process_hb2.py was written to process the information in .hb2 files. .hb2 files are generated with HBPLUS analysis of hydrogen bonds in PDB files. Acquire HBPLUS here: https://www.ebi.ac.uk/thornton-srv/software/HBPLUS/ Generate .hb2 file like so: $ echo file.pdb | clean $ hbplus -d 3.5 -h 2.7 file.new file.pdb
$ python process_hb2.py -h python process_hb2.py -i input.hb2 -p file.pdb -R -P pr|aa|b -S pr|aa|b -d bond_length -o output.txt Options: -h, --help
REQUIRED
-i, --input The input .hb2 file from running hbplus on PDB file. Not required if using -S option.
OPTIONAL
-p, --pdb Original PDB file. Default: file has same root as .hb2 file + ".pdb" extension.
-d, --dadist Specify a threshold donor-acceptor distance above which to ignore reported hydrogen bonds.
[hbplus has its own default for dadist, but you may want a secondary cutoff.]
-o, --output Specify an output file name. Default is "hb2_statistics".
Pick one of:
-P, --protein Summary statistics for the given protein-RNA structure, either RNA (pr), amino acids (aa), or bases (b).
-R, --RNA List each nucleotide in the RNA and the hbonds formed with backbone, sugar, and base.
-H, --hbonds Output information for each protein-RNA hbond in .hb2 file.
-S, --summary [Default] Summary statistics--protein-RNA (pr), amino acids (aa), or bases (b)--by domain type.
Based on provided PDB files categorized by domain (RRM, KH, dsRBD, ZnF, YTH, PUF, DEAD, CSD).