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