| general_setup.txt | A plain-text file with the general settings for the simulation run |
| model_setup.txt | A plain-text file with parameters of the model to be simulated |
| convert_input_parameters.py | The program that reads setup files and creates a set of simple text files easy for loading in Matlab. |
| Simulate.m | Main function. This function runs simulation of a titration series. Run it as Simulate general_setup_fname model_setup_fname |
| load_setup.m | Loading setup from text files |
| model_matrices.m | Selects appropriate model module |
| Spectra.m | This function calculates spectra for the titration series |
| SpectralFigure.m |
Generates a figure of overlayed spectra |
| TextFigure.m | Generates an image with text parameters of the model |
| ITCFigure.m | Plot ITC curve for the model |
Subfolder with the model-specific code Models/
| XXX_model_matrices.m | Specific code for each model XXX % This function builds model-specific matrices to supply to Spectra: This is where I decide whether to use analytical or numeric solving for equilibrium concentrations. If I can do analytical solution - I place equation here. If not - place expression for Ptot in terms of constants and [L] inmodel_numeric.m |
| XXX_model_numeric.m | Specific code for each model XXX The function for numeric solving for [L]: expresses Ptot as a function of all constants plus [L], which is determined by minimization. |
Python code:
| lineshapekin_simulation_report.py | The program generating summary_report.htm, an HTML summary of simulation results viewable in any Web-browser. Simulate calls lineshapekin_simulation_report.py for the current simulation folder defined in setup.m. |
| template_report.htm | a template file in B/test_results used for adjusting HTML output. This file has all figures made by LineShapeKin Simulation linked from the corresponding folders created in simulation. If you want to move this file (say, send it by email) then do Save As in your web browser and choose Complete Page. Then your browser will save the page in different location and collect all images in one folder you can ZIP together with the HTML page and send it. |
| model_name/custom_results_folder/ |
contains results of all case N entries in model_setup.m and summary_report.htm on them |
Graphs in EPS-2, PNG and Matlab FIG format. When opening FIG format in Matlab you can access individual traces labeled with L/R values and rescale as you like. |
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| Parameters of the model saved in text format. | |
| ITC curve is also simulated (not accurately for the models with isomerization or dimerization of a ligand - ligand contribution is not taken into account) | |
| Relaxation dispersion simulation (yet to be done) |