rdworks 0.36.3__tar.gz → 0.36.4__tar.gz

{rdworks-0.36.3 → rdworks-0.36.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.36.3
+Version: 0.36.4
 Summary: Frequently used tasks built on RDKit and other tools
 Author-email: Sung-Hun Bae <sunghun.bae@gmail.com>
 Maintainer-email: Sung-Hun Bae <sunghun.bae@gmail.com>

{rdworks-0.36.3 → rdworks-0.36.4}/src/rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.36.3'
+__version__ = '0.36.4'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

{rdworks-0.36.3 → rdworks-0.36.4}/src/rdworks/mol.py

@@ -1002,6 +1002,7 @@ class Mol:
 
         if torsion_key is None:
             torsion_atoms_indices = self.torsion_atoms()
+            # {0: (5, 4, 3, 1)}
         else:
             torsion_atoms_indices = {torsion_key: self.torsion_atoms()[torsion_key]}
 

{rdworks-0.36.3 → rdworks-0.36.4}/src/rdworks/torsion.py

@@ -453,10 +453,14 @@ def create_torsion_fragment(rdmol: Chem.Mol,
 
     candidates = find_bonds_to_prune(rdmol, torsion_indices)
     
+    if not candidates:
+        # no fragmentation
+        return rdmol, torsion_indices
+    
     if GFN2xTB().version() is not None:
+        # filter candidate(s) by Wiberg bond order (WBO) if xTB is available
         jk = tuple(sorted([j, k]))
         wbo_passed_candidates = {}
-        # filter candidate(s) by Wiberg bond order (WBO)
         parent = GFN2xTB(rdmol).singlepoint()
         assert hasattr(parent, 'wbo'), "create_torsion_fragment() Error: no wbo for parent"
         for bond_idx, (p, q) in candidates.items():
@@ -470,6 +474,7 @@ def create_torsion_fragment(rdmol: Chem.Mol,
                 wbo_passed_candidates[bond_idx] = (p, q)
         frag_multi_breaks = create_fragment_on_bonds(rdmol, wbo_passed_candidates) 
     else:
+        # skip WBO filtering
         frag_multi_breaks = create_fragment_on_bonds(rdmol, candidates)
 
     frag_ijkl = get_fragment_idx(rdmol, (i, j, k, l), frag_multi_breaks)

{rdworks-0.36.3 → rdworks-0.36.4}/src/rdworks.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.36.3
+Version: 0.36.4
 Summary: Frequently used tasks built on RDKit and other tools
 Author-email: Sung-Hun Bae <sunghun.bae@gmail.com>
 Maintainer-email: Sung-Hun Bae <sunghun.bae@gmail.com>

{rdworks-0.36.3 → rdworks-0.36.4}/tests/test_basics.py

@@ -469,12 +469,20 @@ def test_torsion_fragment():
               name="atorvastatin").make_confs(n=1)
     ta = mol.torsion_atoms()
     assert len(ta) == 12
-    # ta[6] = (8, 9, 10, 18, _rot, _fix)
-    # _rot and _fix are not used
-    frag, frag_ijkl = create_torsion_fragment(mol.confs[0].rdmol, (8, 9, 10, 18, None, None))
+    # {0: (0, 1, 3, 7),  1: (3, 4, 32, 33),  2: (4, 5, 26, 27),  3: (7, 6, 19, 20),
+    # 4: (3, 7, 8, 9),  5: (7, 8, 9, 10),   6: (8, 9, 10, 18),   7: (18, 10, 11, 12),
+    # 8: (10, 11, 12, 17),  9: (17, 12, 13, 14),   10: (12, 13, 14, 15),   11: (36, 35, 34, 32)}
+    frag, frag_ijkl = create_torsion_fragment(mol.confs[0].rdmol, ta[6])
     assert frag_ijkl == (5, 6, 7, 12)
 
 
+    mol2 = Mol(molecule='CC(=O)Nc1ccc(O)cc1', name='acetaminophen.3').make_confs(n=1)
+    ta2 = mol2.torsion_atoms()
+    # {0: (5, 4, 3, 1)}
+    assert len(ta2) == 1
+    frag, frag_ijkl = create_torsion_fragment(mol2.confs[0].rdmol, ta2[0])
+
+
 def test_torsion_energies():
     libr = MolLibr(torsion_dataset_smiles, torsion_dataset_names)
     with open(workdir / 'test_torsion_energies.html', 'w') as f: