Usage: pdb2reaction bond-summary [OPTIONS] [EXTRA_INPUTS]...
Detect bond changes between consecutive structures.
Options:
--help-advanced Show all options (including advanced settings) and
exit.
-i, --input TEXT Input structure files (XYZ/PDB/GJF). Repeat -i for
each file.
--device TEXT Compute device for distance calculations.
[default: cpu]
--bond-factor FLOAT Scaling factor for covalent radii sum. [default:
1.2]
--one-based / --zero-based Use 1-based atom indices in output. [default:
one-based]
--out-json / --no-out-json Print machine-readable JSON to stdout instead of
text. [default: no-out-json]
-h, --help Show this message and exit.