Usage: pdb2reaction path-search [OPTIONS]
Multistep MEP search via recursive GSM/DMF segmentation.
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 or more PDB, mmCIF, XYZ, or GJF 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]
--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]
--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. [default: (peak for gsm, minima
for dmf)]
-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 (PDB/mmCIF inputs only).
-m, --multiplicity INTEGER RANGE
Spin multiplicity (2S+1; inherits from a .gjf
template when available). [default: (1 (or
the .gjf template value)); x>=1]
--freeze-links / --no-freeze-links
Freeze parent atoms of cap hydrogens
(PDB/mmCIF input only). [default: freeze-
links]
--freeze-atoms TEXT Comma-separated 1-based atom indices to freeze
(e.g., '1,3,5').
--max-nodes INTEGER Number of movable internal images per GSM/DMF
segment; the complete segment has max_nodes+2
images including endpoints. When not given,
YAML search.max_nodes_segment applies.
[default: 20]
--max-depth INTEGER RANGE Maximum recursive subdivision levels. 0
disables subdivision. Intervals retained at a
positive cap use seg_NNN_maxdepth and may
contain multiple steps. When omitted, YAML
search.max_depth applies. [default: (10);
x>=0]
--gsm-param [equi|energy] GSM node parameterization after string growth.
The energy scheme concentrates nodes in high-
energy regions and may be tried when an
equidistant path skips the reaction-coordinate
region near the HEI. [default: (equi)]
--max-cycles-gsm INTEGER RANGE Maximum GSM string-optimizer cycles for the
MEP stage. [default: (300); x>=1]
--dmf-max-iterations, --max-cycles-dmf INTEGER RANGE
Maximum IPOPT iterations for the DMF MEP
stage. This is a solver iteration count, not a
string-optimizer cycle count. [default:
(3000); x>=1]
--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/CIF/GJF
companions based on the input format.
[default: convert-files]
-o, --out-dir TEXT Output directory. [default:
./result_path_search/]
--thresh [gau_loose|gau|gau_tight|gau_vtight|baker|never]
Convergence preset for single-structure
optimizations only (gau_loose|gau|gau_tight|ga
u_vtight|baker|never). [default: (gau)]
--thresh-gsm [gau_loose|gau|gau_tight|gau_vtight|baker|never]
Convergence preset for the GSM string
optimizer (gau_loose|gau|gau_tight|gau_vtight|
baker|never). [default: (gau_loose)]
--dmf-tol, --thresh-dmf TEXT IPOPT dual-infeasibility tolerance for the DMF
path optimizer: tight (0.04) | middle (0.10) |
loose (0.20) or a positive float. This is not
a Gaussian preset. [default: (tight)]
--config FILE Base YAML configuration file applied before
explicit CLI options.
--show-config / --no-show-config
Print the resolved configuration blocks and
the loaded YAML file, then continue.
[default: no-show-config]
--dry-run / --no-dry-run Validate options and inputs without running
path search. [default: no-dry-run]
--preopt / --no-preopt If True, run initial single-structure
optimizations of inputs. [default: preopt]
--align / --no-align After optional preoptimization, align adjacent
inputs in sequence and match frozen-atom
positions while relaxing the remaining atoms.
[default: align]
--ref-full-pdb FILE Static full-size PDB/mmCIF template for
coordinate merging used for inspection. Use
the template corresponding to the first -i
input.
--write-ref-merge / --no-write-ref-merge
Write mep_w_ref/hei_w_ref coordinate
composites for inspection. Requires --align
and --ref-full-pdb. [default: no-write-ref-
merge]
--ref-pdb FILE Pocket reference PDB/mmCIF files used to write
the PDB outputs for XYZ/GJF inputs and for the
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|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]
--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').
--coord-type [cart|dlc] Optimization coordinate system (cart|dlc).
[default: (cart)]
--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.
