compare-structures: add rigid scores specific chain mapping in json output

actions/ost-compare-structures

@@ -454,7 +454,10 @@ def _ParseArgs():
               "8.0] given these positions and transformation, \"oligo_gdtha\": "
               "same with thresholds [0.5, 1.0, 2.0, 4.0], \"rmsd\": RMSD given "
               "these positions and transformation, \"transform\": the used 4x4 "
-              "transformation matrix that superposes model onto reference."))
+              "transformation matrix that superposes model onto reference, "
+              "\"rigid_chain_mapping\": equivalent of \"chain_mapping\" which "
+              "is used for rigid scores (optimized for RMSD instead of "
+              "QS-score/lDDT)."))
 
     parser.add_argument(
         "--patch-scores",
@@ -895,6 +898,7 @@ def _Process(model, reference, args, model_format, reference_format):
         out["rmsd"] = _RoundOrNone(scorer.rmsd)
         data = scorer.rigid_transform.data
         out["transform"] = [data[i:i + 4] for i in range(0, len(data), 4)]
+        out["rigid_chain_mapping"] = scorer.rigid_mapping.GetFlatMapping()
 
     if args.patch_scores:
         out["model_interface_residues"] = \

modules/doc/actions.rst

@@ -348,7 +348,9 @@ Details on the usage (output of ``ost compare-structures --help``):
                           thresholds [0.5, 1.0, 2.0, 4.0], "rmsd": RMSD given
                           these positions and transformation, "transform": the
                           used 4x4 transformation matrix that superposes model
-                          onto reference.
+                          onto reference, "rigid_chain_mapping": equivalent of
+                          "chain_mapping" which is used for rigid scores
+                          (optimized for RMSD instead of QS-score/lDDT).
     --patch-scores        Local interface quality score used in CASP15. Scores
                           each model residue that is considered in the interface
                           (CB pos within 8A of any CB pos from another chain (CA