Command-line tools¶

ProteinDF_bridge installs a set of small, single-purpose CLI scripts under scripts/. Each one is a thin wrapper around proteindf_bridge that reads one format and writes another, or performs one structure-editing operation on a bridge (.brd) file. Run any of them with -h for full options.

Format conversion¶

Script	Description
`pdb2brd.py`	translate from PDB to bridge file
`brd2pdb.py`	transform bridge file to PDB file
`gro2brd.py`	translate from gro to bridge file
`brd2gro.py`	output gro format from bridge file
`xyz2brd.py`	transform XYZ file to bridge file
`brd2xyz.py`	transform bridge file to XYZ file
`mmcif2txt.py`	parse mmCIF file
`mmcif2mol2.py`	parse mmCIF file to mol2 file
`read_amber_prmtop.py`	parse Amber prmtop
`mpac2yml.py` / `yml2mpac.py`	convert between MsgPack and YAML bridge representations
`mpac2txt.py`	display file formatted by MsgPack using YAML
`brd2txt.py`	print molecular bridge file
`db2txt.py`	print DB (sqlite3) file

Structure editing¶

Script	Description
`brd-select.py`	bridge file selector
`brd-select-path.py`	bridge file selector (by path)
`brd-divide.py`	bridge file divider
`brd-divide-mainchain.py`	bridge file divider (main chain)
`brd-restructure.py`	restructure brd file by reference file
`brd-renumber-resid.py`	renumber resid in bridge file
`brd-setup-bond.py`	setup bonds
`brd-show-bonds.py`	show bonds
`brd-show-res.py`	print residues in the bridge file
`remove_wat.py`	remove water molecules in bridge file
`reorder.py`	reorder protein
`neutralize.py`	neutralize protein
`crystallize.py`	crystallize molecules
`superposer.py`	superpose

Analysis¶

Script	Description
`brd-box.py`	calc box size
`brd-density.py`	calc density
`brd-formula.py`	print molecular formula

Development¶

Script	Description
`doctest_runner.py`	run doctests across `proteindf_bridge`
`module_inspect.py`	inspect module contents