rdworks 0.50.1__py3-none-any.whl → 0.51.1__py3-none-any.whl

rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.50.1'
+__version__ = '0.51.1'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

rdworks/conf.py

@@ -270,6 +270,62 @@ class Conf:
                 return self.sync(ase_atoms.get_positions())
  
     
+    def protonate(self, atom_indices: list[int]) -> Self:
+        """Protonate given non-hydrogen atoms.
+
+        Args:
+            atom_indices (list[int]): atom indices of non-hydrogen atoms to protonate.
+
+        Returns:
+            Self: self.
+        """
+        for idx in atom_indices:
+            atom = self.rdmol.GetAtomWithIdx(idx)
+            h = atom.GetNumExplicitHs()
+            c = atom.GetFormalCharge()
+            atom.SetNumExplicitHs(h+1)
+            atom.SetFormalCharge(c+1)            
+            Chem.SanitizeMol(self.rdmol)
+            self.rdmol = Chem.AddHs(self.rdmol, addCoords=True)
+            # The Chem.AddHs function in RDKit returns a new Mol object with hydrogens added to the molecule. 
+            # It modifies the input molecule by adding hydrogens, 
+            # but the original molecule remains unchanged.
+        
+        return self
+    
+
+    def deprotonate(self, atom_indices: list[int]) -> Self:
+        """Deprotonate given non-hydrogen atoms.
+
+        Args:
+            atom_indices (list[int]): atom indices of non-hydrogen atoms to deprotonate.
+
+        Returns:
+            Self: self.
+        """
+        for idx in atom_indices:
+            bonded_H_idx = None
+            atom = self.rdmol.GetAtomWithIdx(idx)
+            h = atom.GetNumExplicitHs()
+            if h-1 >= 0 :
+                atom.SetNumExplicitHs(h-1) # (h-1) must be unsigned int
+            c = atom.GetFormalCharge()
+            atom.SetFormalCharge(c-1)            
+            neighbors = atom.GetNeighbors()
+            
+            for neighbor in neighbors:
+                if neighbor.GetAtomicNum() == 1:
+                    bonded_H_idx = neighbor.GetIdx()
+                    break
+
+            if bonded_H_idx is not None:
+                edit_mol = Chem.EditableMol(self.rdmol)
+                edit_mol.RemoveAtom(bonded_H_idx)
+                self.rdmol = edit_mol.GetMol()
+                Chem.SanitizeMol(self.rdmol)
+        
+        return self
+
 
     ##################################################
     ### Endpoint methods

rdworks/mol.py

@@ -1619,4 +1619,46 @@ class Mol:
         self.props = data['props']
         self.confs = [Conf().deserialize(_) for _ in data['confs']] # for 3D conformers (iterable)
         
+        return self
+    
+    def from_molblock(self, molblock: str) -> Self:
+        """Initialize a new Mol object from MolBlock.
+
+        Args:
+            molblock (str): MolBlock string
+
+        Raises:
+            ValueError: invalid MolBlock
+
+        Returns:
+            Self: self.
+        """
+        molecule = Chem.MolFromMolBlock(molblock)
+        try:
+            self.rdmol, _ = clean_2d(molecule, reset_isotope=True, remove_H=True)
+            self.smiles = Chem.MolToSmiles(self.rdmol)
+            self.confs = [Conf(x) for x in _]
+        except:
+            raise ValueError(f'Mol() Error: invalid MolBlock string')
+
+        assert self.smiles and self.rdmol, "Mol() Error: invalid molecule"
+        
+        name = self.rdmol.GetProp('_Name')
+
+        rdDepictor.Compute2DCoords(self.rdmol)
+
+        try:
+            self.name = str(name)
+        except:
+            self.name = 'untitled'
+        
+        self.rdmol.SetProp('_Name', self.name) # _Name can't be None        
+        self.InChIKey = generate_inchi_key(self.rdmol)
+        self.props.update({
+            'aka' : [], # <-- to be set by MolLibr.unique()
+            'atoms' : self.rdmol.GetNumAtoms(), # hydrogens not excluded?
+            'charge': rdmolops.GetFormalCharge(self.rdmol),
+            "nrb" : Descriptors.NumRotatableBonds(self.rdmol),
+            })
+        
         return self

{rdworks-0.50.1.dist-info → rdworks-0.51.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.50.1
+Version: 0.51.1
 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-0.50.1.dist-info → rdworks-0.51.1.dist-info}/RECORD

@@ -1,10 +1,10 @@
-rdworks/__init__.py,sha256=cELiDVknzDSz59Afufwk8LssqIuPLWLsxO73NISKfLY,1391
-rdworks/conf.py,sha256=iQLb3Qg3pjGiiMVMJ5-d57BC1id3zxEhEGlhhrLrA_c,34162
+rdworks/__init__.py,sha256=97yHJt3kMGu9bPYMVL98USE3E9kkAxZmupT77BGkX6s,1391
+rdworks/conf.py,sha256=aHpVa3PcbECk-IP6pdxqT2Q9T4eykqoozcgaGRnZdLk,36210
 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/mol.py,sha256=UPLLJbfn1cPhcedrGW7tL_bk1QpG3BfpjCOhop0tmBY,68663
+rdworks/mol.py,sha256=-zjAsBETNUbP4_n8p6how40NhZB24icMYhas1kYPqCc,70064
 rdworks/mollibr.py,sha256=X4UBO6Ga-QmNS7RwUiaDYAx0Q5hnWs71yTkEpH02Qb4,37696
 rdworks/pka.py,sha256=NVJVfpcNEMlX5QRyLBgUM7GIT7VMjO-llAR4LWc8J2c,1656
 rdworks/readin.py,sha256=0bnVcZcAmSLqc6zu1mYcv0LdBv2agQfOpKGwpSRL9VE,11742
@@ -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=w_SX3q7D4_peHERFzONesG8c-a6UTRzfBLx313D8rNE,23638
-rdworks-0.50.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
-rdworks-0.50.1.dist-info/METADATA,sha256=Rh6pJzHolql4Q3OJot3eO8OQ7K2R9nPqpPc3Vwt3l0Y,1967
-rdworks-0.50.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rdworks-0.50.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
-rdworks-0.50.1.dist-info/RECORD,,
+rdworks-0.51.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
+rdworks-0.51.1.dist-info/METADATA,sha256=nlzLbvfGJYCScwVL1Mub2lFFhsDvETxIQFs5UIBdZ90,1967
+rdworks-0.51.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rdworks-0.51.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
+rdworks-0.51.1.dist-info/RECORD,,