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Library functions --- :mod:`MDAnalysis.lib`

.. module:: MDAnalysis.lib
   :synopsis: ``lib`` collects independent code for re-use in MDAnalysis

:mod:`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 :mod:`MDAnalysis.lib` itself (and possibly in :mod:`MDAnalysis.exceptions`) and thus can be easily imported elsewhere.

Overview

:mod:`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).

:mod:`MDAnalysis.lib.transformations` contains a multitude of matrix operations for manipulating coordinate data.

:mod:`MDAnalysis.lib.qcprot` contains a fast implementation of superposition by minimizing the RMSD.

:mod:`MDAnalysis.lib.util` contains various file and string utility functions whereas mathematical functions are to be found in :mod:`MDAnalysis.lib.mdamath`.

A number of modules are concerned with finding neighbors. :mod:`MDAnalysis.lib.NeighborSearch` contains high-level classes to do neighbor searches with MDAnalysis objects. :mod:`MDAnalysis.lib.nsgrid` contains a fast implementation of grid neighbor search whereas :mod:`MDAnalysis.lib.pkdtree` uses KDTrees (with periodic images) for neighbor searching. Some of the functions in :mod:`MDAnalysis.lib.distances` user either of these algorithms to speed up distance calculations.

List of modules

.. toctree::
   :maxdepth: 1

   ./lib/distances
   ./lib/NeighborSearch
   ./lib/nsgrid
   ./lib/pkdtree
   ./lib/log
   ./lib/mdamath
   ./lib/transformations
   ./lib/qcprot
   ./lib/util
   ./lib/correlations
   ./lib/picklable_file_io

Low level file formats

The modules in :mod:`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 :mod:`MDAnalysis.core` or :mod:`MDAnalysis.topology`). This low-level code is used in the :mod:`MDAnalysis.coordinates` module but can also be re-used by other Python-based projects.

.. toctree::
   :maxdepth: 1

   ./lib/formats/libmdaxdr
   ./lib/formats/libdcd

Libmdanalysis

The :file:`__init__.pxd` file in :mod:`MDAnalysis.lib.libmdanalysis` provides a single place to cimport MDAnalysis' public Cython headers. This is recommended for advanced developers only.

For example, imagine we are writing a Cython extension module in :mod:`MDAnalysis.lib` and we would like to make a function that creates a :class:`MDAnalysis.coordinates.timestep.Timestep`

from MDAnalysis.lib.libmdanalysis cimport timestep
# or we could use the relative cimport
# from .libmdanalysis cimport timestep

cdef timestep.Timestep make_timestep(int natoms):
   cdef timestep.Timestep ts = timestep.Timestep(natoms)
   return ts

Currently modules that are exposed as public Cython headers are:

For more details consult the source :mod:`MDAnalysis.lib.libmdanalysis.__init__.pxd`