Usage: pdb2reaction scan3d [OPTIONS]
3D distance scan with harmonic restraints.
Options:
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Input structure file (.pdb, .xyz, _trj.xyz,
...). Required unless --csv is provided.
-s, --scan-lists TEXT Scan targets: inline Python literal or a
YAML/JSON spec file path.
--csv FILE If provided, skip the 3D scan and read a
precomputed surface.csv from this path. When
used, -i/--input and --scan-lists are
optional.
-q, --charge INTEGER Total charge. Required for non-.gjf inputs
unless --ligand-charge is provided (PDB inputs
or XYZ/GJF with --ref-pdb).
--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).
--one-based / --zero-based Interpret (i,j) indices in --scan-lists as
1-based (default) or 0-based. [default: one-
based]
--max-step-size FLOAT Maximum step size per scanned distance [Å].
[default: 0.2]
--bias-k FLOAT Harmonic well strength k [eV/Å^2]. [default:
300.0]
--relax-max-cycles INTEGER Maximum optimizer cycles per grid relaxation.
When explicitly provided, used unless YAML
sets opt.max_cycles. [default: 10000]
--opt-mode [grad|hess] Relaxation mode: grad (=LBFGS) or hess (=RFO).
[default: grad]
--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').
--dump / --no-dump Write inner d3 scan trajectories per (d1,d2)
as TRJ under result_scan3d/grid/. [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 Base output directory. [default:
./result_scan3d/]
--thresh TEXT Convergence preset (gau_loose|gau|gau_tight|ga
u_vtight|baker|never). Defaults to 'baker'.
--config FILE Base YAML configuration file applied before
explicit CLI options.
--preopt / --no-preopt Pre-optimize the initial structure without
bias before the scan. [default: no-preopt]
-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]
--baseline [min|first] Reference for relative energy (kcal/mol):
'min' or 'first' (i=0,j=0,k=0). [default:
min]
--zmin FLOAT Lower bound of color scale for plots
(kcal/mol).
--zmax FLOAT Upper bound of color scale for plots
(kcal/mol).
--print-parsed / --no-print-parsed
Print parsed scan targets after resolving
--scan-lists. [default: no-print-parsed]
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
-h, --help Show this message and exit.