Metadata-Version: 1.1
Name: modelfree-protein15n
Version: 0.0.7
Summary: Model free analysis of protein backbone amide 15N spin relaxation rates.
Home-page: https://github.com/VSchnapka/modelfree-protein15n.git
Author: Vincent Schnapka
Author-email: vincentschnapka@gmail.com
License: UNKNOWN
Description: # modelfree-protein15n
        Model-Free analysis framework for protein backbone amide 15N NMR spin relaxation rates.
        
        This tool fits the relaxation data to a multi-Lorentzian spectral density function.
        One can choose the number of Lorentzians (dynamic modes) for the fit.
        Typically, one can perform 1, 2, and 3 dynamic mode MF analysis and see which model is most relevant for the data.
        IMPACT analysis is also possible by fixing the correlation times and fitting the amplitudes.
        
        ## Relevant litterature
        
        Lipari & Szabo, Journal of the American Chemical Society (1982);
        Halle, The Journal of chemical physics (2009);
        Khan et al., Biophysical journal (2015)
        
        # installation
        
            $ pip install modelfree-protein15n
        
        # usage
        
        The program is able to generate random relaxation data with the command 'modfree generate'.
        The program is able to fit relaxation data to a model with the command 'modfree fit'.
        The program is able to plot the results with the command 'modfree plot'.
        
        ## Data generation
        
        To generate relaxation data, type the following command:
        
            $ modfree generate
            
        The following flags are available:
        -o (str): Output directory containing the generated data.
        -modes (int): number of dynamic modes used to generate the data
        -n (int): number of residues in the data
        -noise (float): between 0 and 1, indicates the proportion of noise to put in the data. (0.03 by default)
        -fields (list, int or float): Magnetic fields used for the rate generation in MHz.
        -rates: relaxation rates to generate. by default R1, R2, NOE, etaXY.
        
        For example, you can type:
        
            $ modfree generate -o Generated -modes 2 -n 70 -noise 0.05 -fields 600 700 850 950 1200 -rates R1 R2 NOE etaXY etaZ
            
        ## Data fitting
        
        To fit relaxation data, you will need your data in a specific format akin to the generated data. Generate some data to see how it's done. You will also need a directory file and a parameter file. type the following command to fit the data generated in the previous section:
        
            $ modfree fit -o Generated_fit -d Generated/directories.toml -p Generated/parameters.toml
            
        You can also fit only part of the data with the flag -r:
        
            $ modfree fit -o Generated_fit -d Generated/directories.toml -p Generated/parameters.toml -r 10 11 12 13 14 15 16 17
            
        Or
        
            $ modfree fit -o Generated_fit -d Generated/directories.toml -p Generated/parameters.toml -r 15
        
        ## Data plotting
        
        To plot the fitted data, just type:
        
            $ modfree plot -o Generated_fit -p all
        
        The following flags are available:
        -o (str): Output directory containing the data.
        -p: What to plot (all, relaxation, parameters, statistics, correlation)
        -format: Format of the plot files (pdf, png, jpg, svg...)
        -dpi (600 by default)
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
