Better error messages with error chains

UCL-CCS · Aug 20, 2023 · 4987266 · 4987266
1 parent c56571b
commit 4987266
Showing 1 changed file with 12 additions and 14 deletions.
diff --git a/ties/ligand.py b/ties/ligand.py
@@ -266,20 +266,18 @@ def antechamber_prepare_mol2(self, **kwargs):
             with open(log_filename, 'w') as LOG:
                 try:
                     subprocess.run([self.config.ambertools_antechamber,
-                                    '-i', self.current, '-fi', self.current.suffix[1:],
-                                    '-o', mol2_target, '-fo', 'mol2',
-                                    '-at', self.config.ligand_ff_name, '-nc', str(self.config.ligand_net_charge),
-                                    '-dr', str(self.config.antechamber_dr)] + self.config.antechamber_charge_type,
-                                   cwd=mol2_cwd,
-                                   stdout=LOG, stderr=LOG,
-                                   check=True, text=True,
-                                   timeout=60 * 30  # 30 minutes
-                                   )
-                except subprocess.CalledProcessError as E:
-                    print('ERROR: occured when creating the input .mol2 file with antechamber. ')
-                    print(f'ERROR: The output was saved in the directory: {mol2_cwd}')
-                    print(f'ERROR: can be found in the file: {log_filename}')
-                    raise E
+                        '-i', self.current, '-fi', self.current.suffix[1:],
+                        '-o', mol2_target, '-fo', 'mol2',
+                        '-at', self.config.ligand_ff_name, '-nc', str(self.config.ligand_net_charge),
+                        '-dr', str(self.config.antechamber_dr)] + self.config.antechamber_charge_type,
+                       cwd=mol2_cwd,
+                       stdout=LOG, stderr=LOG,
+                       check=True, text=True,
+                       timeout=60 * 30  # 30 minutes
+                       )
+                except subprocess.CalledProcessError as ProcessError:
+                    raise Exception(f'Could not convert the input into .mol2 file with antechamber. '
+                                    f'See the log and its directory: {log_filename}') from ProcessError
             print(f'Converted {self.original_input} into .mol2, Log: {log_filename}')
         else:
             print(f'File {mol2_target} already exists. Skipping. ')