Logging breakdown used in the CLI

ties/cli.py

@@ -205,6 +205,8 @@ def command_line_script():
     # generate all pairings
     pairs = [ties.pair.Pair(ligA, ligZ, config) for ligA, ligZ in itertools.combinations(ligands, r=2)]
 
+    config.logging_breakdown = True
+
     # superimpose the paired topologies
     for pair in pairs:
         start_time = time.perf_counter()

ties/config.py

@@ -93,7 +93,7 @@ def __init__(self, **kwargs):
         self.set_configs(**kwargs)
 
         # logging
-        self.logging_breakdown = True
+        self.logging_breakdown = False
         self.logging_formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
         self.logging_level = logging.INFO
 

ties/topology_superimposer.py

@@ -3175,7 +3175,7 @@ def superimpose_topologies(top1_nodes,
     - check if each molecule topology is connected
     """
 
-    if config.logging_breakdown:
+    if config is not None and config.logging_breakdown:
         file_log_handler = logging.FileHandler(config.workdir / f'{logging_key}.log')
         file_log_handler.setLevel(config.logging_level)
         file_log_handler.setFormatter(config.logging_formatter)
@@ -3389,7 +3389,7 @@ def take_largest(x, y):
     logger.info(f'Disappearing atoms: { (len(top1_nodes) - len(suptop.matched_pairs)) / len(top1_nodes) * 100:.1f}%')
     logger.info(f'Appearing atoms: { (len(top2_nodes) - len(suptop.matched_pairs)) / len(top2_nodes) * 100:.1f}%')
 
-    if config.logging_breakdown:
+    if config is not None and config.logging_breakdown:
         logger.removeHandler(file_log_handler)
 
     return suptop