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, --output, --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 RANGE
Spin multiplicity (2S+1). Triggers energy
recomputation when supplied. [default: (1);
x>=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]
--backend-model TEXT Model variant for the selected --backend (e.g.
uma-s-1p2 / uma-m-1p1 for uma,
orb_v3_conservative_omol for orb, MACE-OMOL-0
/ off:small for mace). [default: (the
selected backend's own model)]
--precision [fp32|fp64] MLIP backend precision: fp32 or fp64. Unset
defaults per backend (uma: fp32; orb, mace:
fp64). Routed to backend-specific kwargs (UMA
precision / ORB precision / MACE
default_dtype). aimnet2: fp32 no-op; fp64
rejected. [default: (per backend: uma fp32;
orb, mace fp64)]
--solvent TEXT 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]
--solvent-xtb-cmd TEXT Command for the xTB solvent correction,
including optional xTB arguments. If xTB SCC
convergence is poor, increasing --etemp may
help (for example: 'xtb --etemp 1000').
--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.
