Move pymatgen import to get_primitive() function

hjkgrp · Dec 17, 2023 · 450c8dd · 450c8dd
1 parent 91d0b45
commit 450c8dd
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Showing 4 changed files with 13 additions and 10 deletions.
diff --git a/molSimplify/Informatics/MOF/MOF_descriptors.py b/molSimplify/Informatics/MOF/MOF_descriptors.py
@@ -54,7 +54,6 @@
 
 ### Defining pymatgen function for getting primitive, since molSimplify does not depend on pymatgen.
 # This function is commented out and should be uncommented if used.
-from pymatgen.io.cif import CifParser
 
 
 def get_primitive(datapath, writepath, occupancy_tolerance=1):
@@ -75,10 +74,10 @@ def get_primitive(datapath, writepath, occupancy_tolerance=1):
     None
 
     """
-
+    from pymatgen.io.cif import CifParser
     s = CifParser(datapath, occupancy_tolerance=occupancy_tolerance).get_structures()[0]
     sprim = s.get_primitive_structure()
-    sprim.to("cif", writepath)  # Output structure to a file.
+    sprim.to(writepath, "cif")  # Output structure to a file.
 
 
 '''<<<< END OF CODE TO COMPUTE PRIMITIVE UNIT CELLS >>>>'''

diff --git a/molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional.py b/molSimplify/Informatics/MOF/MOF_descriptors_alternate_functional.py
@@ -23,11 +23,15 @@
 # This MOF RAC generator assumes that pymatgen is installed.                            #
 # Pymatgen is used to get the primitive cell.                                           #
 #########################################################################################
-from pymatgen.io.cif import CifParser
+
+
 def get_primitive(datapath, writepath):
+    from pymatgen.io.cif import CifParser
     s = CifParser(datapath, occupancy_tolerance=1).get_structures()[0]
     sprim = s.get_primitive_structure()
-    sprim.to("cif",writepath)
+    sprim.to("cif", writepath)
+
+
 '''<<<< END OF CODE TO COMPUTE PRIMITIVE UNIT CELLS >>>>'''
 
 #########################################################################################

diff --git a/molSimplify/Informatics/MOF/cluster_extraction.py b/molSimplify/Informatics/MOF/cluster_extraction.py
@@ -19,10 +19,10 @@
 # This MOF RAC generator assumes that pymatgen is installed.                            #
 # Pymatgen is used to get the primitive cell.                                           #
 #########################################################################################
-from pymatgen.io.cif import CifParser
 
 
 def get_primitive(datapath, writepath):
+    from pymatgen.io.cif import CifParser
     s = CifParser(datapath, occupancy_tolerance=1).get_structures()[0]
     sprim = s.get_primitive_structure()
     sprim.to("cif", writepath)

diff --git a/tests/informatics/test_MOF_descriptors.py b/tests/informatics/test_MOF_descriptors.py
@@ -33,24 +33,24 @@ def RACs_names(starts, properties, depth, scope="all"):
 
 
 @pytest.mark.parametrize(
-    "name",
+    "cif_file",
     ["odac-21383.cif",
      "odac-21433.cif",
      "odac-21478.cif",
      "odac-21735.cif",
      "odac-21816.cif"])
-def test_get_MOF_descriptors(resource_path_root, tmpdir, name, ref_names):
+def test_get_MOF_descriptors(resource_path_root, tmpdir, cif_file, ref_names):
     with DebugTimer("get_MOF_descriptors()"):
         full_names, full_descriptors = get_MOF_descriptors(
-            str(resource_path_root / "inputs" / "cif_files" / name),
+            str(resource_path_root / "inputs" / "cif_files" / cif_file),
             depth=3,
             path=str(tmpdir),
             xyzpath=str(tmpdir / "test.xyz"),
             Gval=True,
         )
 
     with open(resource_path_root / "refs" / "MOF_descriptors"
-              / name.replace("cif", "json"), "r") as fin:
+              / cif_file.replace("cif", "json"), "r") as fin:
         ref = json.load(fin)
 
     assert full_names == ref_names