calc_hdx is a Python 3 package used to analyze molecular dynamics trajectories and calculate predicted HDX-MS protection factors and deuterated fractions. The predictions are optionally compared with experimental data, and results plotted in a series of output pdf files. The code currently (v0.1) contains the following files:
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calc_hdx.py : Main executable, usable from the command line with provided arguments, or by importing the calc_hdx package
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Functions.py : Transferable functions for trajectory reading/manipulating topologies and trajectory analysis
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DfPred.py : Parent class for analysis methods. Functions for calculating intrinsic rates from a topology, and for calculating deuterated fractions
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Methods.py : Analysis method classes for calculating protection factors with various models. Currently contains 'Radou' model (identical to Best & Vendruscolo, Structure, 2006, 14 (1), 97-106), and 'Persson-Halle' model (Persson & Halle, PNAS, 2015, 112 (33), 10383-10388).
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Analysis.py : Classes for calculating deuterated fractions and outputting results in tabular and graphical form
In addition to the standard Python 3.7 libraries it has been developed with the following dependencies:
MDtraj 1.9.3 Numpy 1.16.4 Scipy 1.3.0 Matplotlib 3.1.0
No testing has been performed with earlier or later dependency versions.
For a description of calc_hdx command line options, run calc_hdx.py -h
For an example usage and dataset, see DOI: 10.5281/zenodo.3385169