Merge pull request #3 from fxcoudert/load_structure

Document and test the loading of JSON files

src/moxel/utils.py

@@ -117,17 +117,18 @@ def __init__(self, grid_size=25, cutoff=10, epsilon=50, sigma=2.5):
         self.epsilon = epsilon
         self.sigma = sigma
 
-    def load_structure(self, cif_pathname):
+    def load_structure(self, pathname):
         r"""
-        Load a crystal structure from a ``.cif`` file.
+        Load a crystal structure from a file in a format supported by pymatgen
+        (CIF, JSON, etc.)
 
         Parameters
         ----------
-        cif_pathname : str
-           Pathname to the ``.cif`` file.
+        pathname : str
+           Pathname to the file.
         """
-        self.structure = Structure.from_file(cif_pathname)
-        self.structure_name = Path(cif_pathname).stem
+        self.structure = Structure.from_file(pathname)
+        self.structure_name = Path(pathname).stem
 
     def calculate(self, cubic_box=False, length=30, potential='lj', n_jobs=None):
         r"""

tests/test_utils.py

@@ -159,6 +159,15 @@ def test_batch_clean(self):
             # Check that the names have been correctly stored.
             self.assertEqual([names[i] for i in filled_idx], clean_names)
 
+    def test_load_file(self):
+        cif_dir = 'tests/CIFs'
+
+        grid = Grid()
+        grid.load_structure(f'{cif_dir}/IRMOF-1.cif')
+
+        grid = Grid()
+        grid.load_structure(f'{cif_dir}/MnH28C26(N2Cl)2.json')
+
 
 if __name__ == '__main__':
     unittest.main()