turning test into smiles

tests/classic_unifac_groups/test_01_ch2.py

@@ -21,16 +21,15 @@
     ("C1CC1", {"CH2": 3}, "smiles"),
     ("C1CCC1", {"CH2": 4}, "smiles"),
     ("C1C2CC1CCCC2", {"CH2": 6, "CH": 2}, "smiles"),
-    # the space ship
     ("CC12C3CCC4CCC1C234", {"CH3": 1, "CH2": 4, "CH": 3, "C": 2}, "smiles"),
     ("CCC(CC)C(C)(C)C", {"CH3": 5, "CH2": 2, "CH": 1, "C": 1}, "smiles"),
     ("C1CCC2CCCCC2C1", {"CH2": 8, "CH": 2}, "smiles"),
     ("C1CCC(CC1)CC2CCCCC2", {"CH2": 11, "CH": 2}, "smiles"),
-    ("ethane", {"CH3": 2}, "name"),
-    ("hexane", {"CH3": 2, "CH2": 4}, "name"),
-    ("2-methylpropane", {"CH3": 3, "CH": 1}, "name"),
-    ("2,2-dimethylpropane", {"CH3": 4, "C": 1}, "name"),
-    ("cyclohexane", {"CH2": 6}, "name"),
+    ("CC", {"CH3": 2}, "smiles"),  # ethane
+    ("CCCCCC", {"CH3": 2, "CH2": 4}, "smiles"),  # hexane
+    ("CC(C)C", {"CH3": 3, "CH": 1}, "smiles"),  # 2-methylpropane
+    ("CC(C)(C)C", {"CH3": 4, "C": 1}, "smiles"),  # 2,2-dimethylpropane
+    ("C1CCCCC1", {"CH2": 6}, "smiles"),  # cyclohexane
 ]
 
 

tests/classic_unifac_groups/test_02_ceqc.py

@@ -39,13 +39,13 @@
         {"CH3": 1, "CH2": 9, "CH": 3, "CH=CH": 2},
         "smiles",
     ),
-    # cyclohexene
-    ("C1CCC=CC1", {"CH2": 4, "CH=CH": 1}, "smiles"),
-    ("2,3-dimethylbutene-2", {"C=C": 1, "CH3": 4}, "name"),
-    ("2-methyl-2-butene", {"CH=C": 1, "CH3": 3}, "name"),
-    ("2-methyl-1-butene", {"CH2": 1, "CH2=C": 1, "CH3": 2}, "name"),
-    ("2-hexene", {"CH2": 2, "CH=CH": 1, "CH3": 2}, "name"),
-    ("1-hexene", {"CH2": 3, "CH2=CH": 1, "CH3": 1}, "name"),
+    ("C1CCC=CC1", {"CH2": 4, "CH=CH": 1}, "smiles"),  # cyclohexene
+    ("CC(=C(C)C)C", {"C=C": 1, "CH3": 4}, "smiles"),  # 2,3-dimethylbutene-2
+    ("CC=C(C)C", {"CH=C": 1, "CH3": 3}, "smiles"),  # 2-methyl-2-butene
+    # 2-methyl-1-butene
+    ("CCC(=C)C", {"CH2": 1, "CH2=C": 1, "CH3": 2}, "smiles"),
+    ("CCCC=CC", {"CH2": 2, "CH=CH": 1, "CH3": 2}, "smiles"),  # 2-hexene
+    ("CCCCC=C", {"CH2": 3, "CH2=CH": 1, "CH3": 1}, "smiles"),  # 1-hexene
     # impossibles
     ("C=C=C", {}, "smiles"),
     ("CC=CC(C)C(C)=C=C", {}, "smiles"),

tests/classic_unifac_groups/test_03_ach.py

@@ -24,10 +24,9 @@
     ),
     # biphenyl
     ("C1=CC=C(C=C1)C2=CC=CC=C2", {"ACH": 10, "AC": 2}, "smiles"),
-    # Naphthalene
-    ("C1=CC=C2C=CC=CC2=C1", {"ACH": 8, "AC": 2}, "smiles"),
-    ("benzene", {"ACH": 6}, "name"),
-    ("styrene", {"AC": 1, "CH2=CH": 1, "ACH": 5}, "name"),
+    ("C1=CC=C2C=CC=CC2=C1", {"ACH": 8, "AC": 2}, "smiles"),  # Naphthalene
+    ("C1=CC=CC=C1", {"ACH": 6}, "smiles"),  # benzene
+    ("C=CC1=CC=CC=C1", {"AC": 1, "CH2=CH": 1, "ACH": 5}, "smiles"),  # styrene
 ]
 
 

tests/classic_unifac_groups/test_04_acch2.py

@@ -61,10 +61,14 @@
         {"ACH": 4, "ACCH": 1, "ACCH2": 1, "CH3": 3},
         "smiles",
     ),
-    ("Gastrodigenin", {"ACH": 4, "ACOH": 1, "ACCH2": 1, "OH": 1}, "name"),
-    ("cumene", {"CH3": 2, "ACH": 5, "ACCH": 1}, "name"),
-    ("ethylbenzene", {"CH3": 1, "ACH": 5, "ACCH2": 1}, "name"),
-    ("toluene", {"ACH": 5, "ACCH3": 1}, "name"),
+    # Gastrodigenin
+    ("C1=CC(=CC=C1CO)O", {"ACH": 4, "ACOH": 1, "ACCH2": 1, "OH": 1}, "smiles"),
+    # cumene
+    ("CC(C)C1=CC=CC=C1", {"CH3": 2, "ACH": 5, "ACCH": 1}, "smiles"),
+    # ethylbenzene
+    ("CCC1=CC=CC=C1", {"CH3": 1, "ACH": 5, "ACCH2": 1}, "smiles"),
+    # toluene
+    ("CC1=CC=CC=C1", {"ACH": 5, "ACCH3": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_05_oh.py

@@ -17,7 +17,8 @@
     ),
     # (2S,3S)-2-Methyl-1,3-hexanediol
     ("CCCC(C(C)CO)O", {"CH3": 2, "CH2": 3, "CH": 2, "OH": 2}, "smiles"),
-    ("2-propanol", {"CH3": 2, "CH": 1, "OH": 1}, "name"),
+    # 2-propanol
+    ("CC(C)O", {"CH3": 2, "CH": 1, "OH": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_06_ch3oh.py

@@ -8,7 +8,8 @@
 # =============================================================================
 
 # UNIFAC
-trials_unifac = [("methanol", {"CH3OH": 1}, "name")]
+# methanol
+trials_unifac = [("CO", {"CH3OH": 1}, "smiles")]
 
 
 @pytest.mark.CH3OH

tests/classic_unifac_groups/test_07_h2o.py

@@ -8,13 +8,13 @@
 # =============================================================================
 
 # UNIFAC
-trials_unifac = [("water", {"H2O": 1})]
+trials_unifac = [("O", {"H2O": 1}, "smiles")]
 
 
 @pytest.mark.H2O
 @pytest.mark.UNIFAC
-@pytest.mark.parametrize("name, result", trials_unifac)
-def test_h2o_unifac(name, result):
-    groups = ug.Groups(name)
+@pytest.mark.parametrize("identifier, result, identifier_type", trials_unifac)
+def test_h2o_unifac(identifier, result, identifier_type):
+    groups = ug.Groups(identifier, identifier_type)
     assert groups.unifac_groups == result
     assert groups.psrk_groups == result

tests/classic_unifac_groups/test_08_acoh.py

@@ -27,7 +27,7 @@
         {"ACH": 7, "AC": 2, "ACOH": 3},
         "smiles",
     ),
-    ("phenol", {"ACH": 5, "ACOH": 1}, "name"),
+    ("C1=CC=C(C=C1)O", {"ACH": 5, "ACOH": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_09_ch2co.py

@@ -41,9 +41,12 @@
     ),
     # acetophenone
     ("CC(=O)C1=CC=CC=C1", {"ACH": 5, "AC": 1, "CH3CO": 1}, "smiles"),
-    ("acetone", {"CH3CO": 1, "CH3": 1}, "name"),
-    ("3-pentanone", {"CH3": 2, "CH2": 1, "CH2CO": 1}, "name"),
-    ("2-butanone", {"CH3": 1, "CH2": 1, "CH3CO": 1}, "name"),
+    # acetone
+    ("CC(=O)C", {"CH3CO": 1, "CH3": 1}, "smiles"),
+    # 3-pentanones
+    ("CCC(=O)CC", {"CH3": 2, "CH2": 1, "CH2CO": 1}, "smiles"),
+    # 2-butanone
+    ("CCC(=O)C", {"CH3": 1, "CH2": 1, "CH3CO": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_10_cho.py

@@ -40,11 +40,13 @@
     ("CCCCC=O", {"CH3": 1, "CH2": 3, "CHO": 1}, "smiles"),
     # 3-methylbutanal
     ("CC(C)CC=O", {"CH3": 2, "CH2": 1, "CH": 1, "CHO": 1}, "smiles"),
-    ("acetaldehyde", {"CH3": 1, "CHO": 1}, "name"),
+    # acetaldehyde
+    ("CC=O", {"CH3": 1, "CHO": 1}, "smiles"),
+    # 2-Hexyl-3-Phenyl-2-Propenal
     (
-        "2-Hexyl-3-Phenyl-2-Propenal",
+        r"CCCCCC\C(C=O)=C/C1=CC=CC=C1",
         {"ACH": 5, "AC": 1, "CH=C": 1, "CH2": 5, "CH3": 1, "CHO": 1},
-        "name",
+        "smiles",
     ),
 ]
 

tests/classic_unifac_groups/test_11_ccoo.py

@@ -19,8 +19,10 @@
     ("CC(=O)OC(C)(C)C", {"CH3COO": 1, "CH3": 3, "C": 1}, "smiles"),
     # triacetin
     ("CC(=O)OCC(COC(=O)C)OC(=O)C", {"CH3COO": 3, "CH2": 2, "CH": 1}, "smiles"),
-    ("butyl propanoate", {"CH3": 2, "CH2": 3, "CH2COO": 1}, "name"),
-    ("butyl acetate", {"CH3": 1, "CH2": 3, "CH3COO": 1}, "name"),
+    # butyl propanoate
+    ("CCCCOC(=O)CC", {"CH3": 2, "CH2": 3, "CH2COO": 1}, "smiles"),
+    # butyl acetate
+    ("CCCCOC(=O)C", {"CH3": 1, "CH2": 3, "CH3COO": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_12_hcoo.py

@@ -13,7 +13,8 @@
     ("C1=CC=C(C=C1)OC=O", {"ACH": 5, "AC": 1, "HCOO": 1}, "smiles"),
     # methyl formate
     ("COC=O", {"HCOO": 1, "CH3": 1}, "smiles"),
-    ("ethyl formate", {"HCOO": 1, "CH2": 1, "CH3": 1}, "name"),
+    # ethyl formate
+    ("CCOC=O", {"HCOO": 1, "CH2": 1, "CH3": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_13_ch2o.py

@@ -25,19 +25,19 @@
     ("CCOCOCC", {"CH3": 2, "CH2O": 2, "CH2": 1}, "smiles"),
     ("C1COCO1", {"CH2O": 2, "CH2": 1}, "smiles"),
     ("C1COCCOCCOCCOCCOCCO1", {"CH2O": 6, "CH2": 6}, "smiles"),
-    ("tetrahydrofuran", {"THF": 1}, "name"),
-    ("diisopropyl ether", {"CH3": 4, "CH": 1, "CH-O": 1}, "name"),
-    ("diethyl ether", {"CH3": 2, "CH2": 1, "CH2O": 1}, "name"),
-    ("dimethyl ether", {"CH3": 1, "CH3O": 1}, "name"),
+    # tetrahydrofuran
+    ("C1CCOC1", {"THF": 1}, "smiles"),
+    # diisopropyl ether
+    ("CC(C)OC(C)C", {"CH3": 4, "CH": 1, "CH-O": 1}, "smiles"),
+    # diethyl ether
+    ("CCOCC", {"CH3": 2, "CH2": 1, "CH2O": 1}, "smiles"),
+    # dimethyl ether
+    ("COC", {"CH3": 1, "CH3O": 1}, "smiles"),
+    # 2H-Pyran, 2-(cyclohexyloxy)tetrahydro-
     (
-        "SCHEMBL3938062",
-        {"CH2": 4, "CH": 2, "OH": 1, "COO": 1, "CH3O": 1},
-        "name",
-    ),
-    (
-        "2H-Pyran, 2-(cyclohexyloxy)tetrahydro-",
+        "C1CCC(CC1)OC2CCCCO2",
         {"CH2": 8, "CH": 1, "CH2O": 1, "CH-O": 1},
-        "name",
+        "smiles",
     ),
     # Problematic ones
     # Benzyl 2-hydroxyethyl carbonate

tests/classic_unifac_groups/test_14_ch3nh2.py

@@ -9,9 +9,12 @@
 
 # UNIFAC
 trials_unifac = [
-    ("methylamine", {"CH3NH2": 1}, "name"),
-    ("isopropylamine", {"CH3": 2, "CHNH2": 1}, "name"),
-    ("propylamine", {"CH3": 1, "CH2": 1, "CH2NH2": 1}, "name"),
+    # methylamine
+    ("CN", {"CH3NH2": 1}, "smiles"),
+    # isopropylamine
+    ("CC(C)N", {"CH3": 2, "CHNH2": 1}, "smiles"),
+    # propylamine
+    ("CCCN", {"CH3": 1, "CH2": 1, "CH2NH2": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_15_cnh.py

@@ -40,9 +40,12 @@
         {"CH3N": 2, "CH2": 7, "CH": 2, "CH2CO": 1},
         "smiles",
     ),
-    ("dimethylamine", {"CH3": 1, "CH3NH": 1}, "name"),
-    ("diethylamine", {"CH3": 2, "CH2": 1, "CH2NH": 1}, "name"),
-    ("diisopropylamine", {"CH3": 4, "CH": 1, "CHNH": 1}, "name"),
+    # dimethylamine
+    ("CNC", {"CH3": 1, "CH3NH": 1}, "smiles"),
+    # diethylamine
+    ("CCNCC", {"CH3": 2, "CH2": 1, "CH2NH": 1}, "smiles"),
+    # diisopropylamine
+    ("CC(C)NC(C)C", {"CH3": 4, "CH": 1, "CHNH": 1}, "smiles"),
     # Problematics
     ("CC(C)NCN", {"CHNH": 1, "CH3": 2, "CH2NH2": 1}, "smiles"),
     # concatenate amine

tests/classic_unifac_groups/test_16_c3n.py

@@ -18,8 +18,10 @@
     ),
     ("CCN(C(C)C)C(C)C", {"CH2N": 1, "CH3": 5, "CH": 2}, "smiles"),
     ("CCN(C)CC", {"CH3N": 1, "CH2": 2, "CH3": 2}, "smiles"),
-    ("trimethylamine", {"CH3": 2, "CH3N": 1}, "name"),
-    ("triethylamine", {"CH3": 3, "CH2": 2, "CH2N": 1}, "name"),
+    # trimethylamine
+    ("CN(C)C", {"CH3": 2, "CH3N": 1}, "smiles"),
+    # triethylamine
+    ("CCN(CC)CC", {"CH3": 3, "CH2": 2, "CH2N": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_17_acnh2.py

@@ -9,7 +9,8 @@
 
 # UNIFAC
 trials_unifac = [
-    ("aniline", {"ACH": 5, "ACNH2": 1}, "name"),
+    # aniline
+    ("C1=CC=C(C=C1)N", {"ACH": 5, "ACNH2": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_18_pyridine.py

@@ -34,16 +34,18 @@
     ("C1=CC=C(C=C1)C1=CC=NC=C1", {"C5H4N": 1, "AC": 1, "ACH": 5}, "smiles"),
     ("CC(=C)C1=CC=NC=C1", {"C5H4N": 1, "CH2=C": 1, "CH3": 1}, "smiles"),
     ("CC1=NC=CC(O)=C1", {"C5H3N": 1, "CH3": 1, "OH": 1}, "smiles"),
-    ("pyridine", {"C5H5N": 1}, "name"),
-    ("3-methylpyridine", {"C5H4N": 1, "CH3": 1}, "name"),
-    ("2,3-Dimethylpyridine", {"C5H3N": 1, "CH3": 2}, "name"),
+    # pyridine
+    ("C1=CC=NC=C1", {"C5H5N": 1}, "smiles"),
+    # 3-methylpyridine
+    ("CC1=CN=CC=C1", {"C5H4N": 1, "CH3": 1}, "smiles"),
+    # 2,3-Dimethylpyridine
+    ("CC1=C(N=CC=C1)C", {"C5H3N": 1, "CH3": 2}, "smiles"),
 ]
 
 
 @pytest.mark.pyridine
 @pytest.mark.UNIFAC
 @pytest.mark.parametrize("identifier, result, identifier_type", trials_unifac)
-# @pytest.mark.skip
 def test_ch3nh2_unifac(identifier, result, identifier_type):
     groups = ug.Groups(identifier, identifier_type)
     assert groups.unifac_groups == result

tests/classic_unifac_groups/test_19_ccn.py

@@ -9,8 +9,10 @@
 
 # UNIFAC
 trials_unifac = [
-    ("acetonitrile", {"CH3CN": 1}, "name"),
-    ("propionitrile", {"CH3": 1, "CH2CN": 1}, "name"),
+    # acetonitrile
+    ("CC#N", {"CH3CN": 1}, "smiles"),
+    # propionitrile
+    ("CCC#N", {"CH3": 1, "CH2CN": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_20_cooh.py

@@ -15,8 +15,10 @@
         {"COOH": 1, "CHNH2": 1, "CH2": 1, "CH2NH2": 1},
         "smiles",
     ),
-    ("acetic acid", {"CH3": 1, "COOH": 1}, "name"),
-    ("formic acid", {"HCOOH": 1}, "name"),
+    # acetic acid
+    ("CC(=O)O", {"CH3": 1, "COOH": 1}, "smiles"),
+    # formic acid
+    ("C(=O)O", {"HCOOH": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_21_ccl.py

@@ -9,9 +9,12 @@
 
 # UNIFAC
 trials_unifac = [
-    ("1-chlorobutane", {"CH3": 1, "CH2": 2, "CH2CL": 1}, "name"),
-    ("2-chloropropane", {"CH3": 2, "CHCL": 1}, "name"),
-    ("2-chloro-2-methylpropane", {"CH3": 3, "CCL": 1}, "name"),
+    # 1-chlorobutane
+    ("CCCCCl", {"CH3": 1, "CH2": 2, "CH2CL": 1}, "smiles"),
+    # 2-chloropropane
+    ("CC(C)Cl", {"CH3": 2, "CHCL": 1}, "smiles"),
+    # 2-chloro-2-methylpropane
+    ("CC(C)(C)Cl", {"CH3": 3, "CCL": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_22_ccl2.py

@@ -10,9 +10,12 @@
 # UNIFAC
 trials_unifac = [
     ("OC(Cl)Cl", {"CHCL2": 1, "OH": 1}, "smiles"),
-    ("dichloro methane", {"CH2CL2": 1}, "name"),
-    ("1,1-dichloroethane", {"CH3": 1, "CHCL2": 1}, "name"),
-    ("2,2-dichloropropane", {"CH3": 2, "CCL2": 1}, "name"),
+    # dichloro methane
+    ("C(Cl)Cl", {"CH2CL2": 1}, "smiles"),
+    # 1,1-dichloroethane
+    ("CC(Cl)Cl", {"CH3": 1, "CHCL2": 1}, "smiles"),
+    # 2,2-dichloropropane
+    ("CC(C)(Cl)Cl", {"CH3": 2, "CCL2": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_23_ccl3.py

@@ -9,8 +9,10 @@
 
 # UNIFAC
 trials_unifac = [
-    ("chloroform", {"CHCL3": 1}, "name"),
-    ("trichloroethane", {"CH3": 1, "CCL3": 1}, "name"),
+    # chloroform
+    ("C(Cl)(Cl)Cl", {"CHCL3": 1}, "smiles"),
+    # trichloroethane
+    ("CC(Cl)(Cl)Cl", {"CH3": 1, "CCL3": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_24_ccl4.py

@@ -9,7 +9,8 @@
 
 # UNIFAC
 trials_unifac = [
-    ("tetrachloromethane", {"CCL4": 1}, "name"),
+    # tetrachloromethane
+    ("C(Cl)(Cl)(Cl)Cl", {"CCL4": 1}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_25_accl.py

@@ -9,7 +9,8 @@
 
 # UNIFAC
 trials_unifac = [
-    ("chlorobenzene ", {"ACCL": 1, "ACH": 5}, "name"),
+    # chlorobenzene
+    ("C1=CC=C(C=C1)Cl", {"ACCL": 1, "ACH": 5}, "smiles"),
 ]
 
 

tests/classic_unifac_groups/test_26_cno2.py

@@ -15,9 +15,12 @@
         "smiles",
     ),
     ("[O-][N+](=O)CC1=CC=CC=C1", {"ACH": 5, "AC": 1, "CH2NO2": 1}, "smiles"),
-    ("nitromethane", {"CH3NO2": 1}, "name"),
-    ("1-nitropropane", {"CH3": 1, "CH2": 1, "CH2NO2": 1}, "name"),
-    ("2-nitropropane", {"CH3": 2, "CHNO2": 1}, "name"),
+    # nitromethane
+    ("C[N+](=O)[O-]", {"CH3NO2": 1}, "smiles"),
+    # 1-nitropropane
+    ("CCC[N+](=O)[O-]", {"CH3": 1, "CH2": 1, "CH2NO2": 1}, "smiles"),
+    # 2-nitropropane
+    ("CC(C)[N+](=O)[O-]", {"CH3": 2, "CHNO2": 1}, "smiles"),
 ]