Usage: pdb2reaction add-elem-info [OPTIONS]
Add/repair element columns (77–78) in a 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 PDB filepath. [required]
-o, --output, --out FILE Output PDB filepath (default: replace ".pdb"
with "_add_elem.pdb"; when provided,
--overwrite is ignored unless this is the
input file, which requires it).
--overwrite / --no-overwrite Overwrite the input file in-place when
-o/--out is omitted. [default: no-overwrite]
--overwrite-elem / --no-overwrite-elem
Also re-infer element columns that already
hold a valid element (off: only empty or
invalid columns are filled). [default: no-
overwrite-elem]
-h, --help Show this message and exit.
