BilayerAnalyzer analysis: `dc_cluster` - Hiearchical clustering of lipids based on distance.¶

Description¶

Compute lipid clusters using a hiearchical distance based method.

This analysis uses a type of hiearchical clustering where points (lipid centers of mass) are are added to a cluster if they are within a specified distance of any other point within the cluster.

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

Initiated by instance of:¶

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

Syntax¶

dc_cluster analysis-ID keyword value

dc_cluster = 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.
- cutoff (float): The cutoff distance to use for the clustering. Default: 12.0

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('dc_cluster dc_cluster_1') 

Add by string - adjust a setting:

analyzer.add_analysis('dc_cluster dc_cluster_1 resname POPC')

Add by list:

analyzer.add_analysis(list(['dc_cluster', 'dc_cluster_1', dict({'resname':'POPC'})]))

Add by dict:

analyzer.add_analysis(dict({'analysis_key': 'dc_cluster', 'analysis_id': 'dc_cluster_1','analysis_settings':dict({'resname':'POPC'})}))

To remove from analyzer:

analyzer.remove_analysis('dc_cluster_1')

Output Info:¶

Retrieve output after running analyses:

output = analyzer.get_analysis_data('dc_cluster_1')

The output is type <type 'dict'>

Note

Only finds the self clusters for a single lipid type as specified by the ```resname``` setting.

References¶

None

BilayerAnalyzer analysis: dc_cluster - Hiearchical clustering of lipids based on distance.¶