Usage: pdb2reaction path-opt [OPTIONS]
MEP optimization via GSM or DMF.
Options:
--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]
-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 (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').
--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 TEXT 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:
no-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: no-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]
-h, --help Show this message and exit.