Usage: pdb2reaction freq [OPTIONS]
Vibrational frequency analysis and mode writer (+ default thermochemistry
summary).
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 Input structure file (.pdb, .xyz, _trj.xyz,
...). [required]
--workers INTEGER MLIP predictor workers; >1 spawns a parallel
predictor. NOTE: analytical Hessian raises a
RuntimeError when workers>1; pass --hessian-
calc-mode FiniteDifference explicitly.
[default: 1]
--workers-per-node INTEGER Workers per node when using a parallel MLIP
predictor (workers>1). [default: 1]
--freeze-links / --no-freeze-links
Freeze parent atoms of cap 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]
-q, --charge INTEGER Total charge. Required for non-.gjf inputs
unless --ligand-charge is provided (.gjf
templates inherit the charge automatically).
-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).
--precision [fp32|fp64] MLIP backend precision: fp32 (default) or
fp64. Routed to backend-specific kwargs (UMA
precision / ORB precision / MACE
default_dtype). aimnet2: fp32 no-op; fp64
rejected.
--backend-model TEXT Model variant for the selected --backend (e.g.
uma-s-1p1 / uma-m-1p1 for uma,
orb_v3_conservative_omol for orb, MACE-OMOL-0
/ MACE-OFF23_small for mace). Default: the
backend's built-in model.
--calc-file FILE Python file exposing get_calculator(...) -> an
ASE Calculator, used as the energy/gradient
backend (overrides --backend). Couples GFN-xTB
/ DFTB+ / any ASE engine. See --calc-factory.
--calc-factory TEXT Name of the callable in --calc-file that
returns an ASE Calculator (or a module-level
Calculator instance). [default:
get_calculator]
--deterministic / --no-deterministic
Strict bit-reproducible GPU runs
(deterministic algorithms + index_reduce_
shim). Slower; raises if unsupported. Default
off.
--allow-charge-mult-mismatch Skip the cluster charge/multiplicity electron-
parity check (logs that it was skipped). For
an intentional open-shell or modified-residue
cluster.
--coord-type [cart|redund|dlc|tric]
Optimization coordinate system
(cart|redund|dlc|tric). cart is the reliable
default used for the published results; dlc
speeds up torsion-rich optimizations.
-h, --help Show this message and exit.