Usage: pdb2reaction opt [OPTIONS]
Single-structure geometry optimization using LBFGS or 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).
--dist-freeze TEXT Distance restraints: inline Python literal
(e.g. '[(1,5,1.4)]') or a YAML/JSON spec file
path. Same format as --scan-lists:
(i,j,target_A) triples. Target may be omitted
to freeze at the current distance: (i,j).
--one-based / --zero-based Interpret --dist-freeze / --scan-lists indices
as 1-based (default) or 0-based. [default:
one-based]
--bias-k FLOAT Harmonic restraint strength k [eV/Å^2] for
--dist-freeze. [default: 300]
--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]
--opt-mode [grad|hess|lbfgs|rfo]
Optimization mode: grad (lbfgs) or hess (rfo).
Aliases lbfgs/rfo are accepted. [default:
grad]
--flatten / --no-flatten Enable/disable imaginary-mode flatten loop
after optimization. [default: no-flatten]
--dump / --no-dump Write optimization trajectory to
'optimization_trj.xyz'. [default: no-dump]
-o, --out-dir TEXT Output directory. [default: ./result_opt/]
--thresh TEXT Convergence preset (gau_loose|gau|gau_tight|ga
u_vtight|baker|never). Defaults to 'gau' 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]
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
--dry-run / --no-dry-run Validate options and print the execution plan
without running optimization. [default: no-
dry-run]
-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.