file parser

Host: GitHub
URL: https://github.com/orhanbalci/patoz
Owner: orhanbalci
License: mit
Created: 2019-08-21T08:28:27.000Z (about 6 years ago)
Default Branch: master
Last Pushed: 2021-11-12T18:18:48.000Z (almost 4 years ago)
Last Synced: 2025-05-04T06:36:30.670Z (6 months ago)
Topics: bioinformatics, nom, parser, pdb, protein-data-bank, protein-structure, rust
Language: Rust
Homepage:
Size: 779 KB
Stars: 9
Watchers: 1
Forks: 1
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

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README

          # Patoz

Protein Data Bank (pdb) file parser

![Build Status](https://github.com/orhanbalci/patoz/workflows/CI/badge.svg)

![License](https://img.shields.io/github/license/orhanbalci/patoz.svg)

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

# 📦 Cargo.toml

```

patoz = "0.1.0"

```

# 🔧 Examples

```rust

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

- [x] [Header](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#HEADER)

- [x] [Obslte](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#OBSLTE)

- [x] [Title](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#TITLE)

- [x] [Splt](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#SPLIT)

- [x] [Caveat](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#CAVEAT)

- [x] [Compnd](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#COMPND)

- [x] [Source](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#SOURCE)

- [x] [Keywds](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#KEYWDS)

- [x] [Expdta](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#EXPDTA)

- [x] [Nummdl](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#NUMMDL)

- [x] [Mdltyp](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#MDLTYP)

- [x] [Author](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#AUTHOR)

- [x] [Sprsde](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#SPRSDE)

- [x] [Revdat](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#REVDAT)

- [x] [Jrnl](http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#JRNL)

    - [x] Auth

    - [x] Titl

    - [x] Edit

    - [x] Ref

    - [x] Publ

    - [x] Refn

    - [x] Pmid

    - [x] Doi

- [ ] [Remarks](http://www.wwpdb.org/documentation/file-format-content/format33/remarks.html)

### Primary Structure Section

- [x] [Dbref](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#DBREF)

- [x] [Dbref1](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#DBREF1)

- [x] [Seqadv](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#SEQADV)

- [x] [Seqres](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#SEQRES)

- [x] [Modres](http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#MODRES)

### Heterogen Section

- [ ] [Het](http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#HET)

- [ ] [Formul](http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#FORMUL)

- [ ] [Hetnam](http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#HETNAM)

- [ ] [Hetsyn](http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#HETSYN)

### Secondary Structure Section

- [ ] [Helix](http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#HELIX)

- [ ] [Sheet](http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#SHEET)

### Connectivity Annotation Section

- [ ] [Ssbond](http://www.wwpdb.org/documentation/file-format-content/format33/sect6.html#SSBOND)

- [ ] [Link](http://www.wwpdb.org/documentation/file-format-content/format33/sect6.html#LINK)

- [ ] [Cispep](http://www.wwpdb.org/documentation/file-format-content/format33/sect6.html#CISPEP)

### Miscellaneous Features Section

- [ ] [Site](http://www.wwpdb.org/documentation/file-format-content/format33/sect7.html#SITE)

### Crystallographic and Coordinate Transformation Section

- [ ] [Cryst1](http://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1)

- [ ] [MtrixN](http://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#MTRIXn)

- [ ] [OrigxN](http://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#ORIGXn)

- [ ] [ScaleN](http://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#SCALEn)

### Coordinate Section

- [ ] [Model](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL)

- [ ] [Atom](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM)

- [ ] [Anisou](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ANISOU)

- [ ] [Ter](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER)

- [ ] [Hetatm](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#HETATM)

- [ ] [Endmdl](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ENDMDL)

### Connectivity Section

- [ ] [Conect](http://www.wwpdb.org/documentation/file-format-content/format33/sect10.html#CONECT)

### Bookkeeping Section

- [ ] [Master](http://www.wwpdb.org/documentation/file-format-content/format33/sect11.html#MASTER)

- [ ] [End](http://www.wwpdb.org/documentation/file-format-content/format33/sect11.html#END)

## 📝 License

Licensed under MIT License ([LICENSE](LICENSE)).

### 🚧 Contributions

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in this project by you, as defined in the MIT license, shall be licensed as above, without any additional terms or conditions.

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