12. Library functions — MDAnalysis.lib¶
MDAnalysis.lib contains code that is independent of the
specific MDAnalysis framework, such as fast calculators for distances
or simple logging support. Modules do not depend on other code inside
MDAnalysis except in MDAnalysis.lib itself (and possibly in
MDAnalysis.exceptions) and thus can be easily imported
elsewhere.
12.1. Overview¶
MDAnalysis.lib.distances contains many high performance maths
functions. Most of them have the keyword backend that allows one to
either select serial (single threaded) code (backend="serial) or
to use parallelized versions (e.g. backend="OpenMP" for OpenMP
parallelism).
MDAnalysis.lib.transformations contains a multitude of
matrix operations for manipulating coordinate data.
MDAnalysis.lib.qcprot contains a fast implementation of
superposition by minimizing the RMSD.
MDAnalysis.lib.util contains various file and string utility
functions whereas mathematical functions are to be found in
MDAnalysis.lib.mdamath.
MDAnalysis.lib.NeighborSearch contains classes to do neighbor
searches with MDAnalysis objects.
12.2. List of modules¶
- 12.2.1. Fast distance array computation —
MDAnalysis.lib.distances - 12.2.2. Low-level modules for
MDAnalysis.lib.distances - 12.2.3. Neighbor Search wrapper for MDAnalysis —
MDAnalysis.lib.NeighborSearch - 12.2.4. Setting up logging —
MDAnalysis.lib.log - 12.2.5. Mathematical helper functions —
MDAnalysis.lib.mdamath - 12.2.6. Homogeneous Transformation Matrices and Quaternions —
MDAnalysis.lib.transformations - 12.2.7. Fast QCP RMSD structure alignment —
MDAnalysis.lib.qcprot - 12.2.8. Helper functions —
MDAnalysis.lib.util
12.3. Low level file formats¶
The modules in MDAnalysis.lib.formats contain code to access various file
formats in a way that is independent from other MDAnalysis functionality
(i.e., they do not use any classes from MDAnalysis.core or
MDAnalysis.topology). This low-level code is used in the
MDAnalysis.coordinates module but can also be re-used by other
Python-based projects.