Usage: mlmm define-layer [OPTIONS]
Define 3-layer ML/MM system based on distance from ML region.
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 PDB or mmCIF file containing the full
system. [required]
--model-pdb FILE PDB or mmCIF file defining atoms in the ML
region.
--model-indices TEXT Comma-separated atom indices for ML region
(e.g., '1,2,3,4' or '1-10,15,20-25'). Used
when --model-pdb is omitted.
--movable-cutoff, --radius-freeze FLOAT
Distance cutoff (Å) from ML region for movable
MM atoms. Atoms beyond this distance are
frozen. [default: 8.0]
-o, --output FILE Output PDB file with B-factors set to layer
values. Defaults to '<input>_layered.pdb'.
[default: (<input>_layered.pdb)]
--one-based / --zero-based Interpret --model-indices as 1-based or
0-based. [default: one-based]
-h, --help Show this message and exit.
