Vesicles datasets

The MDAnalysisData.vesicles module gives access to structures of vesicle models. These models were constructed with the coarse grained Martini force field. The data can be used to analyze lipid membranes and to test working with large coarse grained systems.

fetch_vesicle_lib([data_home, …])

Load the vesicle library dataset

Large System Vesicle Benchmark Library

Large benchmark systems for MDAnalysis (and other codes)

Coarse-grained (DryMartini force field) vesicle systems were generated with the scripts in the vesicle_library by Ian Kenney. All files are in GRO format and contain a static system. For further details about the data set see [Kenney2015].

The files are placed into the Public Domain (made available under the CC0 license).

system

# particles

1_75M

1748952

3_5M

3497904

10M

10074000

Notes

Data set characteristics:

size

807 MB

number of structures

3

number of frames

1

number of particles

varies

creator

Ian Kenney

URL

10.6084/m9.figshare.3406708.v1

license

CC0

reference

[Kenney2015]

Kenney2015(1,2)

M. Kenney, I. and Beckstein, O. (2015) Technical Report: SPIDAL Summer REU 2015: Biomolecular benchmark systems. figshare. doi: 10.6084/m9.figshare.1588804.v1.

MDAnalysisData.vesicles.fetch_vesicle_lib(data_home=None, download_if_missing=True)[source]

Load the vesicle library dataset

Parameters
  • data_home (optional, default: None) – Specify another download and cache folder for the datasets. By default all MDAnalysisData data is stored in ‘~/MDAnalysis_data’ subfolders. This dataset is stored in <data_home>/vesicle_library.

  • download_if_missing (optional, default=True) – If False, raise a IOError if the data is not locally available instead of trying to download the data from the source site.

Returns

  • dataset (dict-like object with the following attributes:)

  • dataset.structures (list) – list with filenames of the different vesicle systems (in GRO format)

  • dataset.N_structures (int) – number of structures

  • dataset.labels (list) – descriptors of the files in dataset.structures (same order), giving their approximate sizes in number of particles

  • dataset.DESCR (string) – Description of the ensemble

See Large System Vesicle Benchmark Library for description.