Using the clue that the coordinates are perfectly overlapped.

ties/cli.py

@@ -30,17 +30,17 @@ def command_line_script():
                              'If more than 2 ligands are provided, '
                              'Lead Optimisation Mapping (TIES MAP) will be used.')
     parser.add_argument('-dir', '--ties-output-dir', metavar='directory', dest='workdir',
-                        type=pathlib.Path, required=False,
-                        help='If not provided, "ties20" directory will be created in the current directory. ')
+                        type=pathlib.Path, required=False, default="ties",
+                        help='The destination directory for the output. Default: "ties".')
     parser.add_argument('-nc', '--ligand-net-charge', metavar='integer', dest='ligand_net_charge',
                         type=int, required=False,
                         help='An integer representing the net charge of each ligand. '
-                             'All ligands must have the same charge.')
+                             'All ligands must have the same charge. Default: 0.1e.')
     parser.add_argument('-p', '--protein', metavar='file', dest='protein',
                         type=ArgparseChecker.existing_file, required=False,
-                        help='The protein file')
+                        help='The protein file. Not necessary. ')
     parser.add_argument('-qtol', '--q-pair-tolerance', metavar='decimal', dest='atom_pair_q_atol',
-                        type=float, required=False, default=0.1,
+                        type=float, required=False,
                         help='The maximum difference in charge between any two paired atoms (electron unit). '
                              'Default 0.1e')
     parser.add_argument('-netqtol', '--q-net-tolerance', metavar='decimal', dest='net_charge_threshold',
@@ -133,6 +133,12 @@ def command_line_script():
     parser.add_argument('-elements', '--compare-elements', metavar='boolean', dest='use_element',
                         type=ArgparseChecker.str2bool, required=False, default=False,
                         help='Ignore the specific atom types in the superimposition. Use only the elements. ')
+    parser.add_argument('-weights', '--mcs-rmsd-weights', metavar='str', dest='weights_ratio',
+                        type=ArgparseChecker.ratio, required=False,
+                        help='The weights for the weighted sum of 1) MCS overlap size to 2) RMSD '
+                             'when coordinates are used for selection of the best structure. '
+                             'Default it is "1:1" for "MCS:RMSD".  '
+                             'MCS is defined (1 - MCS fraction), so lower value is better.')
 
     # initialise the config class
     args = parser.parse_args()

ties/config.py

@@ -46,6 +46,8 @@ def __init__(self, **kwargs):
         # use only the element in the superimposition rather than the specific atom type
         self._use_element = False
         self._use_element_in_superimposition = True
+        # weights in choosing the best MCS, the weighted sum of "(1 - MCS fraction) and RMSD".
+        self.weights = [1, 0.5]
 
         # coordinates
         self._align_molecules_using_mcs = False
@@ -82,8 +84,7 @@ def __init__(self, **kwargs):
         self.uses_cmd = False
 
         # assign all the initial configuration values
-        for key, value in kwargs.items():
-            setattr(self, key, value)
+        self.set_configs(**kwargs)
 
     @property
     def workdir(self):
@@ -897,4 +898,8 @@ def get_serializable(self):
     def set_configs(self, **kwargs):
         # set all the configs one by one
         for k,v in kwargs.items():
+            # skip None values, these come from the command line
+            if v is None:
+                continue
+
             setattr(self, k, v)

ties/helpers.py

@@ -124,6 +124,13 @@ def str2bool(v):
         else:
             raise argparse.ArgumentTypeError('Boolean value expected.')
 
+    @staticmethod
+    def ratio(v):
+        if ':' not in v:
+            argparse.ArgumentTypeError('The ratio has to be separated by ":".')
+        mcs, rmsd = v.split(':')
+        return [float(mcs), float(rmsd)]
+
     @staticmethod
     def existing_file(v):
         # check ligand arguments

ties/pair.py

@@ -173,9 +173,9 @@ def superimpose(self, **kwargs):
                                          force_mismatch=new_mismatch_names,
                                          starting_node_pairs=starting_node_pairs,
                                          parmed_ligA=parmed_ligA, parmed_ligZ=parmed_ligZ,
-                                         starting_pair_seed=self.config.superimposition_starting_pair)
+                                         starting_pair_seed=self.config.superimposition_starting_pair,
+                                         config=self.config)
 
-        assert len(suptops) == 1
         self.set_suptop(suptops[0], parmed_ligA, parmed_ligZ)
         # attach the used config to the suptop
         suptops[0].config = self.config