Work with protein interfaces

Start from a selected interface ID and rebuild its two-chain coordinate view. Use Query the release tables to select interfaces and Protein interfaces for the column definitions.

import biotite.structure as struc
import pandas as pd

from plinder.core import PlinderInterface

/home/runner/micromamba/envs/plinder/lib/python3.12/site-packages/vcs_versioning/_backends/_git.py:709: UserWarning: "/home/runner/work/plinder/plinder" is shallow and may cause errors
  pre_parse(wd)

Rebuild one interface

PlinderInterface expands the two selected assembly-chain instances from the source mmCIF revision recorded by the release.

interface = PlinderInterface(system_id="7cm8__1__1.A--2.A")
interface

PlinderInterface(system_id='7cm8__1__1.A--2.A')

pd.DataFrame(
    {
        "chain": interface.chains,
        "full_sequence_length": [
            len(interface.sequences[chain]) for chain in interface.chains
        ],
        "resolved_atom_count": [
            len(interface.chain_structures[chain]) for chain in interface.chains
        ],
    }
)

removing non-physical bond O@LEU53 <-> NA@NA1 (3.20 A > 3.16 A); likely inter-residue inference (get_assembly).

removing non-physical bond O@LEU53 <-> NA@NA1 (3.20 A > 3.16 A); likely inter-residue inference (get_assembly).

	chain	full_sequence_length	resolved_atom_count
0	1.A	350	2258
1	2.A	350	2258

sequences contains the full deposited polymer sequences; coordinate arrays contain only resolved atoms.

Interface residues and coordinate views

The residue masks are defined over the complete two-chain atom_array. Their keys match the assembly-chain IDs in interface_annotations.

summary = []
for chain, mask in interface.interface_residue_masks.items():
    atoms = interface.atom_array[mask]
    summary.append(
        {
            "chain": chain,
            "interface_residues": struc.get_residue_count(atoms),
            "interface_atoms": len(atoms),
        }
    )
pd.DataFrame(summary)

	chain	interface_residues	interface_atoms
0	1.A	100	757
1	2.A	100	757

print(f"Two-chain atoms: {len(interface.atom_array):,}")
print(f"Interface atoms: {len(interface.interface_structure):,}")
print(f"Reconstructed mmCIF: {interface.interface_cif}")

Two-chain atoms: 4,516
Interface atoms: 1,514
Reconstructed mmCIF: /home/runner/.local/share/plinder/2026-09/reconstructed_interfaces/7cm8__1__1.A--2.A/interface.cif

interface_cif is a pathlib.Path; atom_array, the values of chain_structures, and interface_structure are Biotite AtomArray objects. The written mmCIF is self-contained and contains only the selected interface chains.