test_bm_get_ref_coord.py

import Bio.PDB
import Bio.PDB.Residue
import pytest
import numpy as np
from src.BioHelpers_FABER.bio_mod import get_reference_coordinates

STRUCTURE = Bio.PDB.PDBParser().get_structure("4pqv", "tests/4pqv_A.pdb")
RESIDUES = list(STRUCTURE.get_residues())


def test_get_ref_coord_reference():
    with pytest.raises(ValueError):
        get_reference_coordinates(RESIDUES[5], RESIDUES[5], reference="bla")


def test_get_ref_coord_nitrogen():
    assert (
        get_reference_coordinates(RESIDUES[5], RESIDUES[5], reference="nitrogen")[0]
        == np.array([16.97, 18.539, 12.012], dtype=np.float32)
    ).all()
    assert (
        get_reference_coordinates(RESIDUES[5], RESIDUES[5], reference="nitrogen")[1]
        == np.array([16.97, 18.539, 12.012], dtype=np.float32)
    ).all()


def test_get_ref_coord_nearest():
    expected_val = np.array([20.483, 18.827, 16.128], dtype=np.float32)
    np.testing.assert_equal(
        get_reference_coordinates(RESIDUES[5], RESIDUES[5], reference="nearest"),
        (
            expected_val,
            expected_val,
        ),
    )