rdworks 0.55.1__tar.gz → 0.56.1__tar.gz

{rdworks-0.55.1 → rdworks-0.56.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.55.1
+Version: 0.56.1
 Summary: Routine 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-0.55.1 → rdworks-0.56.1}/src/rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.55.1'
+__version__ = '0.56.1'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

{rdworks-0.55.1 → rdworks-0.56.1}/src/rdworks/complete.py

@@ -2,6 +2,7 @@ from rdworks import Mol, MolLibr
 from rdworks.stereoisomers import enumerate_stereoisomers, enumerate_ring_bond_stereoisomers
 from rdkit import Chem
 from rdkit.Chem.MolStandardize import rdMolStandardize
+from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions
 
 
 def complete_stereoisomers(molecular_input: str | Chem.Mol | Mol, 
@@ -65,6 +66,18 @@ def complete_stereoisomers(molecular_input: str | Chem.Mol | Mol,
     return libr
 
 
+def can_have_stereo(bond):
+    """Check if a double bond can have E/Z stereochemistry"""
+    atom1, atom2 = bond.GetBeginAtom(), bond.GetEndAtom()
+    
+    # Check if both atoms have at least 2 non-hydrogen neighbors
+    for atom in [atom1, atom2]:
+        non_h_neighbors = [n for n in atom.GetNeighbors() if n.GetAtomicNum() != 1]
+        if len(non_h_neighbors) < 2:
+            return False
+    
+    return True
+
 
 def complete_tautomers(mol: Mol, **kwargs) -> MolLibr:
     """Returns a library of enumerated tautomers.
@@ -76,9 +89,30 @@ def complete_tautomers(mol: Mol, **kwargs) -> MolLibr:
         MolLibr: a library of enumerated tautomers.
     """
     enumerator = rdMolStandardize.TautomerEnumerator()
-    rdmols = list(enumerator.Enumerate(mol.rdmol))
+    enumerator.SetRemoveSp3Stereo(False)
+    enumerator.SetRemoveBondStereo(False)  # Don't remove existing stereo
+    tautomers = list(enumerator.Enumerate(mol.rdmol))
+    
+    all_stereoisomers = []
+    
+    for tautomer in tautomers:
+        # Find unspecified double bonds that could have E/Z stereo
+        unspecified_bonds = []
+        for bond in tautomer.GetBonds():
+            if (bond.GetBondType() == Chem.BondType.DOUBLE and 
+                bond.GetStereo() == Chem.BondStereo.STEREONONE and
+                can_have_stereo(bond)):
+                unspecified_bonds.append(bond.GetIdx())
+        
+        if unspecified_bonds:
+            # Enumerate all possible stereoisomers
+            opts = StereoEnumerationOptions(onlyUnassigned=True, maxIsomers=50)
+            stereoisomers = list(EnumerateStereoisomers(tautomer, options=opts))
+            all_stereoisomers.extend(stereoisomers)
+        else:
+            all_stereoisomers.append(tautomer)
     
-    if len(rdmols) > 1: 
-        return MolLibr(rdmols).unique().rename(mol.name, sep='.').compute(**kwargs)
+    if len(all_stereoisomers) > 1: 
+        return MolLibr(all_stereoisomers).unique().rename(mol.name, sep='.').compute(**kwargs)
     
-    return MolLibr(rdmols).compute(**kwargs)
+    return MolLibr(all_stereoisomers).compute(**kwargs)

{rdworks-0.55.1 → rdworks-0.56.1}/src/rdworks.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.55.1
+Version: 0.56.1
 Summary: Routine 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>