# pdb2reaction extract

```
pdb2reaction ver. 0.2.1.dev116+gff86b942a

Usage: cli extract [OPTIONS]

  Extract a binding pocket around substrate residues (from a PDB or residue
  IDs/names), with biochemically aware truncation and optional link-H; supports
  multi-structure input and multi-MODEL output.

Options:
  --help-advanced           Show all options (including advanced settings) and
                            exit.
  -i, --input TEXT          Protein-substrate complex PDB(s). If multiple, they
                            must have identical atom counts and ordering.
                            [required]
  -c, --center TEXT         Substrate specification: a PDB path, a comma/space-
                            separated residue-ID list like '123,124' or
                            'A:123,B:456' (insertion codes supported), or a
                            residue-name list like 'GPP,SAM'.  [required]
  -o, --output TEXT         Output PDB path(s). One path for multi-MODEL PDB, or
                            N paths for per-file output. If omitted: single
                            input -> pocket.pdb; multiple inputs ->
                            pocket_{filename}.pdb.
  -r, --radius FLOAT        Cutoff (angstrom) around substrate atoms for pocket
                            inclusion.  [default: 2.6]
  -l, --ligand-charge TEXT  Total charge number or per-resname mapping like
                            'GPP:-3,SAM:1'.
  -h, --help                Show this message and exit.
```
