add tests and fix pathfinderTest

Author: bjkreitz

test/rmgpy/molecule/moleculeTest.py

@@ -2139,6 +2139,26 @@ def test_surface_molecules(self):
         assert adsorbed.number_of_surface_sites() == 1
         assert bidentate.number_of_surface_sites() == 2
 
+    def test_is_multidentate(self):
+        """
+        Test that we can identify a multidentate adsorbate
+        """
+        monodentate = Molecule().from_adjacency_list(
+            """
+            1 H u0 p0 c0 {2,S}
+            2 X u0 p0 c0 {1,S}
+            """
+        )
+        adjlist = """
+            1 X u0 p0 c0 {3,S}
+            2 X u0 p0 c0 {4,S}
+            3 C u0 p0 c0 {1,S} {4,T}
+            4 C u0 p0 c0 {2,S} {3,T}
+            """
+        bidentate = Molecule().from_adjacency_list(adjlist)
+        assert not monodentate.is_multidentate()
+        assert bidentate.is_multidentate()
+
     def test_malformed_augmented_inchi(self):
         """Test that augmented inchi without InChI layer raises Exception."""
         malform_aug_inchi = "foo"

test/rmgpy/molecule/pathfinderTest.py

@@ -41,6 +41,8 @@
     find_lone_pair_multiple_bond_paths,
     find_N5dc_radical_delocalization_paths,
     find_shortest_path,
+    find_adsorbate_delocalization_paths,
+    find_adsorbate_conjugate_delocalization_paths,
 )
 
 
@@ -458,7 +460,7 @@ def test_h2nnoo(self):
         assert paths
 
 
-class FindAdjLonePairRadicalDelocalizationPaths:
+class FindAdjLonePairRadicalDelocalizationPathsTest:
     """
     test the find_lone_pair_radical_delocalization_paths method
     """
@@ -490,7 +492,7 @@ def test_double_bond(self):
         assert paths
 
 
-class FindAdjLonePairMultipleBondDelocalizationPaths:
+class FindAdjLonePairMultipleBondDelocalizationPathsTest:
     """
     test the find_lone_pair_multiple_bond_delocalization_paths method
     """
@@ -502,7 +504,7 @@ def test_sho3(self):
         assert paths
 
 
-class FindAdjLonePairRadicalMultipleBondDelocalizationPaths:
+class FindAdjLonePairRadicalMultipleBondDelocalizationPathsTest:
     """
     test the find_lone_pair_radical_multiple_bond_delocalization_paths method
     """
@@ -520,7 +522,7 @@ def test_hso3(self):
         assert paths
 
 
-class FindN5dcRadicalDelocalizationPaths:
+class FindN5dcRadicalDelocalizationPathsTest:
     """
     test the find_N5dc_radical_delocalization_paths method
     """
@@ -530,3 +532,41 @@ def test_hnnoo(self):
         mol = Molecule().from_smiles(smiles)
         paths = find_N5dc_radical_delocalization_paths(mol.atoms[1])
         assert paths
+
+class FindAdsorbateDelocalizationPathsTest:
+    """
+    test the find_adsorbate_delocalization_paths method
+    """
+
+    def test_cch(self):
+        adjlist = """
+1 X u0 p0 c0 {3,D}
+2 X u0 p0 c0 {4,S}
+3 C u0 p0 c0 {1,D} {4,D}
+4 C u0 p0 c0 {2,S} {3,D} {5,S}
+5 H u0 p0 c0 {4,S}  
+        """
+
+        mol = Molecule().from_adjacency_list(adjlist)
+        paths = find_adsorbate_delocalization_paths(mol.atoms[0])
+        assert paths
+
+class FindAdsorbateConjugateDelocalizationPathsTest:
+    """
+    test the find_adsorbate_conjugate_delocalization_paths
+    """
+
+    def test_chchc(self):
+        adjlist = """
+1 X u0 p0 c0 {3,T}
+2 X u0 p0 c0 {5,S}
+3 C u0 p0 c0 {1,T} {4,S}
+4 C u0 p0 c0 {3,S} {5,D} {6,S}
+5 C u0 p0 c0 {2,S} {4,D} {7,S}
+6 H u0 p0 c0 {4,S}
+7 H u0 p0 c0 {5,S}
+        """
+
+        mol = Molecule().from_adjacency_list(adjlist)
+        paths = find_adsorbate_conjugate_delocalization_paths(mol.atoms[0])
+        assert paths

test/rmgpy/molecule/resonanceTest.py

@@ -1363,6 +1363,64 @@ def test_resonance_without_changing_atom_order2(self):
                 atom2_nb = {nb.id for nb in list(atom2.bonds.keys())}
                 assert atom1_nb == atom2_nb
 
+    def test_adsorbate_resonance_cc1(self):
+        """Test if all three resonance structures for X#CC#X are generated"""
+        adjlist = """
+1 X u0 p0 c0 {3,T}
+2 X u0 p0 c0 {4,T}
+3 C u0 p0 c0 {1,T} {4,S}
+4 C u0 p0 c0 {2,T} {3,S}
+        """
+
+        mol = Molecule().from_adjacency_list(adjlist)
+
+        mol_list = generate_resonance_structures(mol)
+        assert len(mol_list) == 3
+
+    def test_adsorbate_resonance_cc2(self):
+        """Test if all three resonance structures for X=C=C=X are generated"""
+        adjlist = """
+1 X u0 p0 c0 {3,D}
+2 X u0 p0 c0 {4,D}
+3 C u0 p0 c0 {1,D} {4,D}
+4 C u0 p0 c0 {2,D} {3,D}
+        """
+
+        mol = Molecule().from_adjacency_list(adjlist)
+
+        mol_list = generate_resonance_structures(mol)
+        assert len(mol_list) == 3
+
+    def test_adsorbate_resonance_cc3(self):
+        """Test if all three resonance structures for XC#CX are generated"""
+        adjlist = """
+1 X u0 p0 c0 {3,S}
+2 X u0 p0 c0 {4,S}
+3 C u0 p0 c0 {1,S} {4,T}
+4 C u0 p0 c0 {2,S} {3,T}
+        """
+
+        mol = Molecule().from_adjacency_list(adjlist)
+
+        mol_list = generate_resonance_structures(mol)
+        assert len(mol_list) == 3
+
+    def test_adsorbate_resonance_chchc(self):
+        """Test if both resonance structures for XCHCHXC are generated"""
+        adjlist = """
+1 X u0 p0 c0 {3,T}
+2 X u0 p0 c0 {5,S}
+3 C u0 p0 c0 {1,T} {4,S}
+4 C u0 p0 c0 {3,S} {5,D} {6,S}
+5 C u0 p0 c0 {2,S} {4,D} {7,S}
+6 H u0 p0 c0 {4,S}
+7 H u0 p0 c0 {5,S}
+        """
+
+        mol = Molecule().from_adjacency_list(adjlist)
+
+        mol_list = generate_resonance_structures(mol)
+        assert len(mol_list) == 2
 
 class ClarTest:
     """