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######### Directory structure ##########
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1. ./SinglePolymer			- Contains all the simulation and output data of the single globular domain polymer BioNet simulations
   ./SinglePolymer/initialise		- Contains all files required to build the simulation input files
   ./SinglePolymer/input		- Contains the simulation input files
   ./SinglePolymer/output		- Contains the raw simulation output files
   ./SinglePolymer/analysis		- Contains Python analysis scripts the BioNet simulations
   ./SinglePolymer/results		- Contains processed data and graphs

2. ./PolyproteinNetwork			- Contains all the simulation and output data of the polyprotein network formation BioNet simulations
   ./PolyproteinNetwork/initialise	- Contains all files required to build the simulation input files
   ./PolyproteinNetwork/input		- Contains the simulation input files
   ./PolyproteinNetwork/output		- Contains the raw simulation output files
   ./PolyproteinNetwork/analysis	- Contains Python analysis scripts the BioNet simulations
   ./PolyproteinNetwork/results		- Contains processed data and graphs

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### Simulation and Analysis Protocol ###
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Dependencies:

	Dependencies for entire simulation and analysis suite. The versions used by us are shown in brackets

	Python (3.7.4 within Anaconda 4.7.11)
		Numpy, Scipy, Matplotlib

	Cmake (3.13.4)
	g++(9.1)
	BioNet(https://bitbucket.org/GokuBH/proteinhydrogelsoftware/branches/, PolyproteinNetworkSims branch)
		Eigen(3.3.7)
		Boost(1.69)
		tinyxml2(https://github.com/leethomason/tinyxml2, master branch)

###### Single polymer simulations ######

1. Build the single polymer simulations for a variety of dl/2R values 

	cd ./SinglePolymer/initialise
	python buildSinglePolymerInputScripts.py

	## Reason - To generate the necessary BioNet input scripts

2. Run the single polymer simulations for a variety of dl/2R values

	cd ./SinglePolymer/input
	
	# For each script
	BioNet -i SinglePolymer_ModelGC0-A_lOn2R0.010000.xml -o ../output/SinglePolymer_ModelGC0-A_lOn2R0.010000.out -t Brownian -l --steric --no-vdw --no-kinetics

	## Reason - To obtain a range of simulation data within which our required models will exist

3. Analyse the parameter sweep of single polymer simulations

	cd ./SinglePolymer/analysis
	python calculatePersistanceLengths.py
	python plotPersistanceLengths.py

	## Reason - To determine where is our paramter range of dl/2R are the required values for subsequent network formation simulations

4. Build the single polymer simulations for the parametrised systems 

	cd ./SinglePolymer/initialise
	python buildSinglePolymerParametrisedInputScripts.py

	## Reason - To generate the necessary BioNet input scripts

5. Run the single polymer simulations for the parametrised systems (Flexible, SemiFlexible and Rigid)

	cd ./SinglePolymer/input
	
	# For each script
	BioNet -i SinglePolymer_ModelGC0-A_Flexible.xml -o ../output/SinglePolymer_ModelGC0-A_Flexible.out -t Brownian -l --steric --no-vdw --no-kinetics

	## Reason - To obtain single polymer simulation data for our required models

6. Analyse the parametrised single polymer simulations

	cd ./SinglePolymer/analysis
	python calculateParameterisedPersistanceLengths.py

	## Reason - To verify the structural properties of these BioNet polymers are what we expect them to be, given our parametrisation

7. Calculate the effective rotational freedom of single polymers

	cd ./SinglePolymer/analysis
	python calculateRotationalFreedom.py

	## Reason - To see whether our polymers are rotationally restricted

###### Polymer network simulations ######

1. Build the polymer network non-interacting equilibration scripts 

	cd ./PolyproteinNetwork/initialise
	python buildConfigRelaxInputScripts.py
	python runConfigRelaxInputScripts.py

	## Reason - To generate the necessary equilibration states

2. Build the polymer network steric equilibration scripts 

	cd ./PolyproteinNetwork/initialise
	python buildStericRelaxInputScripts.py
	python runStericRelaxInputScripts.py

	## Reason - To generate the necessary equilibration states

3. Build the polymer network thermal+steric equilibration scripts 

	cd ./PolyproteinNetwork/initialise
	python buildThermalStericRelaxInputScripts.py
	python runThermalStericRelaxInputScripts.py

	## Reason - To generate the necessary equilibration states

4. Build the polymer network kinetics production scripts 

	cd ./PolyproteinNetwork/initialise
	python buildKineticInputScripts.py
	python runKineticInputScripts.py

	## Reason - To generate the necessary percolated networks

5. Build the polymer network stress production scripts 

	cd ./PolyproteinNetwork/initialise
	python buildStressInputScripts.py
	python runStressInputScripts.py

	## Reason - To generate the necessary statistics for stress calculations

6. Analsye the polymer network coordination properties

	cd ./PolyproteinNetwork/analysis
	python plotCoordination.py
	python plotCoordinationPairs.py

	## Reason - To calculate the average coordination properties of the networks

7. Analyse cluster formation traces

	cd ./PolyproteinNetwork/analysis
	python plotClusterFormationOverTime.py

	## Reason - To test for percolation and percolation speeds

8. Analyse the polymer network fractal dimensions

	cd ./PolyproteinNetwork/analysis
	python plotFractalDimensions.py
	python plotFractalDimensionsOverTime.py

	## To gain a system-wide understanding of the fractal structure properties

8. Analyse the fluctuating forces throughout the network

	cd ./PolyproteinNetwork/analysis
	python plotLocalForces.py

	## To gain insight into how force is distributed around the network