9. 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.
9.1. 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.
9.2. List of modules¶
- 9.2.1. Fast distance array computation —
MDAnalysis.lib.distances
- 9.2.2. Low-level modules for
MDAnalysis.lib.distances
- 9.2.3. Neighbor Search wrapper for MDAnalysis —
MDAnalysis.lib.NeighborSearch
- 9.2.4. Setting up logging —
MDAnalysis.lib.log
- 9.2.5. Mathematical helper functions —
MDAnalysis.lib.mdamath
- 9.2.6. Homogeneous Transformation Matrices and Quaternions —
MDAnalysis.lib.transformations
- 9.2.7. Fast QCP RMSD structure alignment —
MDAnalysis.lib.qcprot
- 9.2.8. Helper functions —
MDAnalysis.lib.util