Usage

To use BioInterface in a Python project:

import biointerface

You can extract a single Protein-DNA interface from a single protein chain.

from Bio.PDB.PDBList import PDBList
from Bio.PDB.MMCIFParser import MMCIFParser
from biointerface import Interface, build_interfaces

# retrive file from PDB using Biopython
pdbl = PDBList()
pdbl.retrieve_pdb_file(pdb_code="1A02", pdir=".")
pdbl.retrieve_assembly_file(pdb_code="1A02", assembly_num=1, pdir=".")
# ... or else use your own

# parse and build structure with Biopython
parser = MMCIFParser()
structure = parser.get_structure(
    structure_id="1A02", filename="1a02-assembly1.cif"
)

# extract interface from a specific protein chain
face = Interface(
    structure=structure,
    protein_chain_id="A",
    search_radius=5.0
)
face

<Interface chains=F:BA contacts=258 search_radius=5.0>

You can also extract all Protein-DNA interface from an entire structure.

face_list = build_interfaces(structure=structure, search_radius=5.0)
face_list

[<Interface chains=J:BA contacts=189 search_radius=5.0>,
 <Interface chains=F:BA contacts=258 search_radius=5.0>,
 <Interface chains=N:BA contacts=529 search_radius=5.0>]