linting

psp/AmorphousBuilder.py

@@ -331,8 +331,13 @@ def get_opls(self, output_fname='amor_opls.lmps'):
 
             try:
                 print("LigParGen working on {}.pdb".format(output_prefix))
-                Converter.convert(pdb=os.path.join(self.OutDir_xyz, output_prefix + '.pdb'),
-                                  resname=output_prefix, charge=0, opt=0, outdir='.')
+                Converter.convert(
+                    pdb=os.path.join(self.OutDir_xyz, output_prefix + '.pdb'),
+                    resname=output_prefix,
+                    charge=0,
+                    opt=0,
+                    outdir='.',
+                )
                 os.rename(lig_output_fname, data_fname)
             except BaseException:
                 print('problem running LigParGen for {}.pdb.'.format(output_prefix))

psp/AmorphousBuilder2.py

@@ -49,7 +49,7 @@ def __init__(
         self.SMILES_col = SMILES_col
         self.LeftCap = LeftCap
         self.RightCap = RightCap
-        self.Nunits_col =  Nunits_col
+        self.Nunits_col = Nunits_col
         self.Mwt_col = Mwt_col
         self.define_BB_col = define_BB_col
         self.Loop_col = Loop_col
@@ -83,9 +83,9 @@ def Build(self):
             box_type_ = "Rectangular"
         print(self.rdkit_conf_param)
 
-#        NumConf = 1
-#        if 'numConfs' in self.rdkit_conf_param.keys():
-#            NumConf = int(self.rdkit_conf_param['numConfs'])
+        #        NumConf = 1
+        #        if 'numConfs' in self.rdkit_conf_param.keys():
+        #            NumConf = int(self.rdkit_conf_param['numConfs'])
 
         print(
             "\n",
@@ -133,16 +133,16 @@ def Build(self):
                 Loop_col=self.Loop_col,
                 OutDir=self.OutDir_xyz,
                 NCores=self.NCores,
-                Output=['xyz','pdb','smi'],
+                Output=['xyz', 'pdb', 'smi'],
                 seed=self.seed,
                 rdkit_conf_param=self.rdkit_conf_param,
             )
             results = mol.Build()
 
             path_to_file = self.OutDir_xyz + df[self.ID_col].values[0] + '_C1.smi'
             with open(path_to_file) as f:
-               contents = f.readlines()
-               smi = contents[0].split()[0]
+                contents = f.readlines()
+                smi = contents[0].split()[0]
 
             results['SMILES'] = smi
             xyz_gen_pd = pd.concat([xyz_gen_pd, results])
@@ -158,7 +158,9 @@ def Build(self):
             # Get a list of filenames for XYZ coordinates
             XYZ_list_ind = glob.glob(self.OutDir_xyz + str(row[self.ID_col]) + "*.pdb")
             XYZ_list.append(XYZ_list_ind)
-            NumConf = len(XYZ_list_ind) # Get number of conformer generated for each system
+            NumConf = len(
+                XYZ_list_ind
+            )  # Get number of conformer generated for each system
 
             # Get number of molecules for each conformer of molecules
             NMol_list += [int(row[self.NumMole] / NumConf)] * NumConf
@@ -342,8 +344,13 @@ def get_opls(self, output_fname='amor_opls.lmps'):
 
             try:
                 print("LigParGen working on {}.pdb".format(output_prefix))
-                Converter.convert(pdb=os.path.join(self.OutDir_xyz, output_prefix + '.pdb'),
-                                  resname=output_prefix, charge=0, opt=0, outdir='.')
+                Converter.convert(
+                    pdb=os.path.join(self.OutDir_xyz, output_prefix + '.pdb'),
+                    resname=output_prefix,
+                    charge=0,
+                    opt=0,
+                    outdir='.',
+                )
                 os.rename(lig_output_fname, data_fname)
             except BaseException:
                 print('problem running LigParGen for {}.pdb.'.format(output_prefix))

psp/CopolymerBuilder.py

@@ -21,7 +21,7 @@ def __init__(
         LeftCapSMI_col='LeftCap',
         RightCapSMI_col='RightCap',
         Nunits_col='Nunits',  # list of numbers (ratios); follow the order of building blocks
-        Tunits_col='Tunits', # Total number units in a polymer chain
+        Tunits_col='Tunits',  # Total number units in a polymer chain
         Mwt_col='Mwt_polymer',  # if > 0, then Nunits will be determined from molar mass of BB and Mwt
         Copoly_type_col='Copoly_type',  # 'homo', # homo, alternating, block, graft, random
         define_BB_col='define_BB',
@@ -55,8 +55,8 @@ def __init__(
         self.IrrStruc = IrrStruc
         self.GAFF2_atom_typing = GAFF2_atom_typing
         self.Subscript = Subscript
-        self.seed = seed,
-        self.rdkit_conf_param = rdkit_conf_param,
+        self.seed = (seed,)
+        self.rdkit_conf_param = (rdkit_conf_param,)
 
     # list of molecules name and CORRECT/WRONG
     def Build(self):

psp/CrystalBuilder.py

@@ -132,9 +132,7 @@ def BuildCrystal(self):
                     self.NumCandidate,
                     NCores_opt,
                 )
-                for VaspInp in tqdm(
-                    self.VaspInp_list, desc="Building models ..."
-                )
+                for VaspInp in tqdm(self.VaspInp_list, desc="Building models ...")
             )
         else:
             result = Parallel(n_jobs=NCores)(
@@ -148,9 +146,7 @@ def BuildCrystal(self):
                     self.NumCandidate,
                     NCores_opt,
                 )
-                for VaspInp in tqdm(
-                    self.VaspInp_list, desc="Building models ..."
-                )
+                for VaspInp in tqdm(self.VaspInp_list, desc="Building models ...")
             )
 
         output = []
@@ -569,9 +565,7 @@ def CrystalBuilderMain(
     # digits = bd.len_digit_number(NSamples ** 8)
 
     count = 0
-    for i in tqdm(
-        samp[0], desc=VaspInp + " Generating models"
-    ):  # Second poly
+    for i in tqdm(samp[0], desc=VaspInp + " Generating models"):  # Second poly
         for j in samp[2]:  # Second poly
             for k in samp[1]:  # Second poly
                 for aX in samp[3]:  # Second poly

psp/PSP2_lib.py

@@ -479,7 +479,7 @@ def build_copoly(
         define_BB_ = df_smiles[df_smiles[ID] == unit_name][define_BB].values[0]
         if define_BB_ == 'R':
             define_BB_ = list(smiles_dict.keys())
-            define_BB_.sort() # to ensure it matches with Nunits
+            define_BB_.sort()  # to ensure it matches with Nunits
 
             # If Mwt is provided, update Nunits
             if Mwt != 0:
@@ -491,7 +491,7 @@ def build_copoly(
                 Nunits = update_Nunits
 
             elif Tunits != 0:
-                Nunits = [round(Tunits*item) for item in Nunits]
+                Nunits = [round(Tunits * item) for item in Nunits]
 
             random_seq = []
             for i in range(len(define_BB_)):
@@ -519,11 +519,11 @@ def build_copoly(
 
                 if Mwt != 0:
                     for i in range(len(unit_list)):
-                            update_Nunits.append(
+                        update_Nunits.append(
                             round((Nunits[i] * Mwt) / OBMol_Mwt_dict[unit_list[i]][0])
                         )
                 elif Tunits != 0:
-                    update_Nunits = [round(Tunits*item) for item in Nunits]
+                    update_Nunits = [round(Tunits * item) for item in Nunits]
 
                 BB_count = []
                 for key in blocks_dict:
@@ -532,7 +532,9 @@ def build_copoly(
                         BB_each_count.append(
                             update_Nunits[(ord(j) - 65)] * (1 / total_units.count(j))
                         )
-                    BB_count.append(round(statistics.mean(BB_each_count))) # Take average
+                    BB_count.append(
+                        round(statistics.mean(BB_each_count))
+                    )  # Take average
                 Nunits = BB_count
 
     else:
@@ -555,21 +557,41 @@ def build_copoly(
         OBMol = optimize_geometry(OBMol)
         result = 'SUCCESS'
 
+    if result == 'SUCCESS':  # Fix seed issue
 
-    if result == 'SUCCESS': # Fix seed issue
-
-        list_conf = OBmolConfSearchRDkit(unit_name, OBMol, 'work_dir/', rdkit_conf_param)
+        list_conf = OBmolConfSearchRDkit(
+            unit_name, OBMol, 'work_dir/', rdkit_conf_param
+        )
 
-        n=1 # Conformer sl number
+        n = 1  # Conformer sl number
         for OBconf in list_conf:
             GenOutput(
-                unit_name, OBconf, output_files, out_dir, Inter_Mol_Dis, GAFF2_atom_typing, n
+                unit_name,
+                OBconf,
+                output_files,
+                out_dir,
+                Inter_Mol_Dis,
+                GAFF2_atom_typing,
+                n,
             )
             n += 1
     return unit_name, result
 
 
-def OBmolConfSearchRDkit(unitname, mol, work_dir, rdkit_conf_param, Nconf=1, NCores_opt=0, seed=None, NAttempt=10000, BasicKnowledge=True, RmsThresh=0.1, ExpTorsionAnglePref=True, enforceChirality=False):
+def OBmolConfSearchRDkit(
+    unitname,
+    mol,
+    work_dir,
+    rdkit_conf_param,
+    Nconf=1,
+    NCores_opt=0,
+    seed=None,
+    NAttempt=10000,
+    BasicKnowledge=True,
+    RmsThresh=0.1,
+    ExpTorsionAnglePref=True,
+    enforceChirality=False,
+):
     list_conf = []
 
     # Set parameters
@@ -614,8 +636,17 @@ def OBmolConfSearchRDkit(unitname, mol, work_dir, rdkit_conf_param, Nconf=1, NCo
     m1 = Chem.MolFromMolFile(path_ini_geo)
     m2 = Chem.AddHs(m1)
     if m2 is not None:
-        cids = AllChem.EmbedMultipleConfs(m2, numConfs=Nconf, numThreads=NCores_opt, randomSeed=seed,
-                                          maxAttempts=NAttempt, useBasicKnowledge=BasicKnowledge, pruneRmsThresh=RmsThresh, useExpTorsionAnglePrefs=ExpTorsionAnglePref, enforceChirality=enforceChirality)
+        cids = AllChem.EmbedMultipleConfs(
+            m2,
+            numConfs=Nconf,
+            numThreads=NCores_opt,
+            randomSeed=seed,
+            maxAttempts=NAttempt,
+            useBasicKnowledge=BasicKnowledge,
+            pruneRmsThresh=RmsThresh,
+            useExpTorsionAnglePrefs=ExpTorsionAnglePref,
+            enforceChirality=enforceChirality,
+        )
         if len(cids) < 1:
             list_conf.append(mol)
             print("Couldn't generate multiple conformers ............")
@@ -638,12 +669,19 @@ def OBmolConfSearchRDkit(unitname, mol, work_dir, rdkit_conf_param, Nconf=1, NCo
                 return list_conf
     return list_conf
 
+
 def GenOutput(
     unitname, OBMol, list_output, output_dir, Inter_Mol_Dis, GAFF2_atom_typing, n
 ):
     # Genrate an XYZ file
     obConversion.SetOutFormat('xyz')
-    OBMol.SetTitle("Generated by OpenBabel@PSP --" + " Conformer: " + str(n) +  " -- Output format: " + 'xyz')
+    OBMol.SetTitle(
+        "Generated by OpenBabel@PSP --"
+        + " Conformer: "
+        + str(n)
+        + " -- Output format: "
+        + 'xyz'
+    )
     out_filename = os.path.join(output_dir, unitname + '_C' + str(n) + '.xyz')
     obConversion.WriteFile(OBMol, out_filename)
 
@@ -699,7 +737,13 @@ def GenOutput(
 def gen_opls_data(unit_name, OBMol, output_dir, unitname, n):
     # Generate a pdb file
     obConversion.SetOutFormat('pdb')
-    OBMol.SetTitle("Generated by OpenBabel@PSP --" + " Conformer: " + str(n) +  " -- Output format: " + 'pdb')
+    OBMol.SetTitle(
+        "Generated by OpenBabel@PSP --"
+        + " Conformer: "
+        + str(n)
+        + " -- Output format: "
+        + 'pdb'
+    )
     out_filename_pdb = os.path.join(output_dir, unitname + '_C' + str(n) + '.pdb')
     obConversion.WriteFile(OBMol, out_filename_pdb)
 
@@ -718,7 +762,13 @@ def gen_opls_data(unit_name, OBMol, output_dir, unitname, n):
 def GenOutputOB(unitname, OBMol, list_OB_output, output_dir, n):
     for i in list_OB_output:
         obConversion.SetOutFormat(i)
-        OBMol.SetTitle("Generated by OpenBabel@PSP --" + " Conformer: " + str(n) +  " -- Output format: " + i)
+        OBMol.SetTitle(
+            "Generated by OpenBabel@PSP --"
+            + " Conformer: "
+            + str(n)
+            + " -- Output format: "
+            + i
+        )
         out_filename = os.path.join(output_dir, unitname + '_C' + str(n) + '.' + i)
         obConversion.WriteFile(OBMol, out_filename)
 
@@ -759,6 +809,7 @@ def combine_A_ntimes(OBMol, first, second, n):
 
     return main_obmol, first, second
 
+
 def combine_A_ntimes_pl(OBMol, first, second, n):
     builder = ob.OBBuilder()
     builder.SetKeepRings()

psp/PSP_lib.py

@@ -2711,8 +2711,8 @@ def gen_conf_xyz_vasp(
             maxAttempts=NAttempt,
         )
 
-    #   if len(cids) > 0:
-    #       break
+        if len(cids) > 0:
+            break
     n = 0
     for cid in cids:
         n += 1