.. -*- coding: utf-8 -*- .. MDAnalysis documentation master file, created by .. sphinx-quickstart on Mon Sep 27 09:39:55 2010. .. You can adapt this file completely to your liking, but it should at least .. contain the root `toctree` directive. ############################### MDAnalysis documentation ############################### :Release: |release| :Date: |today| **MDAnalysis** (`www.mdanalysis.org`_) is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM_, Gromacs_, Amber_, NAMD_, LAMMPS_, `DL_POLY`_ and other packages; it also reads other formats (e.g., PDB_ files and `XYZ format`_ trajectories; see :ref:`Supported coordinate formats` and :ref:`Supported topology formats` for the full lists). It can write most of these formats, too, together with atom selections for use in Gromacs_, CHARMM_, VMD_ and PyMol_ (see :ref:`Selection exporters`). It allows one to read molecular dynamics trajectories and access the atomic coordinates through NumPy_ arrays. This provides a flexible and relatively fast framework for complex analysis tasks. Fairly complete atom :ref:`selection-commands-label` are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out in a range of formats. .. _`www.mdanalysis.org`: https://www.mdanalysis.org .. _NumPy: http://numpy.scipy.org .. _CHARMM: http://www.charmm.org/ .. _Amber: http://ambermd.org/ .. _LAMMPS: http://lammps.sandia.gov/ .. _NAMD: http://www.ks.uiuc.edu/Research/namd/ .. _Gromacs: http://www.gromacs.org/ .. _`DL_POLY`: http://www.scd.stfc.ac.uk//44516.aspx .. _VMD: http://www.ks.uiuc.edu/Research/vmd/ .. _PyMol: http://www.pymol.org/ .. _PDB: http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html .. _XYZ format: http://openbabel.org/wiki/XYZ_%28format%29 Getting involved ================ Please report **bugs** or **enhancement requests** through the `Issue Tracker`_. Questions can also be asked on the `GitHub Discussions`_. The MDAnalysis community subscribes to a `Code of Conduct`_ that all community members agree and adhere to --- please read it. .. _Issue Tracker: https://github.com/MDAnalysis/mdanalysis/issues .. _`GitHub Discussions`: https://github.com/MDAnalysis/mdanalysis/discussions .. _`Code of Conduct`: https://www.mdanalysis.org/pages/conduct/ User Guide ========== The MDAnalysis `User Guide`_ provides comprehensive information on how to use the library. We would recommend that new users have a look at the `Quick Start Guide`_. The User Guide also has a set of `examples`_ on how to use the MDAnalysis library which may be of interest. .. _`User Guide`: https://userguide.mdanalysis.org/stable/index.html .. _`Quick Start Guide`: https://userguide.mdanalysis.org/stable/examples/quickstart.html .. _`examples`: https://userguide.mdanalysis.org/stable/examples/README.html .. _installation-instructions: Installing MDAnalysis ===================== The easiest approach to `install the latest release`_ is to use a package that can be installed either with conda_ or pip_. conda ----- First installation with conda_: .. code-block:: bash conda config --add channels conda-forge conda install mdanalysis which will automatically install a *full set of dependencies*. To upgrade later: .. code-block:: bash conda update mdanalysis pip --- Installation with `pip`_ and a *minimal set of dependencies*: .. code-block:: bash pip install --upgrade MDAnalysis To install with a *full set of dependencies* (which includes everything needed for :mod:`MDAnalysis.analysis`), add the ``[analysis]`` tag: .. code-block:: bash pip install --upgrade MDAnalysis[analysis] Tests ----- If you want to `run the tests`_ or use example files to follow some of the examples in the documentation or the tutorials_, also install the ``MDAnalysisTests`` package: .. code-block:: bash conda install mdanalysistests # with conda pip install --upgrade MDAnalysisTests # with pip .. _install the latest release: https://userguide.mdanalysis.org/stable/installation.html#installation .. _pip: http://www.pip-installer.org/en/latest/index.html .. _conda: http://conda.pydata.org/docs/ .. _run the tests: https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests .. _tutorials: https://www.mdanalysis.org/pages/learning_MDAnalysis/ Source Code =========== **Source code** is available from https://github.com/MDAnalysis/mdanalysis/ and is packaged under the `GNU Public Licence, version 3 or any later version`_. Individual components of the source code are provided under GPL compatible licenses, details can be found in the `MDAnalysis license file`_. Obtain the sources with `git`_. .. code-block:: bash git clone https://github.com/MDAnalysis/mdanalysis.git The `User Guide`_ provides more information on how to `install the development version`_ of MDAnalysis. .. _GNU Public Licence, version 3 or any later version: https://www.gnu.org/licenses/gpl-3.0.en.html .. _MDAnalysis license file: https://github.com/MDAnalysis/mdanalysis/blob/develop/LICENSE .. _git: https://git-scm.com/ .. _`install the development version`: https://userguide.mdanalysis.org/stable/installation.html#development-versions Citation ======== When using MDAnalysis in published work, please cite [Michaud-Agrawal2011]_ and [Gowers2016]_. MDAnalysis also contains specific algorithms and whole analysis modules whose algorithms have also been published in the scientific literature. Please make sure to also reference any :ref:`references-components` in published work. Thank you! .. Hide the contents from the front page because they are already in .. the side bar in the Alabaster sphinx style; requires Alabaster .. config sidebar_includehidden=True (default) .. Contents .. ======== .. toctree:: :maxdepth: 4 :caption: Documentation :numbered: :hidden: ./documentation_pages/overview ./documentation_pages/topology ./documentation_pages/selections ./documentation_pages/analysis_modules ./documentation_pages/topology_modules ./documentation_pages/coordinates_modules ./documentation_pages/converters ./documentation_pages/trajectory_transformations ./documentation_pages/selections_modules ./documentation_pages/auxiliary_modules ./documentation_pages/core_modules ./documentation_pages/visualization_modules ./documentation_pages/lib_modules ./documentation_pages/version ./documentation_pages/units ./documentation_pages/exceptions ./documentation_pages/references Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`