rdworks 0.52.1__py3-none-any.whl → 0.53.1__py3-none-any.whl

rdworks/__init__.py

@@ -1,11 +1,11 @@
-__version__ = '0.52.1'
+__version__ = '0.53.1'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol
 from rdworks.mollibr import MolLibr
 
-from rdworks.stereoisomers import complete_stereoisomers
-from rdworks.tautomers import complete_tautomers
+from rdworks.workflow import complete_stereoisomers, complete_tautomers
+
 from rdworks.ionized import IonizedStates
 
 from rdworks.readin import read_csv, merge_csv, read_dataframe, read_smi, read_sdf, read_mae 

rdworks/mol.py

@@ -28,7 +28,6 @@ from rdkit.Chem import (
     Draw, rdDepictor, inchi,
     rdDistGeom, rdMolAlign, rdMolTransforms, rdmolops
     )
-from rdkit.Chem.Draw import rdMolDraw2D
 from rdkit.ML.Cluster import Butina
 from PIL import Image
 
@@ -43,6 +42,8 @@ from rdworks.autograph import NMRCLUST, DynamicTreeCut, RCKmeans, AutoGraph
 from rdworks.bitqt import BitQT
 from rdworks.torsion import create_torsion_fragment, get_torsion_atoms
 from rdworks.display import render_svg, render_png
+from rdworks.stereoisomers import enumerate_stereoisomers, enumerate_ring_bond_stereoisomers
+
 
 from scour.scour import scourString
 
@@ -329,6 +330,36 @@ class Mol:
         return self
 
 
+    def count_stereoisomers(self) -> int:
+        """Counts number of all possible stereoisomers ignoring the current stereochemistry.
+
+        Returns:
+            int: number of stereoisomers.
+        """
+
+        ring_bond_stereo_info = self.get_ring_bond_stereo()
+        mol = self.copy()
+        # remove stereochemistry
+        mol = mol.remove_stereo()
+        rdmols = enumerate_stereoisomers(mol.rdmol)
+        # ring bond stereo is not properly enumerated
+        # cis/trans information is lost if stereochemistry is removed,
+        # which cannot be enumerated by EnumerateStereoisomers() function
+        # so enumerate_ring_bond_stereoisomers() is introduced
+        if len(ring_bond_stereo_info) > 0:
+            ring_cis_trans = []
+            for rdmol in rdmols:
+                ring_cis_trans += enumerate_ring_bond_stereoisomers(rdmol,
+                                                        ring_bond_stereo_info,
+                                                        override=True)
+            if len(ring_cis_trans) > 0:
+                rdmols = ring_cis_trans
+        
+        unique_rdmols = set([Chem.MolToSmiles(rdmol) for rdmol in rdmols])
+        
+        return len(unique_rdmols)
+   
+
     def make_confs(self, n: int = 50, method: str = 'ETKDG', **kwargs) -> Self:
         """Generates 3D conformers.
 

rdworks/stereoisomers.py

@@ -1,13 +1,8 @@
-from typing import List, Tuple, Union, Optional
-
 from rdkit import Chem
 from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions
 
-from .mol import Mol
-from .mollibr import MolLibr
-
 
-def _enum_stereoisomers(rdmol:Chem.Mol) -> List[Chem.Mol]:
+def enumerate_stereoisomers(rdmol: Chem.Mol) -> list[Chem.Mol]:
     """Returns enumerated stereoisomers.
 
     Args:
@@ -28,8 +23,9 @@ def _enum_stereoisomers(rdmol:Chem.Mol) -> List[Chem.Mol]:
             )))
 
 
-def _enum_ring_bond_stereo(rdmol:Chem.Mol, ring_bond_stereo_info:List[Tuple], 
-                           override:bool=False) -> List[Chem.Mol]:
+def enumerate_ring_bond_stereoisomers(rdmol: Chem.Mol, 
+                                      ring_bond_stereo_info: list[tuple],
+                                      override: bool = False) -> list[Chem.Mol]:
     """Enumerates unspecified double bond stereochemistry (cis/trans).
 
     <pre>
@@ -68,60 +64,4 @@ def _enum_ring_bond_stereo(rdmol:Chem.Mol, ring_bond_stereo_info:List[Tuple],
             # trans
             bond.SetStereo(Chem.BondStereo.STEREOTRANS)
             isomers.append(Chem.Mol(rdmol))
-    return isomers
-
-
-def complete_stereoisomers(molecular_input:Union[Mol, str, Chem.Mol], name:Optional[str]=None, 
-                           std:bool=False, override:bool=False, **kwargs) -> MolLibr:
-    """Completes stereoisomers and returns a rdworks.MolLibr.
-
-    Args:
-        molecular_input (Union[Mol, str, Chem.Mol]): input molecule.
-        name (Optional[str], optional): name of the molecule. Defaults to None.
-        std (bool, optional): whether to standardize the input. Defaults to False.
-        override (bool, optional): whether to override input stereoisomers. Defaults to False.
-
-    Raises:
-        TypeError: if `molecular_input` is not rdworks.Mol, SMILES, or rdkit.Chem.Mol object.
-
-    Returns:
-        MolLibr: a library of complete stereoisomers.
-    """
-    if isinstance(molecular_input, Mol):
-        if name:
-            mol = molecular_input.rename(name)
-        else:
-            mol = molecular_input
-    elif isinstance(molecular_input, str) or isinstance(molecular_input, Chem.Mol):
-        mol = Mol(molecular_input, name, std)
-    else:
-        raise TypeError('complete_stereoisomers() expects rdworks.Mol, SMILES or rdkit.Chem.Mol object')
-    
-    ring_bond_stereo_info = mol.get_ring_bond_stereo()
-    
-    if override:
-        mol = mol.remove_stereo()
-    
-    rdmols = _enum_stereoisomers(mol.rdmol)
-    # ring bond stereo is not properly enumerated
-    # cis/trans information is lost if stereochemistry is removed,
-    # which cannot be enumerated by EnumerateStereoisomers() function
-    # so _enum_bond_stereo() is introduced
-    if len(ring_bond_stereo_info) > 0:
-        ring_cis_trans = []
-        for rdmol in rdmols:
-            ring_cis_trans += _enum_ring_bond_stereo(rdmol,
-                                                     ring_bond_stereo_info,
-                                                     override=override)
-        if len(ring_cis_trans) > 0:
-            rdmols = ring_cis_trans
-    
-    if len(rdmols) > 1:
-        libr = MolLibr(rdmols).unique().rename(mol.name, sep='.').compute(**kwargs)
-    else:
-        libr = MolLibr(rdmols).rename(mol.name).compute(**kwargs)
-    
-    for _ in libr:
-        _.props.update(mol.props)
-    
-    return libr
+    return isomers

rdworks/workflow.py

@@ -0,0 +1,85 @@
+
+from rdworks.stereoisomers import enumerate_stereoisomers, enumerate_ring_bond_stereoisomers
+from rdworks.mol import Mol
+from rdworks.mollibr import MolLibr
+
+from rdkit import Chem
+from rdkit.Chem.MolStandardize import rdMolStandardize
+
+
+def complete_stereoisomers(molecular_input: str | Chem.Mol | Mol, 
+                           name: str | None = None, 
+                           std: bool = False, 
+                           override: bool = False, 
+                           **kwargs) -> MolLibr:
+    """Completes stereoisomers and returns a rdworks.MolLibr.
+
+    Args:
+        molecular_input (Union[Mol, str, Chem.Mol]): input molecule.
+        name (Optional[str], optional): name of the molecule. Defaults to None.
+        std (bool, optional): whether to standardize the input. Defaults to False.
+        override (bool, optional): whether to override input stereoisomers. Defaults to False.
+
+    Raises:
+        TypeError: if `molecular_input` is not rdworks.Mol, SMILES, or rdkit.Chem.Mol object.
+
+    Returns:
+        MolLibr: a library of complete stereoisomers.
+    """
+    if isinstance(molecular_input, Mol):
+        if name:
+            mol = molecular_input.rename(name)
+        else:
+            mol = molecular_input
+    elif isinstance(molecular_input, str) or isinstance(molecular_input, Chem.Mol):
+        mol = Mol(molecular_input, name, std)
+    else:
+        raise TypeError('complete_stereoisomers() expects rdworks.Mol, SMILES or rdkit.Chem.Mol object')
+    
+    ring_bond_stereo_info = mol.get_ring_bond_stereo()
+    
+    if override:
+        mol = mol.remove_stereo()
+    
+    rdmols = enumerate_stereoisomers(mol.rdmol)
+    # ring bond stereo is not properly enumerated
+    # cis/trans information is lost if stereochemistry is removed,
+    # which cannot be enumerated by EnumerateStereoisomers() function
+    # so enumerate_ring_bond_stereoisomers() is introduced
+    if len(ring_bond_stereo_info) > 0:
+        ring_cis_trans = []
+        for rdmol in rdmols:
+            ring_cis_trans += enumerate_ring_bond_stereoisomers(rdmol,
+                                                     ring_bond_stereo_info,
+                                                     override=override)
+        if len(ring_cis_trans) > 0:
+            rdmols = ring_cis_trans
+    
+    if len(rdmols) > 1:
+        libr = MolLibr(rdmols).unique().rename(mol.name, sep='.').compute(**kwargs)
+    else:
+        libr = MolLibr(rdmols).rename(mol.name).compute(**kwargs)
+    
+    for _ in libr:
+        _.props.update(mol.props)
+    
+    return libr
+
+
+
+def complete_tautomers(mol: Mol, **kwargs) -> MolLibr:
+    """Returns a library of enumerated tautomers.
+
+    Args:
+        mol (Mol): input molecule.
+
+    Returns:
+        MolLibr: a library of enumerated tautomers.
+    """
+    enumerator = rdMolStandardize.TautomerEnumerator()
+    rdmols = list(enumerator.Enumerate(mol.rdmol))
+    
+    if len(rdmols) > 1: 
+        return MolLibr(rdmols).unique().rename(mol.name, sep='.').compute(**kwargs)
+    
+    return MolLibr(rdmols).compute(**kwargs)

{rdworks-0.52.1.dist-info → rdworks-0.53.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.52.1
+Version: 0.53.1
 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-0.52.1.dist-info → rdworks-0.53.1.dist-info}/RECORD

@@ -1,23 +1,23 @@
-rdworks/__init__.py,sha256=nSkNkfvjtAeom2f5SYdS-XCnglYeC-wcGuGVubrv3nQ,1391
+rdworks/__init__.py,sha256=iKipZN3E7INKDKEGeK2CbjgwyGu8Vu5a3THRaKNU_NE,1358
 rdworks/conf.py,sha256=eH_a3ywmmJiPtnvgk86ykurYOx879AHg80-Dn8z1X70,36379
 rdworks/descriptor.py,sha256=34T_dQ6g8v3u-ym8TLKbQtxIIV5TEo-d3pdedq3o-cg,2106
 rdworks/display.py,sha256=JR0gR26UpH-JCxVOaqXZCUj2MiGZSrx9Me87FncspVI,13469
 rdworks/ionized.py,sha256=_t-Ajssv1rytV4Y_KsSbxfnsBKqy-EusbhNUtaWcV6o,7681
 rdworks/matchedseries.py,sha256=A3ON4CUpQV159mu9VqgNiJ8uoQ9ePOry9d3ra4NCAgc,10377
 rdworks/microstates.py,sha256=T206JgeB3d23MX3sRCrxVj2arxlSILYecBTKaD1VcoE,5109
-rdworks/mol.py,sha256=-zjAsBETNUbP4_n8p6how40NhZB24icMYhas1kYPqCc,70064
+rdworks/mol.py,sha256=4gNjs_ryNNWThMekV794uwjjBE-JLGGWcdyMaS9-xP8,71369
 rdworks/mollibr.py,sha256=X4UBO6Ga-QmNS7RwUiaDYAx0Q5hnWs71yTkEpH02Qb4,37696
 rdworks/pka.py,sha256=NVJVfpcNEMlX5QRyLBgUM7GIT7VMjO-llAR4LWc8J2c,1656
 rdworks/readin.py,sha256=b1BHchQMC5EgQd3C05n72t_aa_9u0iKQWyyIqjyfkPc,11809
 rdworks/rgroup.py,sha256=ivF2gzmRtt339rxEnkv2KfnCs0CUdBbnSje7Y54rtFI,57996
 rdworks/scaffold.py,sha256=60T5YacyxZsEpDo_J5Qxulm2YNQO4EQR8PcNUwjn1QU,22026
 rdworks/std.py,sha256=qOVS_lGogueLKh4rsbrsYIMR0c7z_xh6BqLEzD4X9sE,7938
-rdworks/stereoisomers.py,sha256=g8hhPI-mbYX-MzbF1uAqo5fDZOCNiKYjxI-kLBGdGgg,4980
-rdworks/tautomers.py,sha256=gtZHZJ-aJbryhBdljHbfjx7xhVW3u_OzdYPtwPail54,610
+rdworks/stereoisomers.py,sha256=2Fp89ItDy5nbZ7FO1KHl0X0yUa2gz95BzbgfQSLnzb0,2686
 rdworks/testdata.py,sha256=TmbNPA-ju6nTBt_Yts4EJUFmL9Cd6DCVXrDF42QLlHw,1732
 rdworks/torsion.py,sha256=UUaYOvNS89SlLFauYiAboUqysy32EN0_Gktc4xxuDQI,18788
 rdworks/units.py,sha256=nljKPHcr6IWoAp0CkL7y1gSNDd6a07NeVfxXwSMuHQM,365
 rdworks/utils.py,sha256=d2Sio8WTlGPsmBOHIYDCMWg_7X4rTWjJQAqzd7ywo2A,14191
+rdworks/workflow.py,sha256=MtP9QUGgCKMyI3G4vp8sokos_UyaQvTHFOEPUJresZU,3139
 rdworks/xml.py,sha256=aaMhwVRGvt1VzasaKDnkYnZ4kp2cIgvGb1CsmMgwQ_c,10704
 rdworks/autograph/__init__.py,sha256=0Qfjwo0h4Q0n08zsqHRbuNOZms6MuNXnWErnQpQ6Px0,140
 rdworks/autograph/autograph.py,sha256=frjsUaCTOD-Z1lYPzOxRoTtqMMiYroWAy6tSwKn3CUA,8769
@@ -67,8 +67,8 @@ 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=p_ddunnjtxe3F2yN7RC2mvSUDnw7fNBhGm1bZVMAWAE,21901
-rdworks-0.52.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
-rdworks-0.52.1.dist-info/METADATA,sha256=M47Khc8DU4es8jrzYzp4x4ZyM6ap6NwHrmbJqw5lK5Y,1967
-rdworks-0.52.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rdworks-0.52.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
-rdworks-0.52.1.dist-info/RECORD,,
+rdworks-0.53.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
+rdworks-0.53.1.dist-info/METADATA,sha256=kErcEEj-I1D5jI8ZTSr3D1jVXfZ-cGRlV_z1bsG7vLA,1967
+rdworks-0.53.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rdworks-0.53.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
+rdworks-0.53.1.dist-info/RECORD,,

rdworks/tautomers.py

@@ -1,20 +0,0 @@
-from rdkit.Chem.MolStandardize import rdMolStandardize
-
-from .mol import Mol
-from .mollibr import MolLibr
-
-
-def complete_tautomers(mol:Mol, **kwargs) -> MolLibr:
-    """Returns a library of enumerated tautomers.
-
-    Args:
-        mol (Mol): input molecule.
-
-    Returns:
-        MolLibr: a library of enumerated tautomers.
-    """
-    enumerator = rdMolStandardize.TautomerEnumerator()
-    rdmols = list(enumerator.Enumerate(mol.rdmol))
-    if len(rdmols) > 1: 
-        return MolLibr(rdmols).unique().rename(mol.name, sep='.').compute(**kwargs)
-    return MolLibr(rdmols).compute(**kwargs)