rdworks 0.49.1__py3-none-any.whl → 0.51.1__py3-none-any.whl

rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.49.1'
+__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/xtb/wrapper.py

@@ -59,6 +59,43 @@ class GFN2xTB:
         return shutil.which('xtb') is not None
 
 
+    @staticmethod
+    def is_optimize_ready() -> bool:
+        try:
+            h2o = [
+                '$coord',
+                ' 0.00000000000000      0.00000000000000     -0.73578586109551      o',
+                ' 1.44183152868459      0.00000000000000      0.36789293054775      h',
+                '-1.44183152868459      0.00000000000000      0.36789293054775      h',
+                '$end',
+            ]
+
+            with tempfile.TemporaryDirectory() as temp_dir:
+                test_geometry = os.path.join(temp_dir, 'coord')
+                with open(test_geometry, 'w') as f:
+                    f.write('\n'.join(h2o))
+                proc = subprocess.run(['xtb', test_geometry, '--opt'], 
+                                      capture_output=True, 
+                                      text=True)
+                assert proc.returncode == 0
+
+            return True
+
+        except:
+            print("""                          
+Conda installed xTB has the Fortran runtime error in geometry optimization. 
+Please install xtb using the compiled binary:
+                    
+$ wget https://github.com/grimme-lab/xtb/releases/download/v6.7.1/xtb-6.7.1-linux-x86_64.tar.xz
+$ tar -xf xtb-6.7.1-linux-x86_64.tar.xz
+$ cp -r xtb-dist/bin/*      /usr/local/bin/
+$ cp -r xtb-dist/lib/*      /usr/local/lib/
+$ cp -r xtb-dist/include/*  /usr/local/include/
+$ cp -r xtb-dist/share      /usr/local/ """)
+            
+            return False
+
+
     @staticmethod
     def is_cpx_ready() -> bool:
         """Checks if the CPCM-X command-line tool, `cpx`, is accessible in the system.
@@ -70,7 +107,7 @@ class GFN2xTB:
     
 
     @staticmethod
-    def is_cpcmx_option_ready() -> bool:
+    def is_cpcmx_ready() -> bool:
         """Checks if xtb works with the `--cpcmx` option.
 
         xtb distributed by the conda does not include CPCM-X function (as of June 17, 2025). 
@@ -101,7 +138,8 @@ class GFN2xTB:
         """
         return all([GFN2xTB.is_xtb_ready(),
                     GFN2xTB.is_cpx_ready(),
-                    GFN2xTB.is_cpcmx_option_ready()])
+                    GFN2xTB.is_cpcmx_ready(),
+                    GFN2xTB.is_optimize_ready()])
     
 
     @staticmethod
@@ -115,10 +153,9 @@ class GFN2xTB:
             cmd = ['xtb', '--version']
             proc = subprocess.run(cmd, capture_output=True, text=True)
             assert proc.returncode == 0, "GFN2xTB() Error: xtb not available"
-            for line in proc.stdout.split('\n'):
-                line = line.strip()
-                if 'version' in line:
-                    return line
+            match = re.search('xtb\s+version\s+(?P<version>[\d.]+)', proc.stdout)
+            if match:
+                return match.group('version')
             
         return None
     
@@ -362,7 +399,7 @@ class GFN2xTB:
                 elif water == 'alpb':
                     options += ['--alpb', 'water']
                     # it does not provide Gsolv contribution to the total energy
-                elif water == 'cpcmx' and self.is_cpcmx_option_ready():
+                elif water == 'cpcmx' and self.is_cpcmx_ready():
                     options += ['--cpcmx', 'water']
 
             if verbose:

{rdworks-0.49.1.dist-info → rdworks-0.51.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.49.1
+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-0.49.1.dist-info → rdworks-0.51.1.dist-info}/RECORD

@@ -1,10 +1,10 @@
-rdworks/__init__.py,sha256=1teH6iycO-shzgeW5KwSDr-CH6CYybv2sDcrSNUBDW0,1391
-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
@@ -65,9 +65,9 @@ rdworks/predefined/misc/reactive-part-2.xml,sha256=0vNTMwWrrQmxBpbgbyRHx8sVs83cq
 rdworks/predefined/misc/reactive-part-3.xml,sha256=LgWHSEbRTVmgBoIO45xbTo1xQJs0Xu51j3JnIapRYo4,3094
 rdworks/predefined/misc/reactive.xml,sha256=syedoQ6VYUfRLnxy99ObuDniJ_a_WhrWAJbTKFfJ6VY,11248
 rdworks/xtb/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-rdworks/xtb/wrapper.py,sha256=Uv5XrC1gbWyVZiUJsoVwn6i76SPrtBCVSja0kOgcSWQ,22125
-rdworks-0.49.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
-rdworks-0.49.1.dist-info/METADATA,sha256=3Z8TiRFULi-sddBb-_bhWh13MYWcjjopn5wnpUORX00,1967
-rdworks-0.49.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rdworks-0.49.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
-rdworks-0.49.1.dist-info/RECORD,,
+rdworks/xtb/wrapper.py,sha256=w_SX3q7D4_peHERFzONesG8c-a6UTRzfBLx313D8rNE,23638
+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,,