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# 3. Analysis modules

The `MDAnalysis.analysis` module contains code to carry out specific analysis functionality. 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.

Please see the individual module documentation for additional references and citation information.

These modules are not imported by default; in order to use them one has to import them from `MDAnalysis.analysis`, for instance

    import MDAnalysis.analysis.align

Note

Some of the modules require additional Python packages such as `scipy` from the SciPy package or `networkx` from NetworkX. These package are not automatically installed (although one can add the `[analysis]` requirement to the easy_install command line to force their installation.

Contents

- 3.1. Coordinate fitting and alignment — `MDAnalysis.analysis.align`
- 3.2. Native contacts analysis — `MDAnalysis.analysis.contacts`
- 3.3. Generating densities from trajectories — `MDAnalysis.analysis.density`
- 3.4. Distance analysis — `MDAnalysis.distances`
- 3.5. Elastic network analysis of MD trajectories — `MDAnalysis.analysis.gnm`
- 3.6. Hydrogen Bond analysis — `MDAnalysis.analysis.hbonds`
- 3.7. HELANAL — analysis of protein helices
- 3.8. Generation and Analysis of HOLE pore profiles — `MDAnalysis.analysis.hole`
- 3.9. Leaflet identification — `MDAnalysis.analysis.leaflet`
- 3.10. Nucleic acid analysis — `MDAnalysis.analysis.nuclinfo`
- 3.11. Calculating root mean square quantities — `MDAnalysis.analysis.rms`

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