1Metadata-Version: 2.1 2Name: MDAnalysis 3Version: 0.19.2 4Summary: An object-oriented toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber. 5Home-page: https://www.mdanalysis.org 6Author: Naveen Michaud-Agrawal 7Author-email: naveen.michaudagrawal@gmail.com 8Maintainer: Richard Gowers 9Maintainer-email: mdnalysis-discussion@googlegroups.com 10License: GPL 2 11Download-URL: https://github.com/MDAnalysis/mdanalysis/releases 12Project-URL: Documentation, https://www.mdanalysis.org/docs/ 13Project-URL: Issue Tracker, https://github.com/mdanalysis/mdanalysis/issues 14Project-URL: User Group, https://groups.google.com/forum/#!forum/mdnalysis-discussion 15Project-URL: Source, https://github.com/mdanalysis/mdanalysis 16Description: .. Summary for PyPI 17 .. https://pypi.python.org/project/MDAnalysis/ 18 19 |build| |cov| |docs| |usergroup| |developergroup| |anaconda| |mybinder| 20 21 22 MDAnalysis_ is an object-oriented python toolkit to analyze molecular 23 dynamics trajectories generated by CHARMM_, Gromacs_, Amber_, NAMD_, 24 or LAMMPS_; it also reads other formats (e.g. PDB_ files and `XYZ 25 format`_ trajectories; see the `Table of Supported Coordinate 26 Formats`_ and `Table of Supported Topology Formats`_ for details). It 27 can write most of the coordinate formats, too, together with atom 28 selections for use in Gromacs_, CHARMM_, VMD_ and PyMOL_ (see 29 `Selection exporters`_). 30 31 MDAnalysis allows one to read molecular dynamics trajectories and 32 access the atomic coordinates through NumPy_ arrays. This provides a 33 flexible and relatively fast framework for complex analysis tasks that 34 integrates well with the wider Python ecosystem. Fairly complete `atom 35 selection commands`_ are implemented. Trajectories can also be 36 manipulated (for instance, fit to a reference structure) and written 37 out in a range of formats. 38 39 40 Availability 41 ============ 42 43 **Source code** is available from https://www.mdanalysis.org under the `GNU 44 Public Licence, version 2`_, together with the `online 45 documentation`_. **Packages** can be downloaded from 46 https://pypi.org/project/MDAnalysis/ or installed/upgraded via PyPI using `pip`_:: 47 48 pip install --upgrade MDAnalysis 49 50 By default MDAnalysis does not install every dependency needed to run every 51 analysis available in the analysis module or read netcdf Amber_ trajectories. 52 To install and update these dependencies as well run :: 53 54 pip install --upgrade 'MDAnalysis[analysis,AMBER] 55 56 Please report **bugs** or **enhancement requests** through the `Issue 57 Tracker`_. Questions can also be asked on the `mdnalysis-discussion mailing 58 list`_. 59 60 In order to run the `Unit Tests`_ it is also necessary to install a 61 separate package MDAnalysisTests_ containing the test and test 62 data. As it contains about 70 MB of molecular dynamics trajectories 63 and simulation system structures it is not included with the library 64 itself. 65 66 67 Citation 68 ======== 69 70 When using MDAnalysis in published work, please cite the following 71 two papers: 72 73 * R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, 74 M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, 75 S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: 76 A Python package for the rapid analysis of molecular 77 dynamics simulations. In S. Benthall and S. Rostrup, 78 editors, Proceedings of the 15th Python in Science 79 Conference, pages 102-109, Austin, TX, 2016. SciPy. 80 81 * N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, 82 and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular 83 Dynamics Simulations. *J. Comput. Chem.* **32** (2011), 2319--2327. 84 doi:`10.1002/jcc.21787`_ 85 86 For citations of included algorithms and sub-modules please see the references_. 87 88 89 .. Links 90 91 .. _MDAnalysis: https://www.mdanalysis.org 92 .. _`10.1002/jcc.21787`: https://dx.doi.org/10.1002/jcc.21787 93 .. _references: https://docs.mdanalysis.org/documentation_pages/references.html 94 .. _GNU Public Licence, version 2: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html 95 .. _Issue Tracker: https://github.com/mdanalysis/mdanalysis/issues 96 .. _`mdnalysis-discussion mailing list`: 97 https://groups.google.com/group/mdnalysis-discussion 98 .. _`online documentation`: 99 https://docs.mdanalysis.org 100 .. _`Table of Supported Coordinate Formats`: 101 https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1 102 .. _`Table of Supported Topology Formats`: 103 https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats 104 .. _`atom selection commands`: 105 https://docs.mdanalysis.org/documentation_pages/selections.html#selection-commands 106 .. _`Selection exporters`: 107 https://docs.mdanalysis.org/documentation_pages/selections_modules.html#selection-exporters 108 .. _NumPy: https://numpy.scipy.org 109 .. _CHARMM: https://www.charmm.org/ 110 .. _Amber: http://ambermd.org/ 111 .. _LAMMPS: http://lammps.sandia.gov/ 112 .. _NAMD: http://www.ks.uiuc.edu/Research/namd/ 113 .. _Gromacs: http://www.gromacs.org/ 114 .. _VMD: http://www.ks.uiuc.edu/Research/vmd/ 115 .. _PyMOL: https://www.pymol.org/ 116 .. _PDB: https://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html 117 .. _XYZ format: https://openbabel.org/wiki/XYZ_%28format%29 118 119 .. _Unit Tests: https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests 120 .. _MDAnalysisTests: https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysisTests 121 122 .. _`pip`: https://www.pip-installer.org/en/latest/index.html 123 124 125 .. badges 126 .. |usergroup| image:: https://img.shields.io/badge/Google%20Group-Users-lightgrey.svg 127 :alt: User Google Group 128 :target: http://users.mdanalysis.org 129 130 .. |developergroup| image:: https://img.shields.io/badge/Google%20Group-Developers-lightgrey.svg 131 :alt: Developer Google Group 132 :target: http://developers.mdanalysis.org 133 134 .. |docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg 135 :alt: Documentation (latest release) 136 :target: https://docs.mdanalysis.org 137 138 .. |build| image:: https://travis-ci.org/MDAnalysis/mdanalysis.svg?branch=develop 139 :alt: Build Status 140 :target: https://travis-ci.org/MDAnalysis/mdanalysis 141 142 .. |cov| image:: https://codecov.io/gh/MDAnalysis/mdanalysis/branch/develop/graph/badge.svg 143 :alt: Coverage Status 144 :target: https://codecov.io/gh/MDAnalysis/mdanalysis 145 146 .. |anaconda| image:: https://anaconda.org/conda-forge/mdanalysis/badges/version.svg 147 :alt: Anaconda 148 :target: https://anaconda.org/conda-forge/mdanalysis 149 150 .. |mybinder| image:: https://mybinder.org/badge.svg 151 :alt: My Binder 152 :target: https://mybinder.org/v2/gh/MDAnalysis/binder-notebook/master 153 154 155Platform: UNKNOWN 156Classifier: Development Status :: 4 - Beta 157Classifier: Environment :: Console 158Classifier: Intended Audience :: Science/Research 159Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2) 160Classifier: Operating System :: POSIX 161Classifier: Operating System :: MacOS :: MacOS X 162Classifier: Operating System :: Microsoft :: Windows 163Classifier: Programming Language :: Python 164Classifier: Programming Language :: Python :: 2 165Classifier: Programming Language :: Python :: 2.7 166Classifier: Programming Language :: Python :: 3 167Classifier: Programming Language :: Python :: 3.4 168Classifier: Programming Language :: Python :: 3.5 169Classifier: Programming Language :: Python :: 3.6 170Classifier: Programming Language :: C 171Classifier: Topic :: Scientific/Engineering 172Classifier: Topic :: Scientific/Engineering :: Bio-Informatics 173Classifier: Topic :: Scientific/Engineering :: Chemistry 174Classifier: Topic :: Software Development :: Libraries :: Python Modules 175Requires: numpy (>=1.10.4) 176Requires: biopython (>= 1.71) 177Requires: mmtf (>=1.0.0) 178Requires: networkx (>=1.0) 179Requires: GridDataFormats (>=0.3.2) 180Requires: joblib 181Requires: scipy (>=1.0.0) 182Requires: matplotlib (>=1.5.1) 183Provides: MDAnalysis 184Description-Content-Type: text/x-rst 185Provides-Extra: analysis 186Provides-Extra: AMBER 187