11.1. Betweenness¶

This is the function that does the betweenness calculation

current_flow_allostery.betweenness.betweenness(inDir, outDir, interactionFileName, outputFileNameBase='NO_NAME', selectionQueryStrings=None, nodeColumns=['Resid_1', 'Resid_2'], energyColumn='TOTAL', sourceNodeNames=None, targetNodeNames=None, writeFullTable=False, writeNodeVector=True, writeMatrixIndexToNodeNameMap=True, dryrun=False, verbose=True, verboseLevel=0)[source]¶

This function is the main function to call for the betweenness calculation. NOTE: This function take a total of 15 variables, make sure to give them a check and see what each option does

inDir INPUT SHOULD BE GIVEN outDir INPUT SHOULD BE GIVEN interactionFileName INPUT MUST BE GIVEN outputFileNameBase ‘NO_NAME’ selectionQueryStrings None nodeColumns [‘Resid_1’,’Resid_2’] energyColumn ‘TOTAL’ sourceNodeNames None ### INPUT MUST BE SET targetNodeNames None ### INPUT MUST BE SET writeFullTable False writeNodeVector True writeMatrixIndexToNodeNameMap True dryrun False verbose True verboseLevel 0

Example

current_flow_allostery.betweenness( ‘{1}’, ‘{2}’, ‘{3}.csv’, ‘{3}.Betweenness’, sourceNodeNames=[‘14’,’240’,’466’,’692’,’918’,’1144’], targetNodeNames=[‘47’,’273’,’499’,’725’,’951’,’1177’], writeFullTable=True, verboseLevel=2 )

If there are multiple files to be run, this can be ran parallel following the example in Step1_Run_GB_Network_Betweenness.slurm.bash.

sourceNodeNames & targetNodeNames format is : [‘#’,’#’,’#’,’#’] keep in mind if following format is used it will produce “key error” [#,#,#,#]