{ "info": { "author": "Woolfson Group, University of Bristol", "author_email": "chris.wood@bristol.ac.uk", "bugtrack_url": null, "classifiers": [ "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Natural Language :: English", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "# AMPAL\nA simple, intuitive and Pythonic framework for representing biomolecular structure.\n\n[![CircleCI](https://circleci.com/gh/isambard-uob/ampal/tree/master.svg?style=shield)](https://circleci.com/gh/isambard-uob/ampal/tree/master)\n[![Python Version](https://img.shields.io/badge/python-3.6-lightgrey.svg)]()\n[![MIT licensed](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/isambard-uob/ampal/blob/master/LICENSE)\n\n## Installation\n\nYou can install AMPAL from pip:\n\n`pip install ampal`\n\nOr from source by downloading/cloning this repository, navigating to the folder\nand typing:\n\n`pip install .`\n\nAMPAL uses Cython, so if you're installing from source make sure you have it\ninstalled.\n\n## Super Quick Start\n\nLoad a PDB file into AMPAL:\n\n```Python\nmy_structure = ampal.load_pdb('3qy1.pdb')\nprint(my_structure)\n# OUT: \n```\n\nSelect regions of the structure in an intuitive manner:\n\n```Python\nmy_atom = my_structure['A']['56']['CA']\nprint(my_structure['A']['56']['CA'])\n# OUT: \n```\n\nThen climb all the way back up the hierachy:\n\n```Python\nprint(my_atom.parent)\n# OUT: \nprint(my_atom.parent.parent)\n# OUT: \nprint(my_atom.parent.parent.parent)\n# OUT: \n```\n\nThis is just a quick introduction, AMPAL contain tonnes of tools for making\ncomplex selections and performing analysis. Take a look at the\n[docs](https://isambard-uob.github.io/ampal/) to find out more.\n\n## Release Notes\n\n## v1.4.0\n\n* **Adds `get_ss_regions` to `ampal.dssp`.** This function can be used to\n extract all regions of a protein in a particular secondary structure.\n* **Fixes bug with DSSP `ss_region` tagging.** End residues used to be missed.\n\n## v1.3.0\n\n* **Adds an interface for NACCESS.** Functions for using NACCESS to calculate\n solvent accessibility.\n\n### v1.2.0\n\n* **Adds an interface for DSSP.** If you have DSSP on your computer and have the\n `mkdssp` command available on your path, you can use the `ampal.tag_dssp_data`\n function to add secondary structure information to the tags dictionary of the\n residues in your structure.\n* **Adds the `ampal.align` module.** Contains a simple class for aligning two\n `Polypeptides` using MMC. 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