BilayerAnalyzer analysis: `disp_vec_nncorr` - Displacement vector nearest neigbor correlations.¶

Description¶

Comute the pair-wise cross correlations for the displacement vectors for each lipid in the specified leaflet(s) of bilayer and its nearest neighbor.

This analysis computes the displacement vectors as in the ‘disp_vec’ analysis (DispVecProtocol), but then continues to compute the pair-wise cross correlation between each vector and its nearest neighbor. i.e. the cos(theta) for the angle theta between the vectors.

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

Initiated by instance of:¶

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

Syntax¶

disp_vec_nncorr analysis-ID keyword value

disp_vec_nncorr = 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’, includes all lipid types.
- interval (int): Sets the frame interval over which to compute the displacement vectors. f
- wrapped (bool): Specify whether to use the wrapped (‘True’) or un-wrapped (‘False’) coordintes for the base of the vectors. Default: False

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('disp_vec_nncorr disp_vec_nncorr_1') 

Add by string - adjust a setting:

analyzer.add_analysis('disp_vec_nncorr disp_vec_nncorr_1 leaflet both')

Add by list:

analyzer.add_analysis(list(['disp_vec_nncorr', 'disp_vec_nncorr_1', dict({'leaflet':'both'})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'disp_vec_nncorr', 'analysis_id': 'disp_vec_nncorr_1','analysis_settings':dict({'leaflet':'both'})}))

To remove from analyzer:

analyzer.remove_analysis('disp_vec_nncorr_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('disp_vec_nncorr_1')

The output is type <type 'list'>

References¶

None

BilayerAnalyzer analysis: disp_vec_nncorr - Displacement vector nearest neigbor correlations.¶