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