4.5.1. HOLE analysis — `MDAnalysis.analysis.hole2`

Author:: Lily Wang
Year:: 2020
Copyright:: Lesser GNU Public License v2.1+

Added in version 1.0.0.

This module provides an updated interface for the HOLE suite of tools [1][2] to analyse an ion channel pore or transporter pathway [3] as a function of time or arbitrary order parameters. It replaces MDAnalysis.analysis.hole.

HOLE must be installed separately and can be obtained in binary form from http://www.holeprogram.org/ or as source from https://github.com/osmart/hole2. (HOLE is open source and available under the Apache v2.0 license.)

Deprecated since version 2.8.0: This module is deprecated in favour of the mdakit mdahole2 and will be removed in MDAnalysis 3.0.0.

4.5.1.1. See Also

mdahole2.analysis.hole

4.5.1.2. Module

4.5.1.2.1. HOLE Analysis — `MDAnalysis.analysis.hole2`

Author:: Lily Wang
Year:: 2020
Copyright:: Lesser GNU Public License v2.1+

Added in version 1.0.0.

This module contains the tools to interface with HOLE [1][2] to analyse an ion channel pore or transporter pathway [3].

4.5.1.3. Utility functions and templates

4.5.1.3.1. HOLE Analysis — `mdahole2.analysis.utils`

Author:: Lily Wang
Year:: 2020
Copyright:: GNU Public License v3

Helper functions used in mdahole2.analysis.hole

4.5.1.3.2. HOLE Analysis — `mdahole2.analysis.templates`

Author:: Lily Wang
Year:: 2020
Copyright:: GNU Public License v3

Templates used in mdahole2.analysis.hole

4.5.1. HOLE analysis — MDAnalysis.analysis.hole2