Usage: pdb2reaction all [OPTIONS]
Run active site model extraction → (optional single-structure staged scan) →
MEP search → merge to full PDBs in one shot. If exactly one input is provided:
(a) with --scan-lists, run staged scan on the active site model (or full
structure when extraction is skipped) and use stage results as inputs for
path_search; (b) with --tsopt True and no --scan-lists, run TSOPT-only mode.
Options:
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Two or more **full structures** (PDB/XYZ/GJF)
in reaction order (reactant [intermediates
...] product), or a single **full structure**
(with --scan-lists or with --tsopt True).
Extraction (-c/--center) requires PDB inputs.
When using --scan-lists without extraction,
the input may be PDB/XYZ/GJF (integer indices
only for non-PDB inputs). Repeat -i/--input
for each file. [required]
-c, --center TEXT Substrate specification for the extractor: a
PDB path, a residue-ID list like '123,124' or
'A:123,B:456' (insertion codes OK: '123A' /
'A:123A'), or a residue-name list like
'GPP,SAM'. When omitted, extraction is skipped
and the **full input structure(s)** are used
directly as active site models.
-o, --out-dir DIRECTORY Top-level output directory for the pipeline.
[default: result_all]
-r, --radius FLOAT Inclusion cutoff (Å) around substrate atoms.
[default: 2.6]
--radius-het2het FLOAT Independent hetero–hetero cutoff (Å) for
non‑C/H pairs. [default: 0.0]
--include-h2o BOOLEAN Include waters (HOH/WAT/TIP3/SOL) in the
active site model. [default: True]
--exclude-backbone BOOLEAN Remove backbone atoms on non‑substrate amino
acids (with PRO/HYP safeguards). [default:
False]
--add-linkh BOOLEAN Add link hydrogens for severed bonds (carbon-
only) in active site models. [default: True]
--selected-resn TEXT Force-include residues (comma/space separated;
chain/insertion codes allowed). [default: ""]
--modified-residue TEXT Comma-separated residue names (with optional
charge) to treat as amino acids for backbone
truncation and charge assignment. Examples:
'HD1,HD2,HD3' or 'HD1:0,SEP:-2'. [default:
""]
-l, --ligand-charge TEXT Total charge (number) or per-resname mapping
like 'GPP:-3,SAM:1'. Used for extractor charge
summaries; when extraction is skipped, PDB
inputs derive the total charge and numeric
values act as a total-charge fallback.
-q, --charge INTEGER Force the total system charge (overrides
extractor/GJF/--ligand-charge-derived values;
emits a warning when used).
--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]
-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]
--verbose BOOLEAN Enable INFO-level logging inside extractor.
[default: True]
-m, --multiplicity INTEGER Spin multiplicity (2S+1). [default: 1]
--freeze-links BOOLEAN Freeze parent atoms of link hydrogens (PDB
input or XYZ/GJF with --ref-pdb). [default:
True]
--mep-mode [gsm|dmf] MEP optimizer: Growing String Method (gsm) or
Direct Max Flux (dmf). [default: gsm]
--max-nodes INTEGER Max internal nodes for **segment** GSM (String
has max_nodes+2 images including endpoints).
[default: 20]
--max-cycles INTEGER Maximum GSM optimization cycles. [default:
300]
--climb BOOLEAN Enable transition-state climbing after growth
for the **first** segment in each pair.
[default: True]
--opt-mode [grad|hess] Optimizer mode forwarded to scan/tsopt and
used for single optimizations: grad
(=LBFGS/Dimer) or hess (=RFO/RSIRFO).
[default: grad]
--opt-mode-post [grad|hess] Optimizer mode override for TSOPT/post-IRC
endpoint optimizations. If unset, uses --opt-
mode when explicitly provided; otherwise falls
back to the default ('hess'). [default: hess]
--dump BOOLEAN Dump GSM/MEP trajectories. Always forwarded to
path_search/path-opt; scan/tsopt receive it
only when explicitly set here. The freq stage
uses dump=True by default; set --dump False
explicitly to disable it. [default: False]
--convert-files BOOLEAN Convert XYZ/TRJ outputs into PDB/GJF
companions based on the input format.
[default: True]
--refine-path BOOLEAN Run recursive path_search on the full ordered
series (default). Use --refine-path False to
run a single-pass path-opt GSM between each
adjacent pair and concatenate the segments (no
path_search). [default: True]
--thresh TEXT Convergence preset (gau_loose|gau|gau_tight|ga
u_vtight|baker|never). Defaults to 'gau' when
not provided.
--thresh-post TEXT Convergence preset for post-IRC endpoint
optimizations (gau_loose|gau|gau_tight|gau_vti
ght|baker|never). [default: baker]
--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 any stage. [default: no-dry-
run]
--resume / --no-resume Resume a previous run from --out-dir.
Completed stages whose output files already
exist are skipped. Useful when a long pipeline
was interrupted. [default: no-resume]
--preopt BOOLEAN If True, run initial single-structure
optimizations of the active site model inputs.
[default: True]
--hessian-calc-mode [finitedifference|analytical]
Common MLIP Hessian calculation mode forwarded
to tsopt and freq. Defaults to
'FiniteDifference'.
--tsopt BOOLEAN TS optimization + IRC per reactive segment (or
TSOPT-only mode for single-structure), and
build energy diagrams. [default: False]
--thermo BOOLEAN Run freq on (R, TS, P) per reactive segment
(or TSOPT-only mode) and build Gibbs free-
energy diagram (MLIP). [default: False]
--dft BOOLEAN Run DFT single-point on (R, TS, P) and build
DFT energy diagram. With --thermo True, also
generate a DFT//MLIP Gibbs diagram. [default:
False]
--tsopt-max-cycles INTEGER Override tsopt --max-cycles value. Defaults to
10000 when not provided.
--tsopt-out-dir DIRECTORY Override tsopt output subdirectory (relative
paths are resolved against the default).
--flatten / --no-flatten Enable the extra-imaginary-mode flattening
loop in tsopt (grad: dimer loop, hess: post-
RSIRFO); --no-flatten forces
flatten_max_iter=0. [default: no-flatten]
--freq-out-dir DIRECTORY Override freq output base directory (relative
paths resolved against the default).
--freq-max-write INTEGER Override freq --max-write value. Defaults to
10.
--freq-amplitude-ang FLOAT Override freq --amplitude-ang (Å). Defaults to
0.8.
--freq-n-frames INTEGER Override freq --n-frames value. Defaults to
20.
--freq-sort [value|abs] Override freq mode sorting. Defaults to
'value'.
--freq-temperature FLOAT Override freq thermochemistry temperature (K).
Defaults to 298.15 K.
--freq-pressure FLOAT Override freq thermochemistry pressure (atm).
Defaults to 1.0 atm.
--dft-out-dir DIRECTORY Override dft output base directory (relative
paths resolved against the default).
--dft-func-basis TEXT Override dft --func-basis value. Defaults to
'wb97m-v/def2-tzvpd'.
--dft-max-cycle INTEGER Override dft --max-cycle value. Defaults to
100.
--dft-conv-tol FLOAT Override dft --conv-tol value. Defaults to
1e-9.
--dft-grid-level INTEGER Override dft --grid-level value. Defaults to
3.
--dft-engine [gpu|cpu] DFT backend: gpu (GPU4PySCF, raises error if
unavailable) or cpu (PySCF). [default: gpu]
-s, --scan-lists TEXT Scan targets: inline Python literal or a
YAML/JSON spec file path. Multiple inline
literals define sequential stages, e.g.
'[(12,45,1.35)]'
'[(10,55,2.20),(23,34,1.80)]'. Indices refer
to the original full input PDB (1-based). When
extraction is used, they are auto-mapped to
the active site model after extraction.
--scan-out-dir DIRECTORY Override the scan output directory (default:
<out-dir>/scan/). Relative paths are resolved
against the default parent.
--scan-one-based BOOLEAN Override the scan subcommand indexing
interpretation (True = 1-based, False =
0-based). Defaults to 1-based.
--scan-max-step-size FLOAT Override scan --max-step-size (Å). Defaults to
0.20 Å.
--scan-bias-k FLOAT Override scan harmonic bias strength k
(eV/Å^2). Defaults to 300.
--scan-relax-max-cycles INTEGER
Override scan relaxation max cycles per step.
Defaults to 10000.
--scan-preopt BOOLEAN Override scan --preopt flag. Inherits from
--preopt when omitted.
--scan-endopt BOOLEAN Override scan --endopt flag. Defaults to
False.
--ref-pdb FILE Reference PDB for topology when -i provides
XYZ inputs. Enables PDB output conversion in
TSOPT-only, scan, and path_search pipelines.
-h, --help Show this message and exit.