rdworks 0.50.1__tar.gz → 0.51.1__tar.gz

{rdworks-0.50.1 → rdworks-0.51.1}/PKG-INFO

@@ -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 → rdworks-0.51.1}/src/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-0.50.1 → rdworks-0.51.1}/src/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-0.50.1 → rdworks-0.51.1}/src/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 → rdworks-0.51.1}/src/rdworks.egg-info/PKG-INFO

@@ -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 → rdworks-0.51.1}/src/rdworks.egg-info/SOURCES.txt

@@ -76,6 +76,7 @@ src/rdworks/xtb/__init__.py
 src/rdworks/xtb/wrapper.py
 tests/test_basics.py
 tests/test_ionized.py
+tests/test_qupkake.py
 tests/test_round.py
 tests/test_torsion.py
 tests/test_xtb.py

rdworks-0.51.1/tests/test_qupkake.py

@@ -0,0 +1,19 @@
+import rdworks
+
+def test_readin_qupkake_output():
+    libr = rdworks.read_sdf('qupkake/output/qupkake_output.sdf', confs=True)
+    # libr contains one molecule because of confs=True
+    assert libr.count() == 1
+    for m in libr:
+        assert m.count() == 4
+        print(m.props)
+        print()
+        for c in m:
+            print(c.props)
+            print()
+
+        print(m.serialize(compressed=True))
+
+
+if __name__ == '__main__':
+    test_readin_qupkake_output()

rdworks-0.51.1/tests/test_xtb.py

@@ -0,0 +1,76 @@
+from rdworks import Mol
+from rdworks.xtb.wrapper import GFN2xTB
+from rdworks.testdata import drugs
+
+from pathlib import Path
+
+
+# In ASE, the default energy unit is eV (electron volt).
+# It will be converted to kcal/mol
+# CODATA 2018 energy conversion factor
+hartree2ev = 27.211386245988
+hartree2kcalpermol = 627.50947337481
+ev2kcalpermol = 23.060547830619026
+
+
+datadir = Path(__file__).parent.resolve() / "data"
+workdir = Path(__file__).parent.resolve() / "outfiles"
+
+workdir.mkdir(exist_ok=True)
+
+name = 'Atorvastatin'
+testmol = Mol(drugs[name], name).make_confs(n=50).optimize_confs()
+testmol = testmol.drop_confs(similar=True, verbose=True).sort_confs()
+
+
+def test_xtb_wrapper():
+    from rdworks.xtb.wrapper import GFN2xTB
+    assert GFN2xTB.is_xtb_ready() == True
+    assert GFN2xTB.is_cpx_ready() == True
+    assert GFN2xTB.is_cpcmx_ready() == True
+    assert GFN2xTB.is_ready() == True
+    assert GFN2xTB.version() is not None
+
+
+def test_singlepoint():        
+    mol = testmol.copy()
+
+    print("number of conformers=", mol.count())
+    print("number of atoms=", mol.confs[0].natoms)
+
+    gfn2xtb = GFN2xTB(mol.confs[0].rdmol)
+
+    print("GFN2xTB.singlepoint()")
+    outdict = gfn2xtb.singlepoint()
+    print(outdict)
+    print()
+
+    print("GFN2xTB.singlepoint(water='gbsa')")
+    outdict = gfn2xtb.singlepoint(water='gbsa')
+    print(outdict)
+    print()
+
+    print("GFN2xTB.singlepoint(water='alpb')")
+    outdict = gfn2xtb.singlepoint(water='alpb')
+    print(outdict)
+    print()
+
+    print("GFN2xTB.singlepoint(water='cpcmx')")
+    outdict = gfn2xtb.singlepoint(water='cpcmx')
+    print(outdict)
+    print()
+
+
+def test_optimize():
+    mol = testmol.copy()
+    print("number of conformers=", mol.count())
+    print("GFN2xTB.optimize()")
+    outdict = GFN2xTB(mol.confs[0].rdmol).optimize(verbose=True)
+    print(outdict)
+    print()
+
+
+if __name__ == '__main__':
+    test_xtb_wrapper()
+    test_singlepoint()
+    test_optimize()

rdworks-0.50.1/tests/test_xtb.py

@@ -1,160 +0,0 @@
-from rdworks import Mol
-from rdworks.xtb.wrapper import GFN2xTB
-from rdworks.testdata import drugs
-
-from pathlib import Path
-
-
-# In ASE, the default energy unit is eV (electron volt).
-# It will be converted to kcal/mol
-# CODATA 2018 energy conversion factor
-hartree2ev = 27.211386245988
-hartree2kcalpermol = 627.50947337481
-ev2kcalpermol = 23.060547830619026
-
-
-datadir = Path(__file__).parent.resolve() / "data"
-workdir = Path(__file__).parent.resolve() / "outfiles"
-
-workdir.mkdir(exist_ok=True)
-
-name = 'Atorvastatin'
-testmol = Mol(drugs[name], name).make_confs(n=50).optimize_confs()
-testmol = testmol.drop_confs(similar=True, verbose=True).sort_confs()
-
-
-def test_xtb_wrapper():
-    from rdworks.xtb.wrapper import GFN2xTB
-    assert GFN2xTB.is_xtb_ready() == True
-    assert GFN2xTB.is_cpx_ready() == True
-    assert GFN2xTB.is_cpcmx_ready() == True
-    assert GFN2xTB.is_ready() == True
-    assert GFN2xTB.version() is not None
-
-
-def test_singlepoint():        
-    mol = testmol.copy()
-
-    print("number of conformers=", mol.count())
-    print("number of atoms=", mol.confs[0].natoms)
-
-    gfn2xtb = GFN2xTB(mol.confs[0].rdmol)
-
-    print("GFN2xTB.singlepoint()")
-    outdict = gfn2xtb.singlepoint()
-    print(outdict)
-    print()
-
-    print("GFN2xTB.singlepoint(water='gbsa')")
-    outdict = gfn2xtb.singlepoint(water='gbsa')
-    print(outdict)
-    print()
-
-    print("GFN2xTB.singlepoint(water='alpb')")
-    outdict = gfn2xtb.singlepoint(water='alpb')
-    print(outdict)
-    print()
-
-    print("GFN2xTB.singlepoint(water='cpcmx')")
-    outdict = gfn2xtb.singlepoint(water='cpcmx')
-    print(outdict)
-    print()
-
-
-def test_optimize():
-    mol = testmol.copy()
-    print("number of conformers=", mol.count())
-    print("GFN2xTB.optimize()")
-    outdict = GFN2xTB(mol.confs[0].rdmol).optimize(verbose=True)
-    print(outdict)
-    print()
-
-
-def test_state_generate():
-    import rdworks
-    import numpy as np
-    import os
-
-    task_queue = 'xtb'
-
-    kT = 0.001987 * 300.0 # (kcal/mol K)
-
-    smiles =  'CCCCNC(=O)[C@@H]1CCCN1[C@@H](CC)c1nnc(Cc2ccc(C)cc2)o1'
-    n = 50
-    method = 'ETKDG'
-
-    standardized = rdworks.Mol(smiles)
-    libr = rdworks.complete_tautomers(standardized)
-
-    PE = []
-    for mol in libr:
-        mol = mol.make_confs(n=n, method=method, verbose=True)
-        mol = mol.optimize_confs(calculator='MMFF94', verbose=True)
-        mol = mol.drop_confs(similar=True, similar_rmsd=0.3, verbose=True)
-        mol = mol.sort_confs(calculator='xTB', verbose=True)
-        mol = mol.drop_confs(k=10, window=15.0, verbose=True) # enforcing both conditions
-        _PE = []
-        for conf in mol.confs:
-            conf = conf.optimize(calculator='xTB', verbose=True)
-            # GFN2xTB requires 3D coordinates
-            xtb = GFN2xTB(conf.rdmol).singlepoint(water='cpcmx', verbose=True)
-            _PE.append(xtb.PE)
-        # SimpleNamespace(
-        #             PE = datadict['total energy'] * hartree2kcalpermol,
-        #             Gsolv = Gsolv,
-        #             charges = datadict['partial charges'],
-        #             wbo = Wiberg_bond_orders,
-        #             )
-        PE.append(_PE)
-        print(_PE)
-    
-    # calculate population
-    PE = np.array(PE)
-    PE = PE - np.min(PE)
-    Boltzmann_factors = np.exp(-PE/kT)
-    # partition function
-    Z = np.sum(Boltzmann_factors)
-    # population
-    p = np.sum(Boltzmann_factors/Z, axis=1)
-
-    sorted_indices = sorted(list(enumerate(p)), key=lambda x: x[1], reverse=True) # [(0,p0), (1,p1), ...]
-
-    molecular_states = []
-    for idx, population in sorted_indices:
-        if population < 0.05:
-            continue
-
-        # state.keys() = ['rdmol','smiles','charge','population','pKa', 'qikprop']
-
-        state_mol = libr[idx].rename(f'state.{idx+1}').qed(
-            properties=['QED', 'MolWt', 'LogP', 'TPSA', 'HBD', 'HBA'])
-        
-        basic_properties = {
-            'QED'      : round(state_mol.props['QED'],   2),
-            'MolWt'    : round(state_mol.props['MolWt'], 2),
-            'LogP'     : round(state_mol.props['LogP'],  2),
-            'TPSA'     : round(state_mol.props['TPSA'],  2),
-            'HBD'      : state_mol.props['HBD'],
-            'HBA'      : state_mol.props['HBA'],
-            }
-        
-        state_props = {
-            'method': task_queue,
-            'PE(kcal/mol)': state_mol.confs[0].props['E_tot(kcal/mol)'],
-            'population' : round(float(population), 3),
-            'basic_properties': basic_properties,
-            'rdkit_version': rdworks.__rdkit_version__,
-            'rdworks_version': rdworks.__version__,
-        }
-        
-        molecular_states.append((state_mol.serialize(compressed=True), state_props))
-    
-    print(molecular_states)
-
-
-
-if __name__ == '__main__':
-    test_xtb_wrapper()
-    test_singlepoint()
-    test_optimize()
-    test_state_generate()