BilayerAnalyzer analysis: apl_grid - Area per lipid using 2D lipid grids.

Description

Estimate the indvidual area per lipid for each lipid type using a gridding procedure.

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

Initiated by instance of:

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

Syntax

apl_grid analysis-ID

  • apl_grid = analysis-Key - keyword/name for this analysis.

  • analysis-ID = The unique name/ID being assigned to this analysis.

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('apl_grid apl_grid_1')

Add by string - adjust a setting:

analyzer.add_analysis('apl_grid apl_grid_1 none None')

Add by list:

analyzer.add_analysis(list(['apl_grid', 'apl_grid_1', dict({'none':None})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'apl_grid', 'analysis_id': 'apl_grid_1','analysis_settings':dict({'none':None})}))

To remove from analyzer:

analyzer.remove_analysis('apl_grid_1')

Output Info:

Retrieve output after running analyses:

output = analyzer.get_analysis_data('apl_grid_1')

The output is type <type 'dict'>

References

  1. Allen et al. Vol. 30, No. 12 Journal of Computational Chemistry

  2. Gapsys et al. J Comput Aided Mol Des (2013) 27:845-858