From e42a13c61f8286769673137fb84ca895c05c7d21 Mon Sep 17 00:00:00 2001
From: Kiyoon Kim <kiyoon@users.noreply.github.com>
Date: Mon, 21 Oct 2024 17:09:57 +0900
Subject: [PATCH] refactor: use biotest

---
 pyproject.toml        |  7 ++++++
 requirements_test.txt |  1 +
 tests/test_helpers.py | 50 +++++--------------------------------------
 3 files changed, 13 insertions(+), 45 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index a9f6081..070639a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -87,6 +87,13 @@ max-line-length = 120
 [tool.ruff.lint.isort]
 # combine-as-imports = true
 known-third-party = ["wandb"]
+known-first-party = [
+  "rust_graph",
+  "bio_data_to_db",
+  "apbs_binary",
+  "slack_helpers",
+  "biotest",
+]
 
 ## Uncomment this if you want to use Python < 3.10
 # required-imports = [
diff --git a/requirements_test.txt b/requirements_test.txt
index 90c22de..4a44ffd 100644
--- a/requirements_test.txt
+++ b/requirements_test.txt
@@ -1,3 +1,4 @@
 pytest
 pytest-cov
 numpy
+biotest @ git+https://github.com/deargen/biotest@master
diff --git a/tests/test_helpers.py b/tests/test_helpers.py
index 9545263..dc52510 100644
--- a/tests/test_helpers.py
+++ b/tests/test_helpers.py
@@ -5,9 +5,9 @@
 from os import PathLike
 from pathlib import Path
 
-import numpy as np
 import pytest
 
+from biotest.compare_files import assert_two_pdb_files_within_tolerance
 from reduce_binary.helpers import protonate
 
 logger = logging.getLogger(__name__)
@@ -15,47 +15,6 @@
 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"),
     [
@@ -81,7 +40,8 @@ def test_protonate(in_pdb_path: str | PathLike, answer_pdb_path: str | PathLike)
             remove_hydrogen_first=True,
         )
 
-        check_pdb_atoms_almost_equal(
-            out_pdb_path.read_text(),
-            answer_pdb_path.read_text(),
+        assert_two_pdb_files_within_tolerance(
+            out_pdb_path,
+            answer_pdb_path,
+            tolerance=1e-3,
         )