.. Contains the formatted docstrings from the analysis modules located in 'mdanalysis/MDAnalysis/analysis', although in some cases the documentation imports functions and docstrings from other files which are also curated to reStructuredText markup. **************** Analysis modules **************** The :mod:`MDAnalysis.analysis` module contains code to carry out specific analysis functionality for MD trajectories. It is based on the core functionality (i.e. trajectory I/O, selections etc). The analysis modules can be used as examples for how to use MDAnalysis but also as working code for research projects; typically all contributed code has been used by the authors in their own work. An analysis using the available modules usually follows the same structure #. Import the desired module, since analysis modules are not imported by default. #. Initialize the analysis class instance from the previously imported module. #. Run the analysis, optionally for specific trajectory slices. #. Access the analysis from the :attr:`results` attribute .. code-block:: python from MDAnalysis.analysis import ExampleAnalysisModule # (e.g. RMSD) analysis_obj = ExampleAnalysisModule.AnalysisClass(universe, ...) analysis_obj.run(start=start_frame, stop=stop_frame, step=step) print(analysis_obj.results) Please see the individual module documentation for any specific caveats and also read and cite the reference papers associated with these algorithms. .. rubric:: Additional dependencies Some of the modules in :mod:`MDAnalysis.analysis` require additional Python packages to enable full functionality. For example, :mod:`MDAnalysis.analysis.encore` provides more options if `scikit-learn`_ is installed. If you installed MDAnalysis with :program:`pip` (see :ref:`installation-instructions`) these packages are *not automatically installed*. Although, one can add the ``[analysis]`` tag to the :program:`pip` command to force their installation. If you installed MDAnalysis with :program:`conda` then a *full set of dependencies* is automatically installed. Other modules require external programs. For instance, the :mod:`MDAnalysis.analysis.hole2.hole` module requires an installation of the HOLE_ suite of programs. You will need to install these external dependencies by following their installation instructions before you can use the corresponding MDAnalysis module. .. _scikit-learn: http://scikit-learn.org/ .. _HOLE: http://www.holeprogram.org/ Building blocks for Analysis ============================ The building block for the analysis modules is :class:`MDAnalysis.analysis.base.AnalysisBase`. To build your own analysis class start by reading the documentation. .. toctree:: :maxdepth: 1 analysis/base Distances and contacts ====================== .. toctree:: :maxdepth: 1 analysis/align analysis/contacts analysis/distances analysis/rms analysis/psa analysis/encore analysis/bat Hydrogen bonding ================ .. toctree:: :maxdepth: 1 analysis/hydrogenbonds analysis/hbond_autocorrel analysis/wbridge_analysis Deprecated modules: .. toctree:: :maxdepth: 1 analysis/hbond_autocorrel_deprecated Membranes and membrane proteins =============================== .. toctree:: :maxdepth: 1 analysis/hole2 analysis/leaflet Nucleic acids ============= .. toctree:: :maxdepth: 1 analysis/nuclinfo analysis/nucleicacids Polymers ======== .. toctree:: :maxdepth: 1 analysis/polymer Structure ========= Macromolecules -------------- .. toctree:: :maxdepth: 1 analysis/gnm analysis/helix_analysis analysis/dihedrals Liquids ------- .. toctree:: :maxdepth: 1 analysis/rdf analysis/msd Volumetric analysis =================== .. toctree:: :maxdepth: 1 analysis/density analysis/lineardensity analysis/waterdynamics analysis/dielectric Dimensionality Reduction ======================== .. toctree:: :maxdepth: 1 analysis/diffusionmap analysis/pca Legacy analysis modules ======================= The :mod:`MDAnalysis.analysis.legacy` module contains code that for a range of reasons is not as well maintained and tested as the other analysis modules. *Use with care.* .. toctree:: :maxdepth: 1 analysis/legacy_modules Data ==== .. toctree:: :maxdepth: 1 analysis/data