BilayerAnalyzer analysis: `disp_vec_corr_avg` - Weighted average of displacement vector correlations.¶

Description¶

Compute the pair-wise cross correlation between pairs of the displacement vectors for each lipid in the specified leaflet(s) of bilayer and do a inverse-distance weighted averaging.

This analysis computes the displacement vectors as in DispVecProtocol, but then continues to compute the pair-wise cross correlations between each vector (i.e. the cos(theta) for the angle theta between the vectors) and averages the values using the inverse of the distance between the vector starting points as a weight.

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

Initiated by instance of:¶

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

Syntax¶

disp_vec_corr_avg analysis-ID keyword value

disp_vec_corr_avg = 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.
- 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_corr_avg disp_vec_corr_avg_1') 

Add by string - adjust a setting:

analyzer.add_analysis('disp_vec_corr_avg disp_vec_corr_avg_1 leaflet both')

Add by list:

analyzer.add_analysis(list(['disp_vec_corr_avg', 'disp_vec_corr_avg_1', dict({'leaflet':'both'})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'disp_vec_corr_avg', 'analysis_id': 'disp_vec_corr_avg_1','analysis_settings':dict({'leaflet':'both'})}))

To remove from analyzer:

analyzer.remove_analysis('disp_vec_corr_avg_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('disp_vec_corr_avg_1')

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

References¶

None

BilayerAnalyzer analysis: disp_vec_corr_avg - Weighted average of displacement vector correlations.¶