Add io tests

molSimplify/Scripts/io.py

@@ -115,12 +115,6 @@ def readdict(fname):
 
 
 def readdict_sub(fname):
-    # Constructor
-    #  @param self The object pointer
-    #  @param subname The name of the substrate
-    class substrate:
-        def __init__(self, subname):
-            self.subname = subname
     d = dict()
     with open(fname, 'r') as f:
         txt = f.read()
@@ -137,8 +131,7 @@ def __init__(self, subname):
                     vv.append(vvs)
                 else:
                     vv += vvs
-            # dict keys are instances of the substrate class
-            d[substrate(key)] = vv
+            d[key] = vv
     return d
 
 # Get ligands in dictionary

tests/test_io.py

@@ -1,5 +1,11 @@
 import numpy as np
-from molSimplify.Scripts.io import lig_load
+from molSimplify.Scripts.io import (lig_load,
+                                    core_load,
+                                    printgeoms,
+                                    getsubstrates,
+                                    readdict_sub,
+                                    )
+from importlib_resources import files as resource_files
 
 
 def test_lig_load(resource_path_root):
@@ -18,3 +24,60 @@ def test_lig_load(resource_path_root):
     print(ref.coordsvect())
     np.testing.assert_allclose(mol.coordsvect(), ref.coordsvect())
     assert mol.charge == ref.charge
+
+
+def test_core_load():
+    file = str(resource_files("molSimplify").joinpath("Cores/ferrcore.xyz"))
+    core, emsg = core_load(file)
+    # Assert that the error message is empty
+    assert not emsg
+    core.convert2mol3D()
+    assert core.make_formula(latex=False) == "Fe1F1C10H9"
+
+    file = str(resource_files("molSimplify").joinpath("Cores/ferrocene.mol"))
+    core, emsg = core_load(file)
+    # Assert that the error message is empty
+    assert not emsg
+    core.convert2mol3D()
+    assert core.make_formula(latex=False) == "Fe1C10H10"
+
+
+def test_printgeoms(capsys):
+    printgeoms()
+    captured = capsys.readouterr()
+
+    ref = (
+        "Coordination: 1, geometry: none,\t short name: no \n"
+        "Coordination: 2, geometry: linear,\t short name: li \n"
+        "Coordination: 3, geometry: trigonal_planar,\t short name: tpl \n"
+        "Coordination: 4, geometry: square_planar,\t short name: sqp \n"
+        "Coordination: 4, geometry: tetrahedral,\t short name: thd \n"
+        "Coordination: 5, geometry: square_pyramidal,\t short name: spy \n"
+        "Coordination: 5, geometry: trigonal_bipyramidal,\t short name: tbp \n"
+        "Coordination: 6, geometry: octahedral,\t short name: oct \n"
+        "Coordination: 6, geometry: trigonal_prismatic,\t short name: tpr \n"
+        "Coordination: 7, geometry: pentagonal_bipyramidal,\t short name: pbp \n"
+        "Coordination: 8, geometry: square_antiprismatic,\t short name: sqap \n\n"
+    )
+    assert captured.out == ref
+
+
+def test_readdict_sub():
+    file = resource_files("molSimplify").joinpath("Substrates/substrates.dict")
+    sub_dict = readdict_sub(file)
+    assert sub_dict["methane"] == ['methane.xyz', 'ch4', '1', ['inter'],
+                                   ['N'], ['0', '#', 'BDH', '=', '104.9(0.1)']]
+    assert sub_dict["ethane"] == ['ethane.xyz', 'c2h6', '2', ['inter'],
+                                  ['B'], ['0', '#', 'BDH', '=', '101.1(0.4)']]
+
+
+def test_getsubstrates():
+    subs = getsubstrates()
+    ref = (
+        "acetaldehyde acetylene benzene biphenyl bromobenzene cumene "
+        "cyclohexene dha diphenylmethane estrogen ethanal ethane ethene "
+        "ethylene fluorene formaldehyde formicacid iodobenzene methanal "
+        "methane methanoicacid methanol methylazide n-quinolinylbutyramidate "
+        "n2 phenyl propane propene propylene propyne tert-butane toluene triazole xanthene"
+        )
+    assert subs == ref