rdworks 0.55.1__py3-none-any.whl → 0.56.1__py3-none-any.whl

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/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.dist-info → rdworks-0.56.1.dist-info}/METADATA

@@ -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.dist-info → rdworks-0.56.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
-rdworks/__init__.py,sha256=uWC5GaxWQpax4cYBDNiFaYul630ZKhLHVvtZTQYX-Dg,1356
-rdworks/complete.py,sha256=rTd7iBGmNwSoylx8VmBqcqqPIEeCHxiCO2TPo00_UnA,3147
+rdworks/__init__.py,sha256=d-zUnWFkFgiYgKXi2hBDA6KX99RDMX4c8RJqrCpQozw,1356
+rdworks/complete.py,sha256=MGNw3O66tPN4I2PIrrjz2ufMako0D1KezvHSNjfpRf8,4642
 rdworks/conf.py,sha256=_4SxHJiaOdK_4KY9adxvQTfzJFudvAQoHRgvejmfyGc,36365
 rdworks/descriptor.py,sha256=34T_dQ6g8v3u-ym8TLKbQtxIIV5TEo-d3pdedq3o-cg,2106
 rdworks/display.py,sha256=JR0gR26UpH-JCxVOaqXZCUj2MiGZSrx9Me87FncspVI,13469
@@ -66,8 +66,8 @@ rdworks/predefined/misc/reactive-part-3.xml,sha256=LgWHSEbRTVmgBoIO45xbTo1xQJs0X
 rdworks/predefined/misc/reactive.xml,sha256=syedoQ6VYUfRLnxy99ObuDniJ_a_WhrWAJbTKFfJ6VY,11248
 rdworks/xtb/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rdworks/xtb/wrapper.py,sha256=YpZY8SJ9Lrp3I3_GAVawSb_4_Zc8hcJtF5l7-I-Wbys,22048
-rdworks-0.55.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
-rdworks-0.55.1.dist-info/METADATA,sha256=9Do_0fPpQCuHbz-hq-OvSeKLcH6Qsf_YPYlyRkQYBZM,1967
-rdworks-0.55.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rdworks-0.55.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
-rdworks-0.55.1.dist-info/RECORD,,
+rdworks-0.56.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
+rdworks-0.56.1.dist-info/METADATA,sha256=4jemVgYRM_UDuGjLUOK8vbboQZiqctnx-rrZgnvAg5k,1967
+rdworks-0.56.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rdworks-0.56.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
+rdworks-0.56.1.dist-info/RECORD,,