Usage: mlmm sp [OPTIONS]
Compute a single-point ML/MM ONIOM energy + forces (and optionally Hessian).
Options:
-v, --verbose LEVEL Console verbosity 0-3 (default 2). 0=silent;
1=milestones only; 2=+detailed step logging
and 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 Layered PDB (or XYZ) defining the ML/MM/Frozen
system. [required]
--parm, --real-parm7 FILE Amber parm7 of the full enzyme (canonical flag
is --parm; --real-parm7 retained as alias).
[required]
--model-pdb FILE PDB defining atoms that belong to the ML
(high-level) region. Optional when --detect-
layer is enabled.
--model-indices TEXT Comma-separated atom indices for the ML region
(ranges allowed like 1-5). Used when --model-
pdb is omitted.
--freeze-atoms TEXT Comma-separated 1-based atom indices to freeze
(e.g., '1,3,5').
--radius-partial-hessian, --hess-cutoff FLOAT
Distance cutoff (Å) from ML region for MM
atoms to include in Hessian calculation.
Applied to movable MM atoms; combinable with
--detect-layer.
--radius-freeze, --movable-cutoff FLOAT
Distance cutoff (Å) from ML region for movable
MM atoms. MM atoms beyond this are frozen.
-q, --charge INTEGER ML region total charge.
-l, --ligand-charge TEXT Per-ligand charge mapping, e.g.
'SAM:1,GPP:-3'.
-m, --multiplicity INTEGER ML region spin multiplicity (2S+1).
-o, --out-dir TEXT Output directory. [default: ./result_sp/]
--hess / --no-hess Also compute the full ONIOM Hessian and save
to hessian.npy. [default: no-hess]
--hessian-calc-mode [analytical|finitedifference]
Hessian backend when --hess is set. Analytical
only works for UMA; other backends fall back
to FiniteDifference.
--convert-files / --no-convert-files
Auto-convert output XYZ-like files into
matching PDB beside them. [default: convert-
files]
--config FILE YAML config file with sections (calc:, geom:,
…).
--show-config / --no-show-config
Print effective merged config and exit.
--dry-run / --no-dry-run Validate options and print the plan without
running.
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
-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
(experimental). [default: no-embedcharge]
--embedcharge-cutoff FLOAT Embed-charge cutoff radius (Å) around the ML
region.
--link-atom-method [scaled|fixed]
Link-atom positioning: scaled (g-factor) or
fixed (1.09/1.01 Å).
--mm-backend [hessian_ff|openmm]
MM backend (default: hessian_ff).
--cmap / --no-cmap Enable CMAP (backbone cross-map) terms in
model parm7.
--detect-layer / --no-detect-layer
Detect ML/MM layers from input PDB B-factors
(ML=0, MovableMM=10, FrozenMM=20). If
disabled, you must provide --model-pdb or
--model-indices. [default: detect-layer]
--model-indices-one-based / --model-indices-zero-based
Interpret --model-indices as 1-based (default)
or 0-based. [default: model-indices-one-
based]
--precision [fp32|fp64] MLIP backend precision: fp32 (default) or
fp64. Routed to backend-specific kwargs (UMA
precision / ORB precision / MACE
default_dtype). aimnet2: fp32 no-op; fp64
rejected.
--backend-model TEXT Model variant for the selected --backend (e.g.
uma-s-1p1 / uma-m-1p1 for uma,
orb_v3_conservative_omol for orb, MACE-OMOL-0
/ MACE-OFF23_small for mace). Default: the
backend's built-in model.
--calc-file FILE Python file exposing get_calculator(...) -> an
ASE Calculator used as the ML-region backend
(overrides --backend). Couples GFN-xTB / DFTB+
/ any ASE engine. See --calc-factory.
--calc-factory TEXT Name of the callable in --calc-file that
returns an ASE Calculator (or a module-level
Calculator instance). [default:
get_calculator]
--deterministic / --no-deterministic
Strict bit-reproducible GPU runs
(deterministic algorithms + index_reduce_
shim). Slower; raises if unsupported. Default
off.
--allow-charge-mult-mismatch Skip the ML-region charge/multiplicity
electron-parity check (logs that it was
skipped). For an intentional open-shell or
covalently-cut ML region.
--print-every INTEGER RANGE Print optimizer status every N cycles (debug
knob). [x>=1]
-h, --help Show this message and exit.