Usage: mlmm bond-summary [OPTIONS] [EXTRA_INPUTS]...
Detect bond changes between consecutive structures.
Options:
-v, --verbose LEVEL Console verbosity 0-3 (default 2). 0=silent;
1=milestones only; 2=+detailed step logging and
deliverable paths; 3=everything (full config
blocks, per-file paths, DEBUG logging). [0<=x<=3]
--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]
--json / --no-json Write the JSON report to stdout; no file is
created. [default: no-json]
-h, --help Show this message and exit.