Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/haddocking/pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.
https://github.com/haddocking/pdb-tools

bioinformatics pdb protein python rcsb structural-bioinformatics structural-biology utrecht-university

Last synced: 20 days ago
JSON representation

A dependency-free cross-platform swiss army knife for PDB files.

Awesome Lists containing this project

README 

        
# pdb-tools



[![PyPI version](https://badge.fury.io/py/pdb-tools.svg)](https://pypi.python.org/pypi/pdb-tools)

[![PyPi Downloads](https://img.shields.io/pypi/dm/pdb-tools.svg)](https://pypi.python.org/pypi/pdb-tools)

[![tests](https://github.com/haddocking/pdb-tools/workflows/ci/badge.svg?branch=master)](https://github.com/haddocking/pdb-tools/actions?workflow=ci)

[![DOI](https://zenodo.org/badge/27217350.svg)](https://doi.org/10.12688/f1000research.17456.1)



A swiss army knife for manipulating and editing PDB files.



## Looking for the _other_ pdb-tools?

The Harms lab maintains a set of tools also called `pdbtools`, which perform a

slightly different set of functions. You can find them [here](https://github.com/harmslab/pdbtools).



## About

Manipulating PDB files is often painful. Extracting a particular chain or set of

residues, renumbering residues, splitting or merging models and chains, or just

ensuring the file is conforming to the PDB specifications are examples of tasks

that can be done using any decent parsing library or graphical interface. These,

however, almost always require 1) scripting knowledge, 2) time, and 3) installing

one or more programs.



`pdb-tools` were designed to be a swiss-knife for the PDB format. They have no

external dependencies, besides obviously the [Python programming language](http://www.python.org).

They are the descendant of a set of old FORTRAN77 programs that had the 

particular advantage of working with streams, i.e. the output of one script 

could be piped into another. Since FORTRAN77 is a pain too, I rewrote them in

Python and added a few more utilities. 



The philosophy of the scripts is simple: one script, one task. If you want to 

do two things, pipe the scripts together. Requests for new scripts will be taken

into consideration - use the Issues button or write them yourself and create a

Pull Request.



## Installation Instructions

`pdb-tools` are available on PyPi and can be installed though `pip`. This is the

recommended way as it makes updating/uninstalling rather simple:

```bash

pip install pdb-tools

```



Because we use semantic versioning in the development of `pdb-tools`, every bugfix

or new feature results in a new version of the software that is automatically published

on PyPI. As such, there is no difference between the code on github and the latest version

you can install with `pip`. To update your installation to the latest version of the code

run:

```bash

pip install --upgrade pdb-tools

```



## What can I do with them?

The names of the tools should be self-explanatory. Their command-line interface

is also pretty consistent. Therefore, here is a couple of examples to get you

started:



* Downloading a structure

   ```bash

   pdb_fetch 1brs > 1brs.pdb  # 6 chains

   pdb_fetch -biounit 1brs > 1brs.pdb  # 2 chains

   ```



* Renumbering a structure

   ```bash

   pdb_reres -1 1ctf.pdb > 1ctf_renumbered.pdb

   ```



* Selecting chain(s)

   ```bash

   pdb_selchain -A 1brs.pdb > 1brs_A.pdb

   pdb_selchain -A,D 1brs.pdb > 1brs_AD.pdb

   ```



* Deleting hydrogens

   ```bash

   pdb_delelem -H 1brs.pdb > 1brs_noH.pdb

   ```



* Selecting backbone atoms

   ```bash

   pdb_selatom -CA,C,N,O 1brs.pdb > 1brs_bb.pdb

   ```



* Selecting chains, removing HETATM, and producing a valid PDB file

  ```bash

  pdb_selchain -A,D 1brs.pdb | pdb_delhetatm | pdb_tidy > 1brs_AD_noHET.pdb

  ```



*Note: On Windows the tools will have the `.exe` extension.*



## What _can't_ I do with them?

Operations that involve coordinates or numerical calculations are usually not in

the scope of `pdb-tools`. Use a proper library for that, it will be much faster

and scalable. Also, although we provide mmCIF<->PDB converters, we do not support

large mmCIF files with more than 99999 atoms, or 9999 residues in a single chain.

Our tools will complain if you try using them on such a molecule. 



## Citation

We finally decided to write up a small publication describing the tools. If you

used them in a project that is going to be published, please cite us:



```

Rodrigues JPGLM, Teixeira JMC, Trellet M and Bonvin AMJJ.

pdb-tools: a swiss army knife for molecular structures. 

F1000Research 2018, 7:1961 (https://doi.org/10.12688/f1000research.17456.1) 

```



If you use a reference manager that supports BibTex, use this record:

```

@Article{ 10.12688/f1000research.17456.1,

AUTHOR = { Rodrigues, JPGLM and Teixeira, JMC and Trellet, M and Bonvin, AMJJ},

TITLE = {pdb-tools: a swiss army knife for molecular structures [version 1; peer review: 2 approved]

},

JOURNAL = {F1000Research},

VOLUME = {7},

YEAR = {2018},

NUMBER = {1961},

DOI = {10.12688/f1000research.17456.1}

}

```



## Requirements

`pdb-tools` should run on Python 2.7+ and Python 3.x. We test on Python 2.7, 3.6,

and 3.7. There are no dependencies.



## Installing from Source

Download the zip archive or clone the repository with git. We recommend the `git`

approach since it makes updating the tools extremely simple.



```bash

# To download

git clone https://github.com/haddocking/pdb-tools

cd pdb-tools



# To update

git pull origin master



# To install

python setup.py install

```



## Contributing

If you want to contribute to the development of `pdb-tools`, provide a bug fix,

or a new tools, read our `CONTRIBUTING` instructions [here](https://github.com/haddocking/pdb-tools/blob/master/CONTRIBUTING.md).



## License

`pdb-tools` are open-source and licensed under the Apache License, version 2.0.

For details, see the LICENSE file.