# deer_lib_gen.m

From Spinach Documentation Wiki

Generates a library of distance distributions and corresponding DEER traces for use in neural network training. Full details are given in our paper on the subject.

## Syntax

[time_grid,dist_grid,dist_distr_lib,... deer_ffact_lib,background_lib,deer_trace_lib,... noise_line_lib,exchange_lib,parameters]=deer_lib_gen(file_name,parameters)

## Arguments

Required fields of the parameters.* structure:

min_dist - lower limit of distance distributions, Angstrom max_dist - upper limit of distance distributions, Angstrom max_time - DEER trace duration, seconds max_exch - maximum exchange coupling, MHz (NMR convention) min_exch - minimum exchange coupling, MHz (NMR convention) ntraces - number of traces you wish to generate ndistmax - maximum number of skewed gaussians in the distance distribution npoints - number of digitisation points in the DEER trace and the distance distribu- tion noise_lvl - RMS noise level as a fraction of the modulation depth min_fwhm - minimum FWHM for a skewed gaussian in the distance distribution, fraction of distance max_fwhm - maximum FWHM for a skewed gaussian in the distance distribution, fraction of distance min_skew - minimum shape parameter for a skewed gaussian in the distance distribution max_skew - maximum shape parameter for a skewed gaussian in the distance distribution max_mdep - minimum DEER modulation depth min_mdep - maximum DEER modulation depth max_brate - maximum background signal decay rate, s^-1 min_brate - minimum background signal decay rate, s^-1 min_bdim - minimum background dimensionality max_bdim - maximum background dimensionality

## Outputs

time_grid - time grid (seconds) as a row vector dist_grid - distance grid (Angsrom) as a row vector dist_distr_lib - all distance distributions as a horizonal stack of row vectors deer_ffact_lib - all DEER form factors as a horizonal stack of row vectors background_lib - all background signals as a horizonal stack of row vectors, shifted and scaled to match DEER traces deer_trace_lib - all complete DEER traces as a horizonal stack of row vectors noise_line_lib - all noise tracks as a horizonal stack of row vectors exchange_lib - exchange interaction (MHz), a row vector conataining the value for each example parameters - parameters array as received

If a file name is provided, these variables are written into that file.

## Examples

The example below loads the parameters from one of the example files and generates a library of 1000 DEER traces.

% Load the training set parameters run('net_set_any_peaks/netset_params.m'); % Specify number of traces to produce parameters.ntraces=1000; % Set the training database name file_name='dlg_example_set.mat'; % Generate the training library [time_grid,dist_grid,dist_distr_lib,... deer_ffact_lib,background_lib,deer_trace_lib,... noise_line_lib,exchange_lib,parameters]=deer_lib_gen(file_name,parameters);

One of the resulting DEER traces is shown below.

## Notes

Multiple caveats exist in the training process. Please read our paper carefully before training your own networks.

## See also

*Version 2.5, authors: Ilya Kuprov, Steve Worswick, Jake Keeley, Gunnar Jeschke*