9. MDAnalysis library¶
MDAnalysis.lib.distances
contains many high performance
maths functions.
MDAnalysis.lib._distances
contains low level access to the
MDAnalysis’ Cython functions in distances. These have little to no
error checking done on inputs so should be used with
caution. MDAnalysis.lib.parallel
contains parallelized
implementations for some these algorithms.
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, string
and mathematical utility functions.
MDAnalysis.lib.NeighborSearch
contains classes to do neighbor searches- with MDAnalysis objects.
- 9.1. Fast distance array computation —
MDAnalysis.lib.distances
- 9.2. Distance calculation library —
MDAnalysis.lib._distances
- 9.3. Neighbor Search wrapper for MDAnalysis — :mod: MDAnalysis.lib.NeighborSearch
- 9.4. Setting up logging —
MDAnalysis.lib.log
- 9.5. Mathematical helper functions —
MDAnalysis.lib.mdamath
- 9.6. Parallel algorithms for MDAnalysis
- 9.7. Homogeneous Transformation Matrices and Quaternions —
MDAnalysis.lib.transformations
- 9.8. Fast QCP RMSD structure alignment —
MDAnalysis.lib.qcprot
- 9.9. Helper functions —
MDAnalysis.lib.util