MATLAB scripts

All scripts can be downloaded from the following .zip file: Discrete_DNA_minicircles.zip.

Energy_min.m

Inputs	bBDNA initial guesses, name: `Initial_guesses/‹seq_name›_guess‹guess_nb›.txt`
Parameters	model for DNA: `models = "cgDNAmin", "cgDNA+min"` or `["cgDNAmin","cgDNA+min"]`
	closure assumption: `boundaries = "NCC", "PC"` or `["NCC","PC"]`
	sequence: `seq`: the sequence `seq_name`: the name of the sequence `range_guesses`: list of `‹guess_nb›`
Outputs	3D views of solutions, name: `Results/3D_views/‹seq_name›_3Dsol‹guess_nb›_‹model›.fig`
	2D plots of solutions, name: `Results/2D_plots/‹seq_name›_2Dsol‹guess_nb›_‹model›.fig`
	MATLAB variables, name: `Results/Variables/‹seq_name›_sol‹guess_nb›_‹model›.mat`

The scripts then runs the discrete energy minimization for all combinations of models and boundaries.
The initial guesses are read from the "Initial_guesses" folder.
The algorithm outputs the solutions in the "Results/3D_views", "Results/2D_plots", "Results/Variables" subfolders.

The codes relative to each combination of model and closure assumption can be found in the "‹boundary›‹model›" subfolder.
The function that runs the minimization is the find_min_e function and the function to compute the energy, its gradient and Hessian is discrete_dna_penalty_en_grad_hess. The definitions of both funcitons can be found in the .m files with the corresponding names.

Visualize_solution.m

Inputs	cgDNAmin solution, name: `Results/Variables/‹seq_name›_sol‹guess_nb›_‹model›.mat`
Parameters	model for DNA: `models = "cgDNAmin"` or `"cgDNA+min"`
	closure assumption: `boundaries = "NCC"` or `"PC"`
	sequence: `seq`: the sequence `seq_name`: the name of the sequence `range_guesses`: list of `‹guess_nb›`
	chose figures to save: `guess_view`: 3D view of the initial guess `solution_view`: 3D view of the solution `plot_coord`: 2D plots of coordinates `plot_diff`: 2D plots of the difference groundstate - circle shape
Outputs (if chosen)	3D views of initial guess, name: `Results/3D_views/‹seq_name›_guess‹guess_nb›_‹model›.png`
	3D views of solution, name: `Results/3D_views/‹seq_name›_3Dsol‹guess_nb›_‹model›.png`
	2D plots of solution, name: `Results/2D_plots/‹seq_name›_2Dsol‹guess_nb›_‹model›.png` In the case cgDNA+min: 2 different plots for cgDNA and phosphate coordinates: `Results/2D_plots/‹seq_name›_2Dsol‹guess_nb›_‹model›_cgDNA-coord.png` `Results/2D_plots/‹seq_name›_2Dsol‹guess_nb›_‹model›_Pho-coord.png`
	2D plots of difference, name: `Results/2D_plots/‹seq_name›_2Ddiff‹guess_nb›_‹model›.png` In the case cgDNA+min: 2 different plots for cgDNA and phosphate coordinates: `Results/2D_plots/‹seq_name›_2Ddiff‹guess_nb›_‹model›_cgDNA-coord.png` `Results/2D_plots/‹seq_name›_2Ddiff‹guess_nb›_‹model›_Pho-coord.png`

The script reads the stored variables of the computed solution and creates the figures. The bBDNA software can be found on the LVCMM software page: link.