rdworks 0.42.1__tar.gz → 0.43.2__tar.gz

{rdworks-0.42.1 → rdworks-0.43.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.42.1
+Version: 0.43.2
 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-0.42.1 → rdworks-0.43.2}/src/rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.42.1'
+__version__ = '0.43.2'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

{rdworks-0.42.1 → rdworks-0.43.2}/src/rdworks/conf.py

@@ -206,11 +206,20 @@ class Conf:
         if isinstance(calculator, str) :
             
             PE_start = self.potential_energy(calculator)
+            PE_final = None
             
             if calculator.lower() == 'xTB'.lower():
                 water = kwargs.get('water', None)
-                PE_final, self.rdmol = GFN2xTB(self.rdmol).optimize(water=water)
-
+                result = GFN2xTB(self.rdmol).optimize(water=water)
+                # SimpleNamespace(
+                #         PE = datadict['total energy'] * hartree2kcalpermol,
+                #         charges = datadict['partial charges'],
+                #         wbo = Wiberg_bond_orders,
+                #         geometry = rdmol_opt,
+                # )
+                self.rdmol = result.geometry
+                PE_final = result.PE
+                
             elif calculator.lower() == 'MMFF94'.lower() or calculator.lower() == 'MMFF'.lower():
                 retcode = Chem.rdForceFieldHelpers.MMFFOptimizeMolecule(self.rdmol, 
                                                                         mmffVariant='MMFF94',
@@ -226,7 +235,8 @@ class Conf:
                                                                        maxIters=max_iter)
                 # returns 0 if the optimization converged
 
-            PE_final = self.potential_energy(calculator)
+            if PE_final is None:
+                PE_final = self.potential_energy(calculator)
             
             self.props.update({
                 'E_tot_init(kcal/mol)': PE_start , # energy before optimization
@@ -681,6 +691,15 @@ class Conf:
                     rdmol.SetProp(k, str(v))
             f.write(rdmol)
         return in_memory.getvalue()
+
+
+    def to_smi(self) -> str:
+        """Returns SMILES containing explicit hydrogens
+
+        Returns:
+            str: SMILES
+        """
+        return Chem.MolToSmiles(self.rdmol)
     
 
     def to_png(self,
@@ -763,4 +782,4 @@ class Conf:
                           highlight_bonds = highlight_bonds,
                           redraw = redraw, 
                           coordgen = coordgen, 
-                          optimize = optimize)
+                          optimize = optimize)

{rdworks-0.42.1 → rdworks-0.43.2}/src/rdworks.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.42.1
+Version: 0.43.2
 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>