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MolClustPy / SpringSaLaD-Python-Viz

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Reproduce Figure 1G for SpringSalad: average number of bonds per site and per molecule #7

Open vcellmike opened 1 month ago

vcellmike commented 1 month ago

See the FIGURE 1G: number of bonds per molecule - take average bonds for all sites of a given molecule, add their occupancies numbers, and divide by the total number of sites in the system. For NWasp the total number of sites is 6*10 (only PRM).

Modify the Figure 1G to display number of bonds per site - take average bonds for the specified type of a given molecule, add their occupancies numbers, and divide by the total number of sites of this type in the system. For Nick the total number of sites of the type SH2 is 120 and SH3 is 320.

vcellmike commented 3 weeks ago

To find average number of bonds, process /Users/mblinov/Software/SpringSaLaD-Python-Viz/Examples/Nephrin-Nck-NWasp/Final_version_test_SIMULATIONS/Simulation0_SIM_FOLDER/data/Simulation0_SIM_AverageBondCounts....txt Sum up over all sites on a given molecule.