Usage: mlmm oniom-import [OPTIONS]
Import ONIOM input (Gaussian g16 or ORCA) and reconstruct XYZ + B-factor
layered PDB.
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 Input ONIOM file (.gjf/.com for g16, .inp for
ORCA). [required]
--mode [g16|orca] Input mode. If omitted, inferred from input
suffix. [default: (inferred from the input
suffix)]
-o, --out-prefix PATH Output prefix. Defaults to input stem in the
current working directory.
--ref-pdb FILE Reference PDB to preserve atom naming/residue
metadata (atom count must match).
--allow-unverified-ref-order / --no-allow-unverified-ref-order
Allow legacy positional --ref-pdb mapping when
repeated elements make atom identity
unverifiable. Use only after independently
checking order. [default: no-allow-
unverified-ref-order]
-h, --help Show this message and exit.