molify 0.2.3__tar.gz → 0.2.5__tar.gz

{molify-0.2.3 → molify-0.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: molify
-Version: 0.2.3
+Version: 0.2.5
 Summary: Molecular Structure Interface with RDKit, ASE, Packmol and NetworkX
 Project-URL: Repository, https://github.com/zincware/molify
 Project-URL: Releases, https://github.com/zincware/molify/releases

{molify-0.2.3 → molify-0.2.5}/src/molify/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.2.3'
-__version_tuple__ = version_tuple = (0, 2, 3)
+__version__ = version = '0.2.5'
+__version_tuple__ = version_tuple = (0, 2, 5)
 
 __commit_id__ = commit_id = None

{molify-0.2.3 → molify-0.2.5}/src/molify/compress.py

@@ -18,7 +18,7 @@ def compress(
     atoms : ase.Atoms
         The Atoms object to compress.
     density : float
-        The target density in g/cm^3.
+        The target density in kg/m^3.
     freeze_molecules : bool
         If True, freeze the internal degrees of freedom of the molecules
         during compression, to prevent bond compression.

{molify-0.2.3 → molify-0.2.5}/src/molify/pack.py

@@ -137,6 +137,9 @@ def _extract_atom_arrays(
     charges = np.concatenate([atom.get_initial_charges() for atom in selected_images])
     if any(charge != 0 for charge in charges):
         packed_atoms.set_initial_charges(charges)
+    tags = np.concatenate([atom.get_tags() for atom in selected_images])
+    if any(tag != 0 for tag in tags):
+        packed_atoms.set_tags(tags)
     return packed_atoms
 
 

{molify-0.2.3 → molify-0.2.5}/tests/test_solvate.py

@@ -109,6 +109,16 @@ def test_pack_charges():
     assert charges == [0, 0, 0, -1, 0, 1] + [1, 0, 0, -1, 0, 0, 0, 0, 0, 0]
 
 
+def test_pack_tags():
+    water = smiles2conformers("O", 1)
+    methane = smiles2conformers("C", 1)
+    water[0].set_tags(range(1, 4))  # O, H, H -> 1, 2, 3
+    methane[0].set_tags(range(4, 9))  # C, H, H, H, H -> 4, 5, 6, 7, 8
+
+    atoms = pack([water, methane], [2, 1], density=1000)
+    npt.assert_array_equal(atoms.get_tags(), [1, 2, 3, 1, 2, 3, 4, 5, 6, 7, 8])
+
+
 def test_pack_ratio():
     water = smiles2conformers("O", 1)
     # pack a cubic box