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 Single-geometry input (.pdb, .cif, .mmcif,
.xyz, or .gjf). Extract a trajectory frame to
.xyz before use. [required]
--uma-workers, --workers INTEGER
MLIP predictor workers; >1 spawns a parallel
predictor. NOTE: with UMA, workers>1 plus an
explicit Analytical Hessian request is an
error; use workers=1 or FiniteDifference.
[default: 1]
--uma-workers-per-node, --workers-per-node INTEGER
Workers per node when using a parallel MLIP
predictor (workers>1). [default: 1]
--distance-restraint, --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 --distance-restraint / --scan-lists
indices as 1-based or 0-based. [default: one-
based]
--restraint-k, --bias-k FLOAT Harmonic restraint strength k [eV/Å^2] for
--distance-restraint. [default: 300]
--freeze-links / --no-freeze-links
Freeze parent atoms of cap hydrogens
(PDB/mmCIF 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/CIF/GJF
companions based on the input format.
[default: convert-files]
--ref-pdb FILE Reference PDB/mmCIF topology to use when the
input is XYZ/GJF (keeps XYZ coordinates).
--max-cycles INTEGER RANGE Maximum number of optimization cycles.
[default: (100000); x>=1]
--opt-mode [grad|hess|lbfgs|rfo]
Optimization mode: grad (lbfgs) or hess (rfo).
Aliases lbfgs/rfo are accepted. [default:
grad]
--reject-uphill / --no-reject-uphill
Opt in to rejecting uphill RFO trials in hess
mode (tolerance: 1e-4 Hartree) and final-check
the retained geometry at the emergency floor.
Ignored in grad/lbfgs mode. [default: no-
reject-uphill]
--stop-plateau / --no-stop-plateau
Stop when the energy stops changing while the
convergence criteria are still unmet, and
report the run as stalled. It never signals
convergence; --max-cycles remains the real
bound. [default: no-stop-plateau]
--stop-plateau-thresh FLOAT Energy range (hartree) below which --stop-
plateau treats the window as flat. [default:
(1e-4)]
--stop-plateau-window INTEGER Number of consecutive cycles --stop-plateau
inspects. [default: (50)]
--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). [default: (gau)]
--config FILE Base YAML configuration file applied before
explicit CLI options.
--show-config / --no-show-config
Print the loaded YAML file and its top-level
keys, then continue. [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 inputs without running
optimization. [default: no-dry-run]
-b, --backend [uma|orb|mace|aimnet2|dft]
Energy/force calculator backend. [default:
uma]
--solvent TEXT Computationally expensive xTB solvent delta
correction for MLIP backends; dft uses native
PySCF PCM/SMD. Examples: water, methanol,
acetonitrile, dmso, thf, toluene. 'none'
disables it. [default: none]
--solvent-model [alpb|cpcmx|pcm|smd]
Solvent model: ALPB/CPCMx for MLIP backends;
PCM/SMD for dft. [default: alpb]
--solvent-xtb-cmd TEXT Command for the xTB solvent correction,
including optional xTB arguments. If xTB SCC
convergence is poor, increasing --etemp may
help (for example: 'xtb --etemp 1000').
--coord-type [cart|redund|dlc|tric]
Optimization coordinate system
(cart|redund|dlc|tric). [default: (cart)]
-q, --charge INTEGER Total charge. Required unless --ligand-charge,
YAML calc.charge, or a .gjf input gives it.
-l, --ligand-charge TEXT Total ligand charge or per-resname mapping
(e.g., GPP:-3,SAM:1) used to derive charge
when -q is omitted (requires PDB/mmCIF input
or --ref-pdb).
-m, --multiplicity INTEGER RANGE
Spin multiplicity (2S+1). [default: (1);
x>=1]
--print-every INTEGER RANGE Print optimizer status every N cycles.
[default: (100); x>=1]
--precision [fp32|fp64] MLIP backend precision: fp32 or fp64. Unset
defaults per backend (uma: fp32; orb, mace:
fp64). Routed to backend-specific kwargs (UMA
precision / ORB precision / MACE
default_dtype). aimnet2: fp32 no-op; fp64
rejected. [default: (per backend: uma fp32;
orb, mace fp64)]
--backend-model TEXT Model variant for the selected --backend (e.g.
uma-s-1p2 / uma-m-1p1 for uma,
orb_v3_conservative_omol for orb, MACE-OMOL-0
/ off:small for mace). [default: (the
selected backend's own 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-file-
func-name.
--calc-factory, --calc-file-func-name TEXT
Name of the callable in --calc-file that
returns an ASE Calculator (or a module-level
Calculator instance). CLI overrides config
YAML; otherwise defaults to get_calculator.
[default: (get_calculator)]
--deterministic / --no-deterministic
Request strict same-stack PyTorch determinism
(deterministic algorithms + index_reduce_
shim). Slower; raises for detected unsupported
ops; custom calculators are outside its scope.
[default: no-deterministic]
--allow-charge-mult-mismatch Skip the cluster charge/multiplicity electron-
parity check (logs that it was skipped). Open-
shell clusters need a matching multiplicity
instead; use this only for an intentionally
nonstandard electron count.
--func-basis TEXT DFT method as FUNCTIONAL/BASIS; HF/BASIS is
also accepted. [default: (wb97m-v/def2-svp)]
--dft-engine, --engine [gpu|cpu]
PySCF execution engine used by --backend dft.
[default: (gpu)]
--save-scf-checkpoint / --no-save-scf-checkpoint
Persist a structure-bound PySCF checkpoint
(default: disabled). [default: (disabled)]
--scf-checkpoint FILE Load/save the optional structure-bound PySCF
checkpoint at PATH.
--scf-stepwise-grid / --no-scf-stepwise-grid
Converge the first SCF on a coarse grid, then
on the final grid (later SCFs reuse the
previous density as usual). [default:
(enabled)]
--dft-low-memory, --lowmem / --no-dft-low-memory, --no-lowmem
Use GPU4PySCF rks_lowmem for closed-shell GPU
DFT; open-shell GPU and CPU use standard
direct JK. --no-dft-low-memory enables density
fitting. [default: (lowmem)]
--dft-nprocs INTEGER RANGE PySCF/OpenMP CPU threads; GPU count is
unaffected. [default: (auto); x>=1]
--dft-memory, --dft-mem TEXT PySCF host RAM limit (for example 64GB or
120000MB). [default: (auto)]
-h, --help Show this message and exit.
