Merge pull request #346 from UCL-CCS/verbosity

Logging

ties/__init__.py

@@ -1,3 +1,4 @@
+import logging
 from pathlib import Path
 
 from . import cli
@@ -10,4 +11,6 @@
 
 from ._version import __version__
 
-__all__ = [Ligand, Protein, Pair, Config, LigandMap, Protein, __version__]
+__all__ = [Ligand, Protein, Pair, Config, LigandMap, Protein, __version__]
+
+logging.basicConfig(encoding='utf-8', level=logging.INFO)

ties/cli.py

@@ -4,6 +4,7 @@
 """
 import time
 import itertools
+import logging
 import pathlib
 import shutil
 import sys
@@ -17,6 +18,9 @@
 import ties.protein
 
 
+logger = logging.getLogger(__name__)
+
+
 def command_line_script():
     parser = argparse.ArgumentParser(description='TIES 20')
     parser.add_argument('-action', '--action', metavar='command', type=str, default='create',
@@ -57,6 +61,11 @@ def command_line_script():
                         type=ArgparseChecker.str2bool, required=False, default=False,
                         help='Align the coordinates in the "END" ligand to the "INITIAL" ligand using '
                              'the generated maximum common substructure (MCS).')
+    parser.add_argument("-v", "--logging-level", metavar="str or bool", dest="logging_level",
+                        type=ArgparseChecker.logging_lvl, required=False, default="WARNING",
+                        help="Logging level. Can be a boolean value "
+                             "(False disables logging by setting it to ERROR). "
+                             "A string should specify a logging level (DEBUG, INFO, WARNING, ERROR, CRITICAL). ")
     parser.add_argument('-ant-dr', '--antechamber-dr', metavar='boolean', dest='antechamber_dr',
                         type=ArgparseChecker.str2bool, required=False, default=False,
                         help='Antechamber dr is turned off by default. It is playing up with .mol2 files. '
@@ -142,6 +151,11 @@ def command_line_script():
 
     # initialise the config class
     args = parser.parse_args()
+
+    logger.setLevel(args.logging_level)
+    for handler in logger.handlers:
+        handler.setLevel(args.logging_level)
+
     command = args.command.lower()
     delattr(args, 'command')
     # assign all the parsed arguments to the Config class
@@ -159,12 +173,12 @@ def command_line_script():
             raise Exception('ERROR: to rename atoms to be unique across two ligands, '
                   'you have to provide exactly two ligands with -l.'
                   'E.g. ties rename -l init.mol2 final.mol2')
-        print('Atom names will be renamed to ensure that the atom names are unique across the two molecules.')
+        logger.info('Atom names will be renamed to ensure that the atom names are unique across the two molecules.')
         pair = ties.pair.Pair(ligands[0], ligands[1], config)
         pair.make_atom_names_unique()
         sys.exit()
     elif command == 'mergecrd':
-        print('Merging coordinates. Will add coordinates from an external file.')
+        logger.info('Merging coordinates. Will add coordinates from an external file.')
         if len(ligands) > 1:
             raise Exception('ERROR: too many ligands ligand (-l). '
                   'Use one ligand when assigning coordinates from another file.')
@@ -190,9 +204,9 @@ def command_line_script():
     pairs = [ties.pair.Pair(ligA, ligZ, config) for ligA, ligZ in itertools.combinations(ligands, r=2)]
 
     # superimpose the paired topologies
-    start_time = time.perf_counter()
     for pair in pairs:
-        print(f'Next ligand pair: {pair.internal_name}')
+        start_time = time.perf_counter()
+        logger.info(f'Next ligand pair: {pair.internal_name}')
 
         # rename the atom names to ensure they are unique across the two molecules
         if args.unique_atom_names:
@@ -207,7 +221,7 @@ def command_line_script():
         hybrid.write_metadata()
         hybrid.write_pdb()
         hybrid.write_mol2()
-    print(f'Compared ligands to each other in: {time.perf_counter() - start_time:.1f} s')
+        logger.info(f'Compared pair of ligands: {time.perf_counter() - start_time:.1f} s')
 
     # transformation hunter
     if len(ligands) == 2:
@@ -227,21 +241,21 @@ def command_line_script():
             continue
 
         pair.suptop.prepare_inputs(protein=None)
-        print(f'Ligand {pair} directory populated successfully')
+        logger.info(f'Ligand {pair} directory populated successfully')
 
     ##########################################################
     # ------------------ Complex  ----------------------------
     if config.protein is not None:
         protein = ties.protein.Protein(config.protein, config)
         for pair in selected_pairs:
             pair.suptop.prepare_inputs(protein=protein)
-            print(f'Protein {pair} directory populated successfully')
+            logger.info(f'Protein {pair} directory populated successfully')
 
     # prepare the post-analysis scripts
     shutil.copy(config.namd_script_dir / "check_namd_outputs.py", config.workdir)
     shutil.copy(config.namd_script_dir / "ddg.py", config.workdir)
 
-    print('TIES 20 Finished')
+    logger.info('TIES finished')
 
 
 if __name__ == '__main__':