.

tests/test_helpers.py

@@ -5,6 +5,7 @@
 from os import PathLike
 from pathlib import Path
 
+import numpy as np
 import pytest
 
 from reduce_binary.helpers import protonate
@@ -14,6 +15,47 @@
 SCRIPT_DIR = Path(__file__).resolve().parent
 
 
+def check_pdb_atoms_almost_equal(
+    pdb1_str: str,
+    pdb2_str: str,
+):
+    # ATOM    998  N   PHE B   9      18.937-159.292 -13.075  1.00 30.49           N
+    pdb1_lines = pdb1_str.splitlines()
+    pdb2_lines = pdb2_str.splitlines()
+    assert len(pdb1_lines) == len(pdb2_lines)
+
+    for pdb1_line, pdb2_line in zip(pdb1_lines, pdb2_lines):
+        if pdb1_line.startswith("ATOM") and pdb2_line.startswith("ATOM"):
+            coord_1 = (
+                float(pdb1_line[32:38]),
+                float(pdb1_line[38:47]),
+                float(pdb1_line[47:56]),
+            )
+            coord_2 = (
+                float(pdb2_line[32:38]),
+                float(pdb2_line[38:47]),
+                float(pdb2_line[47:56]),
+            )
+
+            for c1, c2 in zip(coord_1, coord_2):
+                assert np.isclose(
+                    c1, c2, atol=1e-3
+                ), f"{pdb1_line.rstrip()} and {pdb2_line.rstrip()} are not equal."
+
+            line1_except_coord = pdb1_line[:32] + pdb1_line[56:]
+            line2_except_coord = pdb2_line[:32] + pdb2_line[56:]
+            assert (
+                line1_except_coord.rstrip() == line2_except_coord.rstrip()
+            ), f"{pdb1_line.rstrip()} and {pdb2_line.rstrip()} are not equal."
+
+        else:
+            assert (
+                pdb1_line.rstrip() == pdb2_line.rstrip()
+            ), f"{pdb1_line.rstrip()} and {pdb2_line.rstrip()} are not equal."
+
+    return True
+
+
 @pytest.mark.parametrize(
     ("in_pdb_path", "answer_pdb_path"),
     [
@@ -38,4 +80,8 @@ def test_protonate(in_pdb_path: str | PathLike, answer_pdb_path: str | PathLike)
             out_pdb_path,
             remove_hydrogen_first=True,
         )
-        assert out_pdb_path.read_text() == answer_pdb_path.read_text()
+
+        check_pdb_atoms_almost_equal(
+            out_pdb_path.read_text(),
+            answer_pdb_path.read_text(),
+        )