test2.py

import Bio.PDB
import Bio.PDB.Atom
import numpy as np


def main():
    structure = Bio.PDB.PDBParser().get_structure("4pqv", "tests/4pqv_A.pdb")
    residues = list(structure.get_residues())
    res1 = residues[8]
    res2 = residues[3]
    atoms1 = list(res1.get_atoms())
    atoms2 = list(res2.get_atoms())
    min_dist = 999
    min_atom1 = Bio.PDB.Atom.Atom("dummy", np.zeros(3), 0, 1, 1, "dummy", 0)
    min_atom2 = Bio.PDB.Atom.Atom("dummy", np.zeros(3), 0, 1, 1, "dummy", 0)
    for a1 in atoms1:
        for a2 in atoms2:
            if np.linalg.norm(a1.get_coord() - a2.get_coord()) < min_dist:
                min_dist = np.linalg.norm(a1.get_coord() - a2.get_coord())
                min_atom1 = a1
                min_atom2 = a2

    print(
        f"Minimal distance: {min_dist:.2f}, Coordinate1: {min_atom1}, Coordinate2: {min_atom2}"
    )


if __name__ == "__main__":
    main()