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        "author": "Joao Rodrigues",
        "author_email": "j.p.g.l.m.rodrigues@gmail.com",
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            "Development Status :: 5 - Production/Stable",
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            "License :: OSI Approved :: Apache Software License",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Chemistry"
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        "description": "# pdb-tools\n\n[![PyPI version](https://badge.fury.io/py/pdb-tools.svg)](https://badge.fury.io/py/pdb-tools)\n[![Travis (.org) branch](https://img.shields.io/travis/haddocking/pdb-tools/master.svg?style=flat&label=TravisCI)](https://travis-ci.org/haddocking/pdb-tools)\n[![AppVeyor branch](https://img.shields.io/appveyor/ci/JoaoRodrigues/pdb-tools-2coq6.svg?style=flat&label=AppVeyor)](https://ci.appveyor.com/project/JoaoRodrigues/pdb-tools-2coq6)\n[![codecov](https://codecov.io/gh/haddocking/pdb-tools/branch/master/graph/badge.svg)](https://codecov.io/gh/haddocking/pdb-tools)\n[![DOI](https://zenodo.org/badge/27217350.svg)](https://zenodo.org/badge/latestdoi/27217350)\n\nA swiss army knife for manipulating and editing PDB files.\n\n\n## Looking for the _other_ pdb-tools?\nThe Harms lab maintains a set of tools also called `pdbtools`, which perform a\nslightly different set of functions. You can find them [here](https://github.com/harmslab/pdbtools).\n\n\n## About\nManipulating PDB files is often painful. Extracting a particular chain or set of\nresidues, renumbering residues, splitting or merging models and chains, or just\nensuring the file is conforming to the PDB specifications are examples of tasks\nthat can be done using any decent parsing library or graphical interface. These,\nhowever, almost always require 1) scripting knowledge, 2) time, and 3) installing\none or more programs.\n\n`pdb-tools` were designed to be a swiss-knife for the PDB format. They have no\nexternal dependencies, besides obviously the [Python programming language](http://www.python.org).\nThey are the descendant of a set of old FORTRAN77 programs that had the \nparticular advantage of working with streams, i.e. the output of one script \ncould be piped into another. Since FORTRAN77 is a pain too, I rewrote them in\nPython and added a few more utilities. \n\nThe philosophy of the scripts is simple: one script, one task. If you want to \ndo two things, pipe the scripts together. Requests for new scripts will be taken\ninto consideration - use the Issues button or write them yourself and create a\nPull Request.\n\n\n## Installation Instructions\n`pdb-tools` are available on PyPi and can be installed though `pip`. This is the\nrecommended way as it makes updating/uninstalling rather simple:\n```bash\npip install pdb-tools\n```\n\nIf you want to install the latest development version, which might give you new\nfeatures but also some bugs, see [here](#Installing-from-Source).\n\n\n## What can I do with them?\nThe names of the tools should be self-explanatory. Their command-line interface\nis also pretty consistent. Therefore, here is a couple of examples to get you\nstarted:\n\n* Downloading a structure\n   ```bash\n   pdb_fetch 1brs > 1brs.pdb  # 6 chains\n   pdb_fetch -biounit 1brs > 1brs.pdb  # 2 chains\n   ```\n\n* Renumbering a structure\n   ```bash\n   pdb_reres -1 1ctf.pdb > 1ctf_renumbered.pdb\n   ```\n\n* Selecting chain(s)\n   ```bash\n   pdb_selchain -A 1brs.pdb > 1brs_A.pdb\n   pdb_selchain -A,D 1brs.pdb > 1brs_AD.pdb\n   ```\n\n* Deleting hydrogens\n   ```bash\n   pdb_delelem -H 1brs.pdb > 1brs_noH.pdb\n   ```\n\n* Selecting backbone atoms\n   ```bash\n   pdb_selatom -CA,C,N,O 1brs.pdb > 1brs_bb.pdb\n   ```\n\n* Selecting chains, removing HETATM, and producing a valid PDB file\n  ```bash\n  pdb_selchain -A,D 1brs.pdb | pdb_delhetatm | pdb_tidy > 1brs_AD_noHET.pdb\n  ```\n\n*Note: On Windows the tools will have the `.exe` extension.*\n\n\n## What _can't_ I do with them?\nOperations that involve coordinates or numerical calculations are usually not in\nthe scope of `pdb-tools`. Use a proper library for that, it will be much faster\nand scalable. Also, although we provide mmCIF<->PDB converters, we do not support\nlarge mmCIF files with more than 99999 atoms, or 9999 residues in a single chain.\nOur tools will complain if you try using them on such a molecule. \n\n\n## Citation\nWe finally decided to write up a small publication describing the tools. If you\nused them in a project that is going to be published, please cite us:\n\n```\nRodrigues, J. P. G. L. M., Teixeira, J. M. C., Trellet, M. & Bonvin, A. M. J. J.\npdb-tools: a swiss army knife for molecular structures. bioRxiv (2018). \ndoi:10.1101/483305\n```\n\nIf you use a reference manager that supports BibTex, use this record:\n```\n@article {Rodrigues483305,\n  author = {Rodrigues, Jo{\\~a}o P.G.L.M. and Teixeira, Jo{\\~a}o M.C. and Trellet, Mika{\\\"e}l and Bonvin, Alexandre M.J.J.},\n  title = {pdb-tools: a swiss army knife for molecular structures},\n  elocation-id = {483305},\n  year = {2018},\n  doi = {10.1101/483305},\n  publisher = {Cold Spring Harbor Laboratory},\n  abstract = {The pdb-tools are a collection of Python scripts for working with molecular structure data in the PDB format. They allow users to edit, convert, and validate PDB files, from the command-line, in a simple but efficient manner. The pdb-tools are implemented in Python, without any external dependencies, and are freely available under the open-source Apache License at https://github.com/haddocking/pdb-tools/ and on PyPI (https://pypi.org/project/pdb-tools/).},\n  URL = {https://www.biorxiv.org/content/early/2018/12/04/483305},\n  eprint = {https://www.biorxiv.org/content/early/2018/12/04/483305.full.pdf},\n  journal = {bioRxiv}\n}\n```\n\n## Requirements\n`pdb-tools` should run on Python 2.7+ and Python 3.x. We test on Python 2.7, 3.6,\nand 3.7. There are no dependencies.\n\n\n## Installing from Source\nDownload the zip archive or clone the repository with git. We recommend the `git`\napproach since it makes updating the tools extremely simple.\n\n```bash\n# To download\ngit clone https://github.com/haddocking/pdb-tools\ncd pdb-tools\n\n# To update\ngit pull origin master\n\n# To install\npython setup.py install\n```\n\n## Contributing\nIf you want to contribute to the development of `pdb-tools`, provide a bug fix,\nor a new tools, read our `CONTRIBUTING` instructions [here](https://github.com/haddocking/pdb-tools/blob/master/CONTRIBUTING.md).\n\n## License\n`pdb-tools` are open-source and licensed under the Apache License, version 2.0.\nFor details, see the LICENSE file.\n\n",
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