Usage: pdb2reaction trj2fig [OPTIONS] [EXTRA_OUTS]...
Plot ΔE or E from an XYZ trajectory and export figure/CSV.
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 FILE XYZ trajectory file. [required]
-o, --out FILE Output file(s). You can repeat -o and/or list
extra filenames after options
(.png/.jpg/.jpeg/.html/.svg/.pdf/.csv). If
nothing is given, defaults to energy.png.
--unit [kcal|hartree] Target unit for plotted and exported energy
values. [default: kcal]
-r, --reference TEXT Reference: 'init' (initial frame; last frame
if --reverse-x), 'None' (absolute E), or a
zero-based integer frame index. [default:
init]
-q, --charge INTEGER Total charge. Triggers energy recomputation
when supplied.
-m, --multiplicity INTEGER Spin multiplicity (2S+1). Triggers energy
recomputation when supplied. [default: (1)]
--reverse-x / --no-reverse-x Reverse the x-axis (last frame on the left).
[default: no-reverse-x]
-b, --backend [uma|orb|mace|aimnet2]
MLIP backend. [default: uma]
--solvent TEXT Experimental, computationally expensive xTB
solvent delta correction. Examples: water,
methanol, acetonitrile, dmso, thf, toluene.
'none' disables it. [default: none]
--solvent-model [alpb|cpcmx] xTB solvent model. [default: alpb]
--out-json / --no-out-json Write machine-readable result.json to the
output directory. [default: no-out-json]
-h, --help Show this message and exit.