Usage: pdb2reaction opt [OPTIONS]
Single-structure geometry optimization using LBFGS or RFO.
Options:
-v, --verbose LEVEL Console verbosity 0-3 (default 2). 0=silent;
1=milestones only; 2=+optimizer cycle tables,
per-stage timing, VRAM, 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: the analytical Hessian (used
for RFO seeding) raises a RuntimeError when
workers>1; run with --workers 1 for those
modes. [default: 1]
--workers-per-node INTEGER Workers per node when using a parallel MLIP
predictor (workers>1). [default: 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 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/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 [gau_loose|gau|gau_tight|gau_vtight|baker|never]
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]
--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.
-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).
--print-every INTEGER RANGE Print optimizer status every N cycles (debug
knob). [x>=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.
-h, --help Show this message and exit.