Added tests for MoleculeGraph.

mlspm/graph/_molecule_graph.py

@@ -276,8 +276,10 @@ def transform_xy(
         """
         Transform atom positions in the xy plane.
 
+        Transformations are perfomed in the order: shift, rotate, flip x, flip y
+
         Arguments:
-            shift: Shift atom positions in xy plane. Performed before rotation and flip.
+            shift: Shift atom positions in xy plane.
             rot_xy: Rotate atoms in xy plane by rot_xy degrees around center point.
             flip_x: Mirror atom positions in x direction with respect to the center point.
             flip_y: Mirror atom positions in y direction with respect to the center point.

tests/test_graph.py

@@ -1,13 +1,14 @@
-from pathlib import Path
 import shutil
-import torch
-import pytest
+from pathlib import Path
+
 import numpy as np
+import pytest
+import torch
 
 
 def test_collate_graph():
-    from mlspm.graph import MoleculeGraph
     from mlspm.data_loading import collate_graph
+    from mlspm.graph import MoleculeGraph
 
     # fmt: off
 
@@ -217,7 +218,7 @@ def test_molecule_graph_array():
 
 
 def test_molecule_graph_remove_atoms():
-    from mlspm.graph import MoleculeGraph, Atom
+    from mlspm.graph import Atom, MoleculeGraph
 
     # fmt: off
 
@@ -245,7 +246,7 @@ def test_molecule_graph_remove_atoms():
     assert removed == []
 
     new_molecule, removed = molecule.remove_atoms([1])
-    removed_expected = [(Atom(np.array([1.0, 1.0, 0.0]), 2), [0, 1, 0])]
+    removed_expected = [(Atom(np.array([1.0, 1.0, 0.0]), 'H'), [0, 1, 0])]
     atoms_expected = np.array([
         [0.0, 0.0,  0.0, 1],
         [1.0, 0.0,  0.0, 3],
@@ -333,10 +334,80 @@ def test_molecule_graph_add_atom():
         assert a == b
 
 
-def test_GraphSeqStats():
-    from mlspm.graph import GraphStats
+def test_molecule_graph_transform_xy():
+    from mlspm.graph import MoleculeGraph
+
+    # fmt:off
+    atoms = np.array([
+            [0.0, 0.0,  0.0, 1],
+            [1.0, 1.0,  1.0, 2],
+            [1.0, 0.0,  0.0, 3],
+            [2.0, 0.0, -1.0, 4]
+    ])
+    # fmt:on
+    bonds = [(0, 2), (1, 2), (2, 3)]
+    molecule = MoleculeGraph(atoms, bonds)
+
+    molecule_transformed = molecule.transform_xy(shift=(1, 1), rot_xy=90, flip_x=True, flip_y=True, center=(1, 1))
+
+    xyz_transformed = molecule_transformed.array(xyz=True)
+    # fmt:off
+    xyz_expected = np.array(
+        [
+            [1.0,  1.0,  0.0],
+            [2.0,  0.0,  1.0],
+            [1.0,  0.0,  0.0],
+            [1.0, -1.0, -1.0]
+        ]
+    )
+    # fmt:on
+
+    assert np.allclose(xyz_transformed, xyz_expected)
+
+
+def test_molecule_graph_crop_atoms():
+    from mlspm.graph import MoleculeGraph
+
+    # fmt:off
+    atoms = np.array([
+            [0.0, 0.0,  0.0, 1],
+            [1.0, 1.0,  1.0, 2],
+            [1.0, 0.0,  0.0, 3],
+            [2.0, 0.0, -1.0, 4]
+    ])
+    # fmt:on
+    bonds = [(0, 2), (1, 2), (2, 3)]
+    molecule = MoleculeGraph(atoms, bonds)
+    box_borders = np.array([[-0.5, -0.5, -0.5], [1.5, 1.5, 0.5]])
+
+    molecule_cropped = molecule.crop_atoms(box_borders)
+
+    xyz_cropped = molecule_cropped.array(xyz=True)
+    # fmt:off
+    xyz_expected = np.array(
+        [
+            [0.0, 0.0,  0.0],
+            [1.0, 0.0,  0.0],
+        ]
+    )
+    # fmt:on
+
+    assert np.allclose(xyz_cropped, xyz_expected)
+    assert molecule_cropped.bonds == [(0, 1)]
+
+
+def test_molecule_graph_randomize_positions():
     from mlspm.graph import MoleculeGraph
 
+    molecule = MoleculeGraph(np.zeros((3, 4)), [])
+    molecule_randomized = molecule.randomize_positions()
+
+    assert not np.allclose(molecule_randomized.array(xyz=True), 0.0)
+
+
+def test_GraphSeqStats():
+    from mlspm.graph import GraphStats, MoleculeGraph
+
     classes = [[0], [1], [2]]
 
     # fmt:off