doc: SCHWED-5954 document unassigned ligand reporting

actions/ost-compare-ligand-structures

@@ -48,7 +48,8 @@ options, this is a dictionary with three keys:
 
 Each score is opt-in and, be enabled with optional arguments and is added
 to the output. Keys correspond to the values in "model_ligands" above.
-Only assigned (mapped) ligands are reported.
+Unassigned ligands are reported with a message in "unassigned_model_ligands"
+and "unassigned_reference_ligands".
 """
 
 import argparse
@@ -199,8 +200,9 @@ def _ParseArgs():
         dest="unassigned",
         default=False,
         action="store_true",
-        help=("Report unassigned ligands in the output together with assigned "
-              "ligands."))
+        help=("Report unassigned model ligands in the output together with "
+              "assigned ligands, with a null score, and reason for not being "
+              "assigned."))
 
     parser.add_argument(
         "--lddt-pli",

modules/doc/actions.rst

@@ -353,7 +353,8 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
 
     Each score is opt-in and, be enabled with optional arguments and is added
     to the output. Keys correspond to the values in "model_ligands" above.
-    Only assigned (mapped) ligands are reported.
+    Unassigned ligands are reported with a message in
+    "unassigned_model_ligands" and "unassigned_reference_ligands".
 
     options:
       -h, --help            show this help message and exit
@@ -406,6 +407,10 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
                             if global-chain-mapping flag is set.
       -ra, --rmsd-assignment
                             Use RMSD for ligand assignment.
+      -u, --unassigned      Report unassigned model ligands in the output
+                            together with assigned ligands, with a null score,
+                            and reason for not being assigned.
+
       --lddt-pli            Compute lDDT-PLI score and store as key "lddt-pli".
       --rmsd                Compute RMSD score and store as key "rmsd".
       --radius RADIUS       Inclusion radius for the binding site. Any residue

modules/mol/alg/pymod/ligand_scoring.py

@@ -229,10 +229,9 @@ class LigandScorer:
                         the optimum. A heuristic is used otherwise.
     :type n_max_naive: :class:`int`
     :param unassigned: If True, unassigned model ligands are reported in
-                       the output together with assigned ligands, with the
-                       a score of None, and reason for not being assigned
-                       in the \*_details matrix.
-                       Defaults to False.
+                       the output together with assigned ligands, with a score
+                       of None, and reason for not being assigned in the
+                       \*_details matrix. Defaults to False.
     :type unassigned: :class:`bool`
     """
     def __init__(self, model, target, model_ligands=None, target_ligands=None,