add box to molecule when parsing gro files

marrink-lab · Apr 25, 2023 · 954cd36 · 954cd36
1 parent 99a936f
commit 954cd36
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Showing 2 changed files with 6 additions and 1 deletion.
diff --git a/vermouth/gmx/gro.py b/vermouth/gmx/gro.py
@@ -107,6 +107,11 @@ def read_gro(file_name, exclude=('SOL',), ignh=False):
 
             molecule.add_node(idx, **properties)
             idx += 1
+        box = np.array(line.strip().split(), dtype=float)
+        # not pretty but the parser is out of touch with the rest of the parsing
+        # infrastructure already
+        molecule.box = box
+
     return molecule
 
 

diff --git a/vermouth/tests/gmx/test_gro.py b/vermouth/tests/gmx/test_gro.py
@@ -540,7 +540,7 @@ def test_read_gro(gro_reference, exclude, ignh):  # pylint: disable=redefined-ou
     molecule = gro.read_gro(filename, exclude=exclude, ignh=ignh)
     pprint(list(molecule.nodes.items()))
     assert_molecule_equal(molecule, reference)
-
+    assert all(molecule.box == np.array([10.0, 11.1, 12.2]))
 
 def test_read_gro_wrong_atom_number(gro_wrong_length):  # pylint: disable=redefined-outer-name
     """