BilayerAnalyzer analysis: `lipid_length` - Lipid length using the lipid vectors.¶

Description¶

Estimate the lipids length using the defined lipid vector.

This analysis is used to compute the mean lipid length using the vector represetation of the specified lipids.

This protocol is identified by the analysis key: ‘lipid_length’

Initiated by instance of:¶

<class 'pybilt.bilayer_analyzer.analysis_protocols.LipidLengthProtocol'>

Syntax¶

lipid_length analysis-ID keyword value

lipid_length = analysis-Key - keyword/name for this analysis.
analysis-ID = The unique name/ID being assigned to this analysis.
keyword value = settings keyword value pairs
- leaflet (str: ‘both’, ‘upper’, or ‘lower’): Specifies the bilayer leaflet to include in the estimate. Default: ‘both’
- resname (str): Specify the resname of the lipid type to include in this analysis. Default: ‘all’, averages over all lipid types.

Examples¶

Construct analyzer:

analyzer = BilayerAnalyzer(structure='name_of_structure_file',
                           trajectory='name_of_traj_file',
                           selection='resname POPC DOPC')

Add by string - use default settings:

analyzer.add_analysis('lipid_length lipid_length_1') 

Add by string - adjust a setting:

analyzer.add_analysis('lipid_length lipid_length_1 leaflet both')

Add by list:

analyzer.add_analysis(list(['lipid_length', 'lipid_length_1', dict({'leaflet':'both'})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'lipid_length', 'analysis_id': 'lipid_length_1','analysis_settings':dict({'leaflet':'both'})}))

To remove from analyzer:

analyzer.remove_analysis('lipid_length_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('lipid_length_1')

The output is type <type 'numpy.ndarray'>

References¶

Anton O. Chugunov, Pavel E. Volynsky, Nikolay A. Krylov, Ivan A. Boldyrev, and Roman G. Efremov, Liquid but Durable: Molecular Dynamics Simulations Explain the Unique Properties of Archaeal-Like Membranes, Scientific Reports, 4:7462, 2014, doi:10.1038/srep07462 (https://www.nature.com/articles/srep07462)

BilayerAnalyzer analysis: lipid_length - Lipid length using the lipid vectors.¶