Usage: pdb2reaction tsopt [OPTIONS]
Transition state optimization (Dimer or RS-I-RFO).
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/GJF
companions based on the input format.
[default: convert-files]
--ref-pdb FILE Reference PDB topology to use when the input
is XYZ/GJF (keeps XYZ coordinates).
--max-cycles INTEGER Maximum number of optimization cycles.
[default: 10000]
--flatten / --no-flatten Enable the extra-imaginary-mode flattening
loop (grad: dimer loop, hess: post-RSIRFO).
[default: no-flatten]
--opt-mode [grad|hess|dimer|rsirfo]
TS optimizer: 'grad'/'dimer' → Hessian Guided
Dimer; 'hess'/'rsirfo' → RS-I-RFO. [default:
hess]
--dump / --no-dump Write optimization trajectory to
'tsopt_trj.xyz' in the output directory.
[default: no-dump]
-o, --out-dir TEXT Output directory. [default: ./result_tsopt/]
--thresh TEXT Convergence preset for the active optimizer (g
au_loose|gau|gau_tight|gau_vtight|baker|never)
. Defaults to 'baker' when not provided.
--config FILE Base YAML configuration file applied before
explicit CLI options.
--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 TS optimization. [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]
Choose MLIP Hessian evaluation mode (used
unless YAML sets calc.hessian_calc_mode).
Defaults to 'FiniteDifference'.
-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.