This code can be used to analyse files generated by VMD (Visual Molecular Dynamics) using the Timeline plugin for secondary structure. Currently, this code is set-up to work with the protein ProP; specifically, it analyses the secondary structure of the c-terminus in E. coli (Ec) and X. campestris (Xc).
This code is written in python 3. There are two parts to the code: timelineMain_v*.py and functionsTimeline_v*.py, where * indicates the version number. To run the code, go to where your timeline files (extension .tml) are stored using either command prompt (windows) or the terminal (linux/mac). Type "python timelineMain_v*.py" and press enter. Respond to the prompts as given. If you wish to quit the program at any time, type "q" and press enter.
This file is an R script that can be used to make boxplots. It is intended for use with .csv files that have been generated using whole files. It takes three command line arguments: (1) the .csv file name, (2) the name of the simulation (used in the boxplot title), and (3) the length of the simulation in ns.
The script is run using Rscript, which is set to default at the top of the code (if running using UNIX system). Open the terminal, make the script executable (chmod u+x make_boxplot.R), and type
$ ./make_boxplot.R filename.csv "simulation name" 50
Alternatively, open command prompt and type:
$ Rscript make_boxplot.R filename.csv "simulation name" 50
If you are not in the directory where the file is stored, you will have to provide the path to the file as well as the filename in the arguments. Note: the simulation name presented here is in quotes, which allows for the use of spaces in the title. If your simulation name is one word or a string of non-empty characters, you don't need to include the quotes.