Usage: pdb2reaction path-opt [OPTIONS]
MEP optimization via GSM or DMF.
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... Two endpoint structures (reactant and
product); accepts .pdb or .xyz. [required]
--mep-mode [gsm|dmf] MEP optimizer: Growing String Method (gsm) or
Direct Max Flux (dmf). [default: gsm]
--dmf-backend [cpu|gpu] DMF compute backend (--mep-mode dmf only): gpu
(dmf.torch / CUDA) or cpu (dmf / NumPy). On a
GPU out-of-memory error, retry with cpu.
[default: gpu]
-q, --charge INTEGER Total charge. Required unless a .gjf template
provides charge metadata or --ligand-charge is
supplied for PDB inputs.
--workers INTEGER MLIP predictor workers; >1 spawns a parallel
predictor. NOTE: the analytical Hessian raises
a RuntimeError when workers>1; run with
--workers 1 for Hessian-based modes.
[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 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').
--max-nodes INTEGER Maximum number of internal nodes (string has
up to max_nodes+2 images including endpoints).
[default: 20]
--max-cycles INTEGER Maximum string optimizer cycles (GSM/DMF path
optimization). [default: 300]
--climb / --no-climb Search for a transition state (climbing image)
after path growth. [default: climb]
--opt-mode [grad|hess] Single-structure optimizer for endpoint
preoptimization: grad (=LBFGS) or hess (=RFO).
[default: grad]
--dump / --no-dump Write optimizer trajectory and restarts during
the run. [default: no-dump]
--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).
-o, --out-dir TEXT Output directory. [default:
./result_path_opt/]
--thresh [gau_loose|gau|gau_tight|gau_vtight|baker|never]
Convergence preset for endpoint
preoptimization only (gau_loose|gau|gau_tight|
gau_vtight|baker|never). Defaults to 'gau'
when not provided.
--thresh-stopt TEXT Convergence preset for the string optimizer
(stopt) (gau_loose|gau|gau_tight|gau_vtight|ba
ker|never). Defaults to 'gau_loose' 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 path optimization. [default:
no-dry-run]
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
--preopt / --no-preopt Preoptimize each endpoint via the selected
single-structure optimizer (LBFGS/RFO) before
alignment and path optimization. [default:
preopt]
--preopt-max-cycles INTEGER Maximum cycles for each endpoint
preoptimization pass (LBFGS or RFO; only used
when --preopt is enabled). [default: 10000]
--fix-ends / --no-fix-ends Fix structures of input endpoints during path
optimization (GSM/DMF). [default: fix-ends]
-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|dlc] Optimization coordinate system (cart|dlc).
cart is the reliable default used for the
published results; dlc speeds up torsion-rich
optimizations.
--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.