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+title: 'pdb-tools'
+headline: ''
+
+logo: /logo/pdb-tools.png
+show_downloads: true
+description: 'A swiss army knife for editing PDB files.'
+theme: jekyll-theme-minimal
+github:
+  zip_url: https://github.com/JoaoRodrigues/pdb-tools/archive/2.0.0-beta.1.zip
+  tar_url: https://github.com/JoaoRodrigues/pdb-tools/archive/2.0.0-beta.1.tar.gz

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+---
+---
+
+@import "{{ site.theme }}";
+
+/* Pad image bottom */
+.wrapper img {
+    padding-bottom: 1%;
+}
+
+/* Remove bullets from ordered lists */
+ul {
+  list-style-type: none;
+  padding: 0;
+  margin: 0;
+}

docs/index.md

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+---
+layout: default
+---
+
+A swiss army knife for manipulating and editing PDB files.
+
+
+## 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
+```
+
+If you want to install the latest development version, which might give you new
+features but also some bugs, see [here](#Installing-from-Source).
+
+
+## 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. 
+
+
+## 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 army knife for the PDB format. 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.
+
+
+## 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).
+
+
+## Citation
+There is no publication (yet!) for pdb-tools, but if you use them and want to
+cite them use this [DOI](http://dx.doi.org/10.5281/zenodo.31158) item.
+
+[![DOI](https://zenodo.org/badge/18453/haddocking/pdb-tools.svg)](https://zenodo.org/badge/latestdoi/18453/haddocking/pdb-tools)
+
+
+## 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/JoaoRodrigues/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/JoaoRodrigues/pdb-tools/blob/version2/CONTRIBUTING.md).
+
+## License
+`pdb-tools` are open-source and licensed under the Apache License, version 2.0.
+For details, see the LICENSE file.