Usage: mlmm all [OPTIONS]
Run pocket extraction → (optional single-structure staged scan) → MEP search
in one shot. If exactly one input is provided: (a) with --scan-lists, stage
results feed into 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** PDBs in reaction order
(reactant [intermediates ...] product), or a
single **full** PDB (with --scan-lists or with
--tsopt True). You may pass a single '-i'
followed by multiple space-separated files
(e.g., '-i A.pdb B.pdb C.pdb'). [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,MMT'. When omitted, extraction is skipped
and full structures are used directly.
-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, --include-h2o BOOLEAN
Include waters (HOH/WAT/TIP3/SOL) in the
pocket. [default: True]
--exclude-backbone BOOLEAN Remove backbone atoms on non‑substrate amino
acids (with PRO/HYP safeguards). [default:
True]
--add-linkH BOOLEAN Add link hydrogens for severed bonds (carbon-
only) in pockets. [default: False]
--selected-resn TEXT Force-include residues (comma/space separated;
chain/insertion codes allowed). [default: ""]
-l, --ligand-charge TEXT Either a total charge (number) to distribute
across unknown residues or a mapping like
'GPP:-3,MMT:-1'.
-q, --charge INTEGER Force total system charge. Highest priority
over derived charges.
--parm FILE Pre-built AMBER parm7 topology file. When
provided, mm_parm generation is skipped.
--model-pdb FILE Pre-built ML-region PDB (with B-factor layer
info). When provided, ml_region generation is
skipped.
--auto-mm-ff-set [ff19sb|ff14sb]
Force-field set forwarded to mm_parm (ff19SB
uses OPC3; ff14SB uses TIP3P). [default:
ff19SB]
--auto-mm-add-ter / --auto-mm-no-add-ter
Control mm_parm TER insertion around
ligand/water/ion blocks. [default: auto-mm-
add-ter]
--auto-mm-keep-temp Keep the mm_parm temporary working directory
(for debugging).
--auto-mm-ligand-mult TEXT Spin multiplicity mapping forwarded to mm_parm
(e.g., 'GPP:2,SAM:1'). If omitted, mm_parm
defaults to 1 for all ligands.
--verbose BOOLEAN Enable INFO-level logging inside extractor.
[default: True]
-m, --multiplicity INTEGER Multiplicity (2S+1). [default: 1]
--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/path-search
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 tsopt defaults. [default: hess]
--dump BOOLEAN Dump GSM / single-structure trajectories
during the run, forwarding the same flag to
scan/tsopt/freq. [default: False]
--refine-path / --no-refine-path
If True, run recursive path_search on the full
ordered series; if False, run a single-pass
path-opt GSM between each adjacent pair and
concatenate the segments (no path_search).
[default: refine-path]
--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]
--preopt BOOLEAN If False, skip initial single-structure
optimizations of the pocket inputs. [default:
True]
--hessian-calc-mode [analytical|finitedifference]
Common MLIP Hessian calculation mode forwarded
to tsopt and freq. Default:
'FiniteDifference'. Use 'Analytical' when VRAM
is sufficient.
--detect-layer / --no-detect-layer
Detect ML/MM layers from input PDB B-factors
(B=0/10/20) in downstream tools. If disabled,
downstream tools require --model-pdb or
--model-indices. [default: detect-layer]
--tsopt BOOLEAN TS optimization + pseudo-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.
--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]
--tsopt-out-dir DIRECTORY Override tsopt output subdirectory (relative
paths are resolved against the default).
--freq-out-dir DIRECTORY Override freq output base directory (relative
paths resolved against the default).
--freq-max-write INTEGER Override freq --max-write value.
--freq-amplitude-ang FLOAT Override freq --amplitude-ang (Å).
--freq-n-frames INTEGER Override freq --n-frames value.
--freq-sort [value|abs] Override freq mode sorting.
--freq-temperature FLOAT Override freq thermochemistry temperature (K).
--freq-pressure FLOAT Override freq thermochemistry pressure (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.
--dft-max-cycle INTEGER Override dft --max-cycle value.
--dft-conv-tol FLOAT Override dft --conv-tol value.
--dft-grid-level INTEGER Override dft --grid-level value.
-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 PDB (1-based) or PDB atom
selectors like "TYR,285,CA"; they are auto-
mapped to the pocket 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 scan indexing interpretation (True =
1-based, False = 0-based).
--scan-max-step-size FLOAT Override scan --max-step-size (Å).
--scan-bias-k FLOAT Override scan harmonic bias strength k
(eV/Å^2).
--scan-relax-max-cycles INTEGER
Override scan relaxation max cycles per step.
--scan-preopt BOOLEAN Override scan --preopt flag.
--scan-endopt BOOLEAN Override scan --endopt flag.
--convert-files / --no-convert-files
Convert XYZ/TRJ outputs to PDB format using
reference topology; forwarded to all
subcommands. [default: convert-files]
--ref-pdb FILE Reference PDB for topology/B-factor layer
information when -i provides XYZ inputs. Used
for define-layer, mm_parm, ml_region, and
forwarded to downstream tools (tsopt, irc,
freq, path_search) as --ref-pdb.
-b, --backend [uma|orb|mace|aimnet2]
ML backend for the ONIOM high-level region
(default: uma).
--embedcharge / --no-embedcharge
Enable xTB point-charge embedding correction
for MM→ML environmental effects. [default:
no-embedcharge]
--embedcharge-cutoff FLOAT Distance cutoff (Å) from ML region for MM
point charges in xTB embedding. Default: 12.0
Å when --embedcharge is enabled.
-h, --help Show this message and exit.