Usage: pdb2reaction scan [OPTIONS]
Internal-coordinate scan with harmonic restraints and relaxation.
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 Input structure file (.pdb, .cif, .mmcif,
.xyz, ...). [required]
-s, --scan-lists TEXT Required. Distance targets (i,j,target), or
scan ranges: distance (i,j,low,high), angle
(i,j,k,low,high), or dihedral
(i,j,k,l,low,high). A YAML/JSON spec file path
is also accepted. Atom strings accept
positional CHAIN:RESNAME:RESSEQ[ICODE]:ATOM.
Multiple inline literals define sequential
stages.
--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').
-q, --charge INTEGER Total charge. Required unless --ligand-charge,
YAML calc.charge, or a .gjf input gives it.
--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]
-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]
--one-based / --zero-based Interpret atom indices in --scan-lists as
1-based or 0-based. [default: one-based]
--max-step-size FLOAT Maximum scanned distance change per step [Å].
[default: 0.2]
--max-angle-step-size FLOAT RANGE
Maximum scanned angle change per step
[degree]. [default: 5.0; x>0.0]
--max-dihedral-step-size FLOAT RANGE
Maximum scanned dihedral change per step
[degree]. [default: 10.0; x>0.0]
--restraint-k, --bias-k FLOAT Harmonic well strength k [eV/Å^2 for
distances; eV/rad^2 for angles]. YAML bias.k
applies when this option is omitted; explicit
CLI wins. [default: (300.0)]
--relax-max-cycles INTEGER RANGE
Maximum optimizer cycles per grid relaxation.
An explicitly provided value overrides YAML
opt.max_cycles. [default: (100000); x>=1]
--opt-mode [grad|hess] Relaxation mode: grad (=LBFGS) or hess (=RFO).
[default: grad]
--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').
--dump / --no-dump Write per-step optimizer trajectory files.
scan_trj.xyz is always written; PDB/CIF
companions additionally require conversion
topology. [default: no-dump]
--convert-files / --no-convert-files
Convert XYZ/TRJ outputs into PDB/CIF/GJF
companions based on the input
topology/template. [default: convert-files]
--ref-pdb FILE Reference PDB/mmCIF topology to use when the
input is XYZ/GJF (keeps XYZ coordinates).
-o, --out-dir TEXT Base output directory. [default:
./result_scan/]
--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.
--preopt / --no-preopt Pre-optimize the initial structure without
bias before the scan. [default: no-preopt]
-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]
--endopt / --no-endopt After each stage, run an additional unbiased
optimization of the stage result. [default:
no-endopt]
--out-json / --no-out-json Write result.json to the output directory.
[default: no-out-json]
--dry-run / --no-dry-run Resolve and validate options (input,
charge/spin parity, --scan-lists parse) and
print the planned scan, then exit without
running any optimization. [default: no-dry-
run]
--coord-type [cart|redund|dlc|tric]
Optimization coordinate system
(cart|redund|dlc|tric). [default: (cart)]
--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.
