PEP-8 other corrections

rdmc/conf.py

@@ -733,9 +733,11 @@ def check_dihed_angle_diff(self,
 
         if mask:
             # Allowing mask some dimensions
-            def masked_tor(tor): return np.ma.masked_array(tor, mask)
+            def masked_tor(tor):
+                return np.ma.masked_array(tor, mask)
         else:
-            def masked_tor(tor): return tor
+            def masked_tor(tor):
+                return tor
 
         # Create an array to store cluster indexes
         # Initializing all elements to -1

rdmc/conformer_generation/ts_optimizers.py

@@ -271,7 +271,7 @@ def extract_frequencies(self,
         if freq_idx:
             freqs = orca_data[freq_idx - 4 - dof: freq_idx - 4]
             freqs.reverse()
-            return np.array([float(l.split()[1]) for l in freqs])
+            return np.array([float(line.split()[1]) for line in freqs])
         else:
             return None
 

rdmc/external/logparser/qchem.py

@@ -35,8 +35,8 @@ def _update_status(self):
             if 'Thank you very much for using Q-Chem.  Have a nice day.' in line:
                 self._finished = True
                 time_str = re.search(self.time_regex, reverse_lines[i + 4]).group()
-                for l in reverse_lines[i + 1:]:
-                    if 'MAXIMUM OPTIMIZATION CYCLES REACHED' in l:
+                for rline in reverse_lines[i + 1:]:
+                    if 'MAXIMUM OPTIMIZATION CYCLES REACHED' in rline:
                         self._success = False
                         break
                 else:

rdmc/external/xtb_tools/opt.py

@@ -193,7 +193,7 @@ def run_xtb_calc(mol, confId=0, job="", return_optmol=False, method="gfn2", leve
         if job == "--hess":
             with open(xtb_g98) as f:
                 data = f.readlines()
-            frequencies = np.array([l.split()[-3:] for l in data if "Frequencies" in l], dtype=float).ravel()
+            frequencies = np.array([line.split()[-3:] for line in data if "Frequencies" in line], dtype=float).ravel()
             props.update({"frequencies": frequencies})
             not save_dir and rmtree(temp_dir)
             return props

rdmc/external/xyz2mol.py

@@ -300,12 +300,12 @@ def BO2mol(mol, BO_matrix, atoms, atomic_valence_electrons,
 
     """
 
-    l = len(BO_matrix)
+    l1 = len(BO_matrix)
     l2 = len(atoms)
     BO_valences = list(BO_matrix.sum(axis=1))
 
-    if (l != l2):
-        raise RuntimeError('sizes of adjMat ({0:d}) and Atoms {1:d} differ'.format(l, l2))
+    if (l1 != l2):
+        raise RuntimeError('sizes of adjMat ({0:d}) and Atoms {1:d} differ'.format(l1, l2))
 
     rwMol = Chem.RWMol(mol)
 
@@ -315,8 +315,8 @@ def BO2mol(mol, BO_matrix, atoms, atomic_valence_electrons,
         3: Chem.BondType.TRIPLE
     }
 
-    for i in range(l):
-        for j in range(i + 1, l):
+    for i in range(l1):
+        for j in range(i + 1, l1):
             bo = int(round(BO_matrix[i, j]))
             if (bo == 0):
                 continue

rdmc/mol.py

@@ -1906,8 +1906,8 @@ def generate_vdw_mat(rd_mol,
             else:
                 atom2 = rd_mol.GetAtomWithIdx(atom2_ind)
                 vdw_mat[atom1_ind, atom2_ind] = threshold * \
-                    (vdw_radii[atom1.GetAtomicNum()] +
-                        vdw_radii[atom2.GetAtomicNum()])
+                    (vdw_radii[atom1.GetAtomicNum()]
+                     + vdw_radii[atom2.GetAtomicNum()])
     return vdw_mat
 
 

rdmc/ts.py

@@ -106,8 +106,8 @@ def get_all_changing_bonds(r_mol: Union['RDKitMol', 'Mol'],
     r_bonds, p_bonds = _get_bonds_as_sets(r_mol, p_mol)
     formed_bonds, broken_bonds = p_bonds - r_bonds, r_bonds - p_bonds
     changed_bonds = [bond for bond in (r_bonds & p_bonds)
-                     if r_mol.GetBondBetweenAtoms(*bond).GetBondTypeAsDouble() !=
-                     p_mol.GetBondBetweenAtoms(*bond).GetBondTypeAsDouble()]
+                     if (r_mol.GetBondBetweenAtoms(*bond).GetBondTypeAsDouble()
+                         != p_mol.GetBondBetweenAtoms(*bond).GetBondTypeAsDouble())]
     return list(formed_bonds), list(broken_bonds), changed_bonds
 
 

rdmc/view.py

@@ -163,14 +163,16 @@ def interactive_conformer_viewer(mol, **kwargs):
         py3Dmol.view: The molecule viewer with slider to view different conformers.
     """
     if isinstance(mol, list) or isinstance(mol, tuple):
-        def viewer(confId): return mol_viewer(obj=mol[confId], confId=0, **kwargs)
+        def viewer(confId):
+            return mol_viewer(obj=mol[confId], confId=0, **kwargs)
         return interact(
             viewer,
             confId=IntSlider(min=0, max=len(mol) - 1, step=1)
         )
 
     else:
-        def viewer(confId): return mol_viewer(obj=mol, confId=confId, **kwargs)
+        def viewer(confId):
+            return mol_viewer(obj=mol, confId=confId, **kwargs)
         return interact(
             viewer,
             confId=IntSlider(min=0, max=mol.GetNumConformers() - 1, step=1)