Usage: pdb2reaction path-search [OPTIONS]
Multistep MEP search via recursive GSM/DMF segmentation.
Options:
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Two or more structures in reaction order.
Repeat -i/--input for each path. [required]
--mep-mode [gsm|dmf] MEP optimizer: Growing String Method (gsm) or
Direct Max Flux (dmf). [default: gsm]
--refine-mode [peak|minima] Refinement seed selection around the highest-
energy image: 'peak' uses HEI±1, 'minima' uses
the nearest local minima in each direction.
Defaults to peak for gsm and minima for dmf
when omitted.
-q, --charge INTEGER Total charge. Required for non-.gjf inputs
unless --ligand-charge derives it from 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 (PDB inputs only).
-m, --multiplicity INTEGER Spin multiplicity (2S+1; defaults from a .gjf
template when available, otherwise 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 Number of internal nodes (string has
max_nodes+2 images including endpoints). Used
for *segment* GSM unless overridden by YAML
search.max_nodes_segment. [default: 20]
--max-cycles INTEGER Maximum GSM optimization cycles. [default:
300]
--climb / --no-climb Enable climbing image for standard GSM
segments (bridge segments always disable
climbing). [default: climb]
--opt-mode [grad|hess] Single-structure optimizer: grad (=LBFGS) or
hess (=RFO). [default: grad]
--dump / --no-dump Write GSM/single-optimization trajectories
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]
-o, --out-dir TEXT Output directory. [default:
./result_path_search/]
--thresh TEXT Convergence preset for single-structure
optimizations only (gau_loose|gau|gau_tight|ga
u_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 search. [default: no-
dry-run]
--preopt / --no-preopt If True, run initial single-structure
optimizations of inputs. [default: no-preopt]
--align / --no-align After preoptimization, align all inputs to the
*first* input and match freeze_atoms using the
align_freeze_atoms API. When --align is True
and --ref-full-pdb is provided, the first
reference PDB will be used for all pairs in
the final merge. [default: align]
--ref-full-pdb FILE Full-size template PDBs in the same reaction
order as --input. With --align True, only the
*first* provided reference PDB is used for all
pairs in the final merge (you may pass just
one).
--ref-pdb FILE Pocket reference PDBs used only for the final
full-system merge. Useful when --input uses
XYZ/GJF intermediates but PDB snapshots exist
for merging. Must match the number and order
of --input.
-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.