CG primary structures finished

ipqa-research · Apr 22, 2024 · 0e90e02 · 0e90e02
1 parent 6c96c18
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Showing 31 changed files with 277 additions and 64 deletions.
diff --git a/tests/classic_unifac_groups/test_17_acnh2.py b/tests/classic_unifac_groups/test_17_acnh2.py
@@ -36,4 +36,7 @@ def test_ch3nh2_psrk(identifier, result, identifier_type):
 def test_ch3nh2_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
     assert mol.subgroups == result
-    assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+    assert (
+        fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+        != {}
+    )
diff --git a/tests/classic_unifac_groups/test_18_pyridine.py b/tests/classic_unifac_groups/test_18_pyridine.py
@@ -70,10 +70,15 @@ def test_ch3nh2_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
 
     if identifier != "C1=CC=NC=C1":
-        
+
         assert mol.subgroups == result
 
         if mol.subgroups != {}:
-            assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+            assert (
+                fit_atoms(
+                    mol.mol_object, mol.subgroups, constantinou_gani_primary
+                )
+                != {}
+            )
     else:
         assert mol.subgroups == {}
diff --git a/tests/classic_unifac_groups/test_19_ccn.py b/tests/classic_unifac_groups/test_19_ccn.py
@@ -37,10 +37,12 @@ def test_ccn_psrk(identifier, result, identifier_type):
 @pytest.mark.parametrize("identifier, result, identifier_type", trials_unifac)
 def test_ccn_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
-    
+
     if identifier != "CC#N":
         assert mol.subgroups == result
-        assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
     else:
         assert mol.subgroups == {}
-
diff --git a/tests/classic_unifac_groups/test_20_cooh.py b/tests/classic_unifac_groups/test_20_cooh.py
@@ -45,9 +45,12 @@ def test_cooh_psrk(identifier, result, identifier_type):
 @pytest.mark.parametrize("identifier, result, identifier_type", trials_unifac)
 def test_cooh_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
-    
+
     if identifier != "C(=O)O":
         assert mol.subgroups == result
-        assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
     else:
         assert mol.subgroups == {}
diff --git a/tests/classic_unifac_groups/test_21_ccl.py b/tests/classic_unifac_groups/test_21_ccl.py
@@ -40,4 +40,7 @@ def test_ccl_psrk(identifier, result, identifier_type):
 def test_ccl_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
     assert mol.subgroups == result
-    assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+    assert (
+        fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+        != {}
+    )
diff --git a/tests/classic_unifac_groups/test_22_ccl2.py b/tests/classic_unifac_groups/test_22_ccl2.py
@@ -40,9 +40,12 @@ def test_ccl2_psrk(identifier, result, identifier_type):
 @pytest.mark.parametrize("identifier, result, identifier_type", trials_unifac)
 def test_ccl2_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
-    
+
     if identifier != "C(Cl)Cl":
         assert mol.subgroups == result
-        assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
     else:
         assert mol.subgroups == {}
diff --git a/tests/classic_unifac_groups/test_23_ccl3.py b/tests/classic_unifac_groups/test_23_ccl3.py
@@ -37,9 +37,12 @@ def test_ccl3_psrk(identifier, result, identifier_type):
 @pytest.mark.parametrize("identifier, result, identifier_type", trials_unifac)
 def test_ccl3_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
-    
+
     if identifier != "C(Cl)(Cl)Cl":
         assert mol.subgroups == result
-        assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
     else:
-        assert mol.subgroups == {}
+        assert mol.subgroups == {}
diff --git a/tests/classic_unifac_groups/test_25_accl.py b/tests/classic_unifac_groups/test_25_accl.py
@@ -36,4 +36,7 @@ def test_accl_psrk(identifier, result, identifier_type):
 def test_accl_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
     assert mol.subgroups == result
-    assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+    assert (
+        fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+        != {}
+    )
diff --git a/tests/classic_unifac_groups/test_26_cno2.py b/tests/classic_unifac_groups/test_26_cno2.py
@@ -45,9 +45,12 @@ def test_cno2_psrk(identifier, result, identifier_type):
 @pytest.mark.parametrize("identifier, result, identifier_type", trials_unifac)
 def test_cno2_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
-    
+
     if identifier != "C[N+](=O)[O-]":
         assert mol.subgroups == result
-        assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
-    else: 
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
+    else:
         assert mol.subgroups == {}
diff --git a/tests/classic_unifac_groups/test_27_acno2.py b/tests/classic_unifac_groups/test_27_acno2.py
@@ -43,4 +43,7 @@ def test_acno2_cg(identifier, result, identifier_type):
     assert mol.subgroups == result
 
     if mol.subgroups != {}:
-        assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
diff --git a/tests/classic_unifac_groups/test_29_ch3sh.py b/tests/classic_unifac_groups/test_29_ch3sh.py
@@ -72,7 +72,11 @@ def test_ch3sh_cg(identifier, result, identifier_type):
         assert mol.subgroups == result
 
         if mol.subgroups != {}:
-            assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+            assert (
+                fit_atoms(
+                    mol.mol_object, mol.subgroups, constantinou_gani_primary
+                )
+                != {}
+            )
     else:
         assert mol.subgroups == {}
-
diff --git a/tests/classic_unifac_groups/test_32_i.py b/tests/classic_unifac_groups/test_32_i.py
@@ -38,4 +38,7 @@ def test_i_psrk(identifier, result, identifier_type):
 def test_i_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
     assert mol.subgroups == result
-    assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+    assert (
+        fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+        != {}
+    )
diff --git a/tests/classic_unifac_groups/test_33_br.py b/tests/classic_unifac_groups/test_33_br.py
@@ -38,5 +38,7 @@ def test_br_psrk(identifier, result, identifier_type):
 def test_br_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
     assert mol.subgroups == result
-    assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
-
+    assert (
+        fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+        != {}
+    )
diff --git a/tests/classic_unifac_groups/test_34_alquine.py b/tests/classic_unifac_groups/test_34_alquine.py
@@ -39,4 +39,7 @@ def test_alquine_psrk(identifier, result, identifier_type):
 def test_alquine_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
     assert mol.subgroups == result
-    assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+    assert (
+        fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+        != {}
+    )
diff --git a/tests/classic_unifac_groups/test_37_clceqc.py b/tests/classic_unifac_groups/test_37_clceqc.py
@@ -36,9 +36,12 @@ def test_cleqc_psrk(identifier, result, identifier_type):
     assert fit_atoms(mol.mol_object, mol.subgroups, psrk) != {}
 
 
-@pytest.mark.ConstantinougGani
+@pytest.mark.ConstantinouGani
 @pytest.mark.parametrize("identifier, result, identifier_type", trials_unifac)
 def test_cleqc_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
     assert mol.subgroups == result
-    assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+    assert (
+        fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+        != {}
+    )
diff --git a/tests/classic_unifac_groups/test_38_acf.py b/tests/classic_unifac_groups/test_38_acf.py
@@ -40,12 +40,20 @@ def test_acf_psrk(identifier, result, identifier_type):
 @pytest.mark.parametrize("identifier, result, identifier_type", trials_unifac)
 def test_acf_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
-    
+
     if identifier != "FC1=CC=NC=C1":
         assert mol.subgroups == result
 
         if mol.subgroups != {}:
-            assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+            assert (
+                fit_atoms(
+                    mol.mol_object, mol.subgroups, constantinou_gani_primary
+                )
+                != {}
+            )
     else:
         mol.subgroups == {"C5H4N": 1, "F": 1}
-        assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
diff --git a/tests/classic_unifac_groups/test_40_cf2.py b/tests/classic_unifac_groups/test_40_cf2.py
@@ -83,4 +83,7 @@ def test_cf2_cg(identifier, result, identifier_type):
     assert mol.subgroups == result
 
     if mol.subgroups != {}:
-        assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
diff --git a/tests/classic_unifac_groups/test_41_coo.py b/tests/classic_unifac_groups/test_41_coo.py
@@ -71,4 +71,7 @@ def test_coo_psrk(identifier, result, identifier_type):
 def test_coo_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
     assert mol.subgroups == result
-    assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+    assert (
+        fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+        != {}
+    )
diff --git a/tests/classic_unifac_groups/test_45_cclf.py b/tests/classic_unifac_groups/test_45_cclf.py
@@ -55,10 +55,19 @@ def test_cclf_cg(identifier, result, identifier_type):
         assert mol.subgroups == {}
     elif identifier == "C(F)(Cl)Cl":
         assert mol.subgroups == {"CHCL2": 1, "F": 1}
-        assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
     elif identifier == "C(F)(F)Cl":
         assert mol.subgroups == {"CHCL": 1, "F": 2}
-        assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
     else:
         assert mol.subgroups == result
-        assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
diff --git a/tests/classic_unifac_groups/test_46_con.py b/tests/classic_unifac_groups/test_46_con.py
@@ -1,6 +1,6 @@
 import pytest
 
-from ugropy import get_groups, psrk, unifac
+from ugropy import constantinou_gani_primary, get_groups, psrk, unifac
 from ugropy.core import fit_atoms
 
 
@@ -81,3 +81,70 @@ def test_con_psrk(identifier, result, identifier_type):
 
     if mol.subgroups != {}:
         assert fit_atoms(mol.mol_object, mol.subgroups, psrk) != {}
+
+
+trials_cg = [
+    # acetamide
+    ("CC(=O)N", {"CH3": 1, "CONH2": 1}, "smiles"),
+    # N-Methylacetamide
+    ("CC(=O)NC", {"CH3": 1, "CONHCH3": 1}, "smiles"),
+    # N-Ethylacetamide
+    ("CCNC(=O)C", {"CH3": 2, "CONHCH2": 1}, "smiles"),
+    # N,N-Dimethylacetamide
+    ("CC(=O)N(C)C", {"CH3": 1, "CON(CH3)2": 1}, "smiles"),
+    # N-ethyl-N-methylacetamide
+    ("CCN(C)C(=O)C", {"CH3": 2, "CONCH3CH2": 1}, "smiles"),
+    # N,N-Diethylacetamide
+    ("CCN(CC)C(=O)C", {"CH3": 3, "CON(CH2)2": 1}, "smiles"),
+    # di amide + amine
+    ("CCN(C(C)C)C(=O)NC(C)C", {}, "smiles"),
+    ("CC(C)NC(=O)N(C)C(C)C", {}, "smiles"),
+    ("CCN(CC)C(=O)NC(C)C", {"CON(CH2)2": 1, "CHNH": 1, "CH3": 4}, "smiles"),
+    ("CCN(C)C(=O)NC(C)C", {"CONCH3CH2": 1, "CHNH": 1, "CH3": 3}, "smiles"),
+    ("CC(C)NC(=O)N(C)C", {"CON(CH3)2": 1, "CHNH": 1, "CH3": 2}, "smiles"),
+    (
+        "CCNC(=O)N(CC)C(C)C",
+        {"CONHCH2": 1, "CH2N": 1, "CH3": 4, "CH": 1},
+        "smiles",
+    ),
+    (
+        "CCNC(=O)N(C)C(C)C",
+        {"CONHCH2": 1, "CH3N": 1, "CH3": 3, "CH": 1},
+        "smiles",
+    ),
+    ("CCNC(=O)N(CC)CC", {"CON(CH2)2": 1, "CH2NH": 1, "CH3": 3}, "smiles"),
+    ("CCNC(=O)N(C)CC", {"CONCH3CH2": 1, "CH2NH": 1, "CH3": 2}, "smiles"),
+    ("CCNC(=O)N(C)C", {"CON(CH3)2": 1, "CH2NH": 1, "CH3": 1}, "smiles"),
+    (
+        "CCN(C(C)C)C(=O)NC",
+        {"CONHCH3": 1, "CH2N": 1, "CH": 1, "CH3": 3},
+        "smiles",
+    ),
+    (
+        "CNC(=O)N(C)C(C)C",
+        {"CONHCH3": 1, "CH3N": 1, "CH": 1, "CH3": 2},
+        "smiles",
+    ),
+    ("CCN(CC)C(=O)NC", {"CON(CH2)2": 1, "CH3NH": 1, "CH3": 2}, "smiles"),
+    ("CCN(C)C(=O)NC", {"CONCH3CH2": 1, "CH3NH": 1, "CH3": 1}, "smiles"),
+    ("CNC(=O)N(C)C", {"CON(CH3)2": 1, "CH3NH": 1}, "smiles"),
+    ("CC(C)NC(=O)NC(C)C", {}, "smiles"),
+    ("CCNC(=O)NC(C)C", {"CONHCH2": 1, "CHNH": 1, "CH3": 3}, "smiles"),
+    ("CCNC(=O)NCC", {"CONHCH2": 1, "CH2NH": 1, "CH3": 2}, "smiles"),
+    ("CNC(=O)NC(C)C", {"CONHCH3": 1, "CHNH": 1, "CH3": 2}, "smiles"),
+    ("CCNC(=O)NC", {"CONHCH3": 1, "CH2NH": 1, "CH3": 1}, "smiles"),
+    ("CNC(=O)NC", {"CONHCH3": 1, "CH3NH": 1}, "smiles"),
+]
+
+
+@pytest.mark.ConstantinouGani
+@pytest.mark.parametrize("identifier, result, identifier_type", trials_cg)
+def test_con_cg(identifier, result, identifier_type):
+    mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
+    assert mol.subgroups == result
+
+    if mol.subgroups != {}:
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
diff --git a/tests/classic_unifac_groups/test_47_occoh.py b/tests/classic_unifac_groups/test_47_occoh.py
@@ -38,5 +38,7 @@ def test_occoh_psrk(identifier, result, identifier_type):
 def test_occoh_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
     assert mol.subgroups == result
-    assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
-
+    assert (
+        fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+        != {}
+    )
diff --git a/tests/classic_unifac_groups/test_48_ch2s.py b/tests/classic_unifac_groups/test_48_ch2s.py
@@ -40,4 +40,7 @@ def test_ch2s_psrk(identifier, result, identifier_type):
 def test_ch2s_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
     assert mol.subgroups == result
-    assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+    assert (
+        fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+        != {}
+    )
diff --git a/tests/classic_unifac_groups/test_50_thiophene.py b/tests/classic_unifac_groups/test_50_thiophene.py
@@ -44,9 +44,12 @@ def test_thiophene_psrk(identifier, result, identifier_type):
 @pytest.mark.parametrize("identifier, result, identifier_type", trials_unifac)
 def test_thiophene_cg(identifier, result, identifier_type):
     mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
-    
+
     if identifier != "C1=CSC=C1":
         assert mol.subgroups == result
-        assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
     else:
         assert mol.subgroups == {}
diff --git a/tests/classic_unifac_groups/test_composed.py b/tests/classic_unifac_groups/test_composed.py
@@ -115,12 +115,22 @@ def test_composed_psrk(identifier, result, identifier_type):
 @pytest.mark.ConstantinouGani
 @pytest.mark.parametrize("identifier, result, identifier_type", trials_unifac)
 def test_composed_cg(identifier, result, identifier_type):
-    cg_result = get_groups(constantinou_gani_primary, identifier, identifier_type)
+    cg_result = get_groups(
+        constantinou_gani_primary, identifier, identifier_type
+    )
     try:
-        mol = get_groups(constantinou_gani_primary, identifier, identifier_type)
+        mol = get_groups(
+            constantinou_gani_primary, identifier, identifier_type
+        )
         assert mol.subgroups == result
-        assert fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary) != {}
+        assert (
+            fit_atoms(mol.mol_object, mol.subgroups, constantinou_gani_primary)
+            != {}
+        )
     except ValueError:
         for psrk_r, sol in zip(cg_result.subgroups, result):
             assert psrk_r == sol
-            assert fit_atoms(mol.mol_object, psrk_r, constantinou_gani_primary) != {}
+            assert (
+                fit_atoms(mol.mol_object, psrk_r, constantinou_gani_primary)
+                != {}
+            )