Using Scripts

We use scripts to use the functionalities offered by cytocalc. Scripts provide an interface for using cytocalc while maintaining a relatively stable ‘core’ functions. System specific information (file structure, folder names etc.) are handled using the scripts, which hence change more often than code in the src folder (eg: function for computing network radius) which doesn’t have to be modified a lot.

The scripts directory provides a few pre-made scripts for some common systems. These are intended to be used as a starting point for creating more complex scripts.

Example

Suppose we would like to measure the Mean Squared Displacement of brownian particles using the diffusing_bead_msd.py script. The simulation details which the script has been designed for are as follows:

• Initialize N beads, non interacting

• Run the simulation for T time

• Use reportF to produce report files in <directory>

To run the script, we must first ensure that the cytocalc is available in the current python environment. This can be done by switching to the virtual environment created during Installation.

$ source $CYTOCALCPATH/.venv/bin/activate

where $CYTOCALCPATH is the path to the local Cytocalc repository. We can now run the script with the directory location as the argument.

(.venv) $ $CYTOCALCPATH/scripts/diffusing_bead_msd.py <directory>