Specific and minimum logging

ties/config.py

@@ -119,7 +119,7 @@ def workdir(self, cwd):
             # current directory
             self._workdir = pathlib.Path(os.getcwd()) / 'ties'
             self._workdir.mkdir(exist_ok=True)
-        logger.info(f'Working Directory: {self._workdir}')
+        logger.debug(f'Working Directory: {self._workdir}')
 
     # --------------- general
     @property
@@ -492,7 +492,7 @@ def ligands_contain_q(self):
             if ligand_ext in {'.mol2', '.ac', '.prep'}:
                 # if all charges are 0, then recompute
                 self._ligands_contain_q = self._guess_ligands_contain_q()
-                logger.info('Appears that charges are provided based on the filetype .ac/.mol2')
+                logger.info(f'Existing atom charges detected (filetype .ac/.mol2). ')
             elif ligand_ext == '.pdb':
                 self._ligands_contain_q = False
                 logger.debug('Assuming that charges are not provided in the given .pdb ligand files. ')

ties/ligand.py

@@ -245,10 +245,8 @@ def antechamber_prepare_mol2(self, **kwargs):
         """
         self.config.set_configs(**kwargs)
 
-        if self.config.ligands_contain_q:
-            logger.info('Antechamber: Generating .mol2 file with BCC charges')
-        if not self.config.antechamber_charge_type:
-            logger.info('Antechamber: Ignoring atom charges. The user-provided atom charges will be used. ')
+        if self.config.ligands_contain_q or not self.config.antechamber_charge_type:
+            logger.info(f'Antechamber: User-provided atom charges will be reused ({self.current.name})')
 
         mol2_cwd = self.config.lig_dir / self.internal_name
 

ties/topology_superimposer.py

@@ -1523,7 +1523,7 @@ def remove_node_pair(self, node_pair):
         for bound_pair, bond_type in bound_pairs:
             if bond_type[0] != bond_type[1]:
                 # fixme - this requires more attention
-                logger.info('While removing a pair noticed that it has a different bond type')
+                logger.debug('While removing a pair noticed that it has a different bond type')
             # remove their binding to the removed pair
             bound_pair_bonds = self.matched_pairs_bonds[bound_pair]
             bound_pair_bonds.remove((node_pair, bond_type))
@@ -3223,7 +3223,7 @@ def superimpose_topologies(top1_nodes,
         def take_largest(x, y):
             return x if len(x) > len(y) else y
         reduce(take_largest, suptops).align_ligands_using_mcs()
-        logger.info(f'RMSD of the best suptop: {suptops[0].align_ligands_using_mcs()}')
+        logger.info(f'RMSD of the best overlay: {suptops[0].align_ligands_using_mcs():.2f}')
 
     # fixme - you might not need because we are now doing this on the way back
     # if useCoords:
@@ -3378,7 +3378,7 @@ def take_largest(x, y):
 
     # print a general summary
     logger.info('-------- Summary -----------')
-    logger.info(f'Final number of matched pairs: {len(suptop.matched_pairs)} out of {len(top1_nodes)}L/{len(top2_nodes)}R')
+    logger.info(f'Number of matched pairs: {len(suptop.matched_pairs)} out of {len(top1_nodes)}L/{len(top2_nodes)}R')
     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}%')
 
@@ -3656,7 +3656,7 @@ def get_starting_configurations(left_atoms, right_atoms, fraction=0.2, filter_ri
         right_count_by_type = sum([1 for right_atom in right_atoms if right_atom.type == atom_type])
         per_type_max_counter[atom_type] = min(left_count_by_type, right_count_by_type)
     max_overlap_size = sum(per_type_max_counter.values())
-    logger.info(f'Superimposition - simple max overlap size: {max_overlap_size}')
+    logger.info(f'Largest MCS size: {max_overlap_size}')
 
     left_atoms_starting = left_atoms_noh[:]
     right_atoms_starting = right_atoms_noh[:]
@@ -3824,7 +3824,7 @@ def _superimpose_topologies(top1_nodes, top2_nodes, mda1_nodes=None, mda2_nodes=
     # clean the overlays by removing sub_overlays.
     # ie if all atoms in an overlay are found to be a bigger part of another overlay,
     # then that overlay is better
-    logger.info(f"Found altogether overlays {len(suptops)}")
+    logger.info(f"Found overlays: {len(suptops)}")
 
     # finally, once again, order the suptops and return the best one
     suptops = extract_best_suptop(suptops, ignore_coords, weights, get_list=True)