Usage: pdb2reaction freq [OPTIONS]
Vibrational frequency analysis and mode writer (+ default thermochemistry
summary).
Options:
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Input structure file (.pdb, .xyz, _trj.xyz,
...). [required]
-q, --charge INTEGER Total charge. Required for non-.gjf inputs
unless --ligand-charge is provided (PDB inputs
or XYZ/GJF with --ref-pdb).
--workers INTEGER MLIP predictor workers; >1 spawns a parallel
predictor (Hessian computation not supported
with workers>1). [default: 1]
--workers-per-node INTEGER Workers per node when using a parallel MLIP
predictor (workers>1). [default: 1]
-l, --ligand-charge TEXT Total charge or per-resname mapping (e.g.,
GPP:-3,SAM:1) used to derive charge when -q is
omitted (requires PDB input or --ref-pdb).
-m, --multiplicity INTEGER Spin multiplicity (2S+1).
--freeze-links / --no-freeze-links
Freeze parent atoms of link hydrogens (PDB
input or XYZ/GJF with --ref-pdb). [default:
freeze-links]
--freeze-atoms TEXT Comma-separated 1-based atom indices to freeze
(e.g., '1,3,5').
--convert-files / --no-convert-files
Convert XYZ/TRJ outputs into PDB companions
when a PDB template is available. [default:
convert-files]
--ref-pdb FILE Reference PDB topology to use when the input
is XYZ/GJF (keeps XYZ coordinates).
--max-write INTEGER How many modes to export (after sorting per
--sort). [default: 10]
--amplitude-ang FLOAT Animation amplitude (Å) used for both _trj.xyz
and .pdb. [default: 0.8]
--n-frames INTEGER Number of frames per mode animation.
[default: 20]
--sort [value|abs] Sort modes by 'value' (cm^-1) or by absolute
value. [default: value]
-o, --out-dir TEXT Output directory. [default: ./result_freq/]
--config FILE Base YAML configuration file applied before
explicit CLI options.
--temperature FLOAT Temperature (K) for thermochemistry summary.
[default: 298.15]
--pressure FLOAT Pressure (atm) for thermochemistry summary.
[default: 1.0]
--dump / --no-dump When True, write 'thermoanalysis.yaml' under
out-dir. [default: no-dump]
--show-config / --no-show-config
Print resolved configuration and continue
execution. [default: no-show-config]
--dry-run / --no-dry-run Validate options and print the execution plan
without running frequency analysis. [default:
no-dry-run]
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
--hessian-calc-mode [finitedifference|analytical]
How the ML backend computes Hessian. Defaults
to 'FiniteDifference' (can also be set via
YAML).
-b, --backend [uma|orb|mace|aimnet2]
MLIP backend. [default: uma]
--solvent TEXT Implicit solvent name for xTB correction (e.g.
'water'). 'none' to disable. [default: none]
--solvent-model [alpb|cpcmx] xTB solvent model. [default: alpb]
-h, --help Show this message and exit.