Calculate per-position deuteration levels from HDX (hydrogen-deuterium exchange) data.
HDX data are measured per-fragment. This utility calculates the level of deuteration at each position of the protein. It uses deuteration levels of all the fragments. It also takes into the account the fact that N-termini of the fragments do not contribute to the deuteration levels, as well as proline residues.
python3 setup.py build
python3 setup.py install
hdxmooth -i <input_file> -o <output_file> [options]
-t --times <time1,time2,time3...>: a comma-separated list of time points to process. Default: process all time points
-p --protein <protein1,protein2,protein3...>: a comma-separated list of protein names to use. These must match input column names. Defautl: process all proteins
-d --delimiter <delimiter>: a delimiter to be used in both input and output .csv files. Default: comma (,)
The software accepts .csv files containing exactly these columns in this order:
Protein,Start,End,Sequence,Deut Time (sec),maxD,#D,%D,Conf Interval (#D),#Pts,Confidence,Stddev,p
Columns can have arbitrary names.
The output is a .csv file with these columns:
Position,Time(sec),protein1,protein2,...