Write simple tests

MDAnalysis · Oct 2, 2024 · 950cfcf · 950cfcf
1 parent 27c10d6
commit 950cfcf
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Showing 2 changed files with 26 additions and 8 deletions.
diff --git a/testsuite/MDAnalysisTests/coordinates/test_mmcif.py b/testsuite/MDAnalysisTests/coordinates/test_mmcif.py
@@ -1,6 +1,4 @@
 import glob
-import os
-from io import StringIO
 
 import MDAnalysis as mda
 import numpy as np
@@ -34,11 +32,28 @@ def test_works_without_explicit_format(mmcif_filename):
     [
         (f"{MMCIF_FOLDER}/1YJP.cif", 59, 66),
         (f"{MMCIF_FOLDER}/1YJP.cif.gz", 59, 66),
-        (f"{MMCIF_FOLDER}/7ETN.cif", 70, 70),
-        (f"{MMCIF_FOLDER}/7ETN.cif.gz", 70, 70),
+        (f"{MMCIF_FOLDER}/7ETN.cif", 150, 150),
+        (f"{MMCIF_FOLDER}/7ETN.cif.gz", 150, 150),
     ],
 )
 def test_n_atoms(mmcif_filename, natoms_protein, natoms_total):
     u = mda.Universe(mmcif_filename)
     assert len(u.atoms) == natoms_total
-    assert len(u.select("protein").atoms) == natoms_protein
+    assert len(u.select_atoms("protein").atoms) == natoms_protein
+
+
+@pytest.mark.parametrize(
+    "mmcif_filename,cell",
+    [
+        (
+            f"{MMCIF_FOLDER}/1YJP.cif.gz",
+            np.array([21.937, 4.866, 23.477, 90.00, 107.08, 90.00]),
+        ),
+        (
+            f"{MMCIF_FOLDER}/7ETN.cif.gz",
+            np.array([5.264, 24.967, 20.736, 90.00, 94.85, 90.00]),
+        ),
+    ],
+)
+def test_cell(mmcif_filename, cell):
+    assert np.allclose(mda.Universe(mmcif_filename).coord._unitcell, cell)
diff --git a/testsuite/MDAnalysisTests/topology/test_mmcif.py b/testsuite/MDAnalysisTests/topology/test_mmcif.py
@@ -34,15 +34,18 @@ def test_chains(mmcif_filename, n_chains):
 @pytest.mark.parametrize(
     "mmcif_filename,sequence",
     [
-        (f"{MMCIF_FOLDER}/1YJP.cif", ["GLY", "ASN", "ASN", "GLN", "GLN", "ASN", "TRY"]),
+        (f"{MMCIF_FOLDER}/1YJP.cif", ["GLY", "ASN", "ASN", "GLN", "GLN", "ASN", "TYR"]),
         (
             f"{MMCIF_FOLDER}/1YJP.cif.gz",
-            ["GLY", "ASN", "ASN", "GLN", "GLN", "ASN", "TRY"],
+            ["GLY", "ASN", "ASN", "GLN", "GLN", "ASN", "TYR"],
         ),
         (f"{MMCIF_FOLDER}/7ETN.cif", ["PRO", "PHE", "LEU", "ILE"]),
         (f"{MMCIF_FOLDER}/7ETN.cif.gz", ["PRO", "PHE", "LEU", "ILE"]),
     ],
 )
 def test_sequence(mmcif_filename, sequence):
     u = mda.Universe(mmcif_filename)
-    assert [res.resname for res in u.residues] == sequence
+    in_structure = [
+        str(res.resname) for res in u.select_atoms("protein and chainid A").residues
+    ]
+    assert in_structure == sequence, ":".join(in_structure)