4. Analysis modules¶
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
Some of the modules require additional Python packages such as
from the SciPy package. These package are not automatically installed
(although one can add the
[analysis] requirement to the pip
command line to force their installation.
4.1. Building blocks for Analysis¶
4.2. Distances and contacts¶
- 4.2.1. Coordinate fitting and alignment —
- 4.2.2. Native contacts analysis —
- 4.2.3. Distance analysis —
- 4.2.4. Calculating root mean square quantities —
- 4.2.5. Calculating path similarity —
- 4.2.6. ENCORE Ensemble Similarity Calculations —
4.3. Hydrogen bonding¶
4.4. Membranes and membrane proteins¶
4.5. Nucleic acids¶
4.8. Volumetric analysis¶
4.9. Dimensionality Reduction¶
4.10. Legacy analysis modules¶
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.