Improved --silent option.

durrantlab · Jun 4, 2020 · f888d30 · f888d30
1 parent ca78cde
commit f888d30
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/dimorphite_dl.py b/dimorphite_dl.py
@@ -480,7 +480,7 @@ def next(self):
             # into a canonical form. Filter if failed.
             mol = UtilFuncs.convert_smiles_str_to_mol(smiles_str)
             if mol is None:
-                if not self.args["silent"]:
+                if "silent" in self.args and not self.args["silent"]:
                     UtilFuncs.eprint(
                         "WARNING: Skipping poorly formed SMILES string: " + line
                     )
@@ -489,7 +489,7 @@ def next(self):
             # Handle nuetralizing the molecules. Filter if failed.
             mol = UtilFuncs.neutralize_mol(mol)
             if mol is None:
-                if not self.args["silent"]:
+                if "silent" in self.args and not self.args["silent"]:
                     UtilFuncs.eprint(
                         "WARNING: Skipping poorly formed SMILES string: " + line
                     )
@@ -499,14 +499,14 @@ def next(self):
             try:
                 mol = Chem.RemoveHs(mol)
             except:
-                if not self.args["silent"]:
+                if "silent" in self.args and not self.args["silent"]:
                     UtilFuncs.eprint(
                         "WARNING: Skipping poorly formed SMILES string: " + line
                     )
                 return self.next()
 
             if mol is None:
-                if not self.args["silent"]:
+                if "silent" in self.args and not self.args["silent"]:
                     UtilFuncs.eprint(
                         "WARNING: Skipping poorly formed SMILES string: " + line
                     )
@@ -630,7 +630,7 @@ def next(self):
                 new_mols = ProtSubstructFuncs.protonate_site(new_mols, site)
                 if len(new_mols) > self.args["max_variants"]:
                     new_mols = new_mols[: self.args["max_variants"]]
-                    if not self.args["silent"]:
+                    if "silent" in self.args and not self.args["silent"]:
                         UtilFuncs.eprint(
                             "WARNING: Limited number of variants to "
                             + str(self.args["max_variants"])
@@ -913,7 +913,7 @@ def set_protonation_charge(mols, idx, charges, prot_site_name):
                 try:
                     mol_copy = Chem.RemoveHs(mol_copy)
                 except:
-                    if not ProtSubstructFuncs.args["silent"]:
+                    if "silent" in ProtSubstructFuncs.args and not ProtSubstructFuncs.args["silent"]:
                         UtilFuncs.eprint(
                             "WARNING: Skipping poorly formed SMILES string: "
                             + Chem.MolToSmiles(mol_copy)