small fixes in outputs, remove DockQ_F1

bjornwallner · Aug 12, 2024 · 90578a9 · 90578a9
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Showing 12 changed files with 68 additions and 86 deletions.
diff --git a/README.md b/README.md
@@ -162,7 +162,7 @@ Small molecules in PDB or mmCIF files can be scored and the mapping optimized in
 $ DockQ examples/1HHO_hem.cif examples/2HHB_hem.cif --small_molecule --mapping :ABEFG --short
 
 Total DockQ-small_molecules over 4 native interfaces: 0.659 with ABDCF:ABEFG model:native mapping
-DockQ 0.950 IRMSD 0.455 LRMSD 1.451 fnat 0.964 fnonnat 0.070 clashes 0.000 F1 0.946 DockQ_F1 0.945 mapping AB:AB examples/1HHO_hem.cif A B -> examples/2HHB_hem.cif A B
+DockQ 0.950 iRMSD 0.455 LRMSD 1.451 fnat 0.964 fnonnat 0.070 clashes 0.000 F1 0.946 DockQ_F1 0.945 mapping AB:AB examples/1HHO_hem.cif A B -> examples/2HHB_hem.cif A B
 LRMSD 0.585 mapping AD:AE (HEM) examples/1HHO_hem.cif A D -> examples/2HHB_hem.cif A E
 LRMSD 28.096 mapping BC:BF (PO4) examples/1HHO_hem.cif B C -> examples/2HHB_hem.cif B F
 LRMSD 1.311 mapping BF:BG (HEM) examples/1HHO_hem.cif B F -> examples/2HHB_hem.cif B G

diff --git a/src/DockQ/DockQ.py b/src/DockQ/DockQ.py
@@ -76,12 +76,6 @@ def parse_args():
         metavar="CHUNK",
         help="Maximum size of chunks given to the cores, actual chunksize is min(max_chunk,combos/cpus)",
     )
-    parser.add_argument(
-        "--optDockQF1",
-        default=False,
-        action="store_true",
-        help="Optimize on DockQ_F1 instead of DockQ",
-    )
     parser.add_argument(
         "--allowed_mismatches",
         default=0,
@@ -255,9 +249,8 @@ def calc_sym_corrected_lrmsd(
         if lrms < min_lrms:
             best_mapping = isomorphism
             min_lrms = lrms
-    dockq_f1 = dockq = dockq_formula(0, 0, min_lrms)
+    dockq = dockq_formula(0, 0, min_lrms)
     info = {
-        "DockQ_F1": dockq_f1,
         "DockQ": dockq,
         "LRMSD": min_lrms,
         "mapping": best_mapping,
@@ -379,7 +372,6 @@ def calc_DockQ(
 
     info = {}
     F1 = f1(nat_correct, nonnat_count, nat_total)
-    info["DockQ_F1"] = dockq_formula(F1, irms, lrms)
     info["DockQ"] = dockq_formula(fnat, irms, lrms)
     if low_memory:
         return info
@@ -632,7 +624,6 @@ def run_on_all_native_interfaces(
     no_align=False,
     capri_peptide=False,
     low_memory=False,
-    optDockQF1=False,
 ):
     """Given a native-model chain map, finds all non-null native interfaces
     and runs DockQ for each native-model pair of interfaces"""
@@ -670,7 +661,7 @@ def run_on_all_native_interfaces(
                 result_mapping[chain_pair] = info
     total_dockq = sum(
         [
-            result["DockQ_F1" if optDockQF1 else "DockQ"]
+            result["DockQ"]
             for result in result_mapping.values()
         ]
     )
@@ -1023,16 +1014,15 @@ def print_results(
                     "LRMSD",
                     "fnat",
                     "fnonnat",
-                    "clashes",
                     "F1",
-                    "DockQ_F1",
+                    "clashes",
                 ]
                 if not results["is_het"]
                 else ["LRMSD"]
             )
             hetname = f" ({results['is_het']})" if results["is_het"] else ""
             score_str = " ".join(
-                [f"{item} {results[item]:.3f}" for item in reported_measures]
+                [f"{item} {results[item]:.3f}" if item != "clashes" else f"{item} {results[item]}" for item in reported_measures]
             )
             print(
                 f"{score_str} mapping {results['chain1']}{results['chain2']}:{chains[0]}{chains[1]}{hetname} {info['model']} {results['chain1']} {results['chain2']} -> {info['native']} {chains[0]} {chains[1]}"
@@ -1052,9 +1042,8 @@ def print_results(
                     "LRMSD",
                     "fnat",
                     "fnonnat",
-                    "clashes",
                     "F1",
-                    "DockQ_F1",
+                    "clashes",
                 ]
                 if not results["is_het"]
                 else ["LRMSD"]
@@ -1064,7 +1053,7 @@ def print_results(
             print(f"\tModel chains: {results['chain1']}, {results['chain2']}")
             print(
                 "\n".join(
-                    [f"\t{item}: {results[item]:.3f}" for item in reported_measures]
+                    [f"\t{item}: {results[item]:.3f}" if item != "clashes" else f"\t{item}: {results[item]}" for item in reported_measures]
                 )
             )
 

diff --git a/testdata/1A2K.dockq b/testdata/1A2K.dockq
@@ -21,26 +21,23 @@ Native chains: A, B
 	LRMSD: 0.000
 	fnat: 0.983
 	fnonnat: 0.008
-	clashes: 0.000
 	F1: 0.987
-	DockQ_F1: 0.996
+	clashes: 0
 Native chains: A, C
 	Model chains: B, C
 	DockQ: 0.511
 	iRMSD: 1.237
 	LRMSD: 6.864
 	fnat: 0.333
 	fnonnat: 0.000
-	clashes: 0.000
 	F1: 0.500
-	DockQ_F1: 0.567
+	clashes: 0
 Native chains: B, C
 	Model chains: A, C
 	DockQ: 0.453
 	iRMSD: 2.104
 	LRMSD: 8.131
 	fnat: 0.500
 	fnonnat: 0.107
-	clashes: 0.000
 	F1: 0.641
-	DockQ_F1: 0.500
+	clashes: 0
diff --git a/testdata/1EXB.dockq b/testdata/1EXB.dockq
@@ -1,17 +1,17 @@
 Total DockQ over 16 native interfaces: 0.852 with BACDFHEG:ABDCEGFH model:native mapping
-DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 1.000 mapping BC:AD examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb A D
-DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping BD:AC examples/1EXB_r_l_b.model.pdb B D -> examples/1EXB_r_l_b.pdb A C
-DockQ 0.552 iRMSD 1.458 LRMSD 3.757 fnat 0.304 fnonnat 0.000 clashes 0.000 F1 0.467 DockQ_F1 0.606 mapping BF:AE examples/1EXB_r_l_b.model.pdb B F -> examples/1EXB_r_l_b.pdb A E
-DockQ 0.694 iRMSD 0.793 LRMSD 2.831 fnat 0.400 fnonnat 0.000 clashes 0.000 F1 0.571 DockQ_F1 0.751 mapping BH:AG examples/1EXB_r_l_b.model.pdb B H -> examples/1EXB_r_l_b.pdb A G
-DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping AC:BD examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb B D
-DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping AD:BC examples/1EXB_r_l_b.model.pdb A D -> examples/1EXB_r_l_b.pdb B C
-DockQ 0.742 iRMSD 0.850 LRMSD 3.426 fnat 0.609 fnonnat 0.176 clashes 0.000 F1 0.700 DockQ_F1 0.772 mapping AE:BF examples/1EXB_r_l_b.model.pdb A E -> examples/1EXB_r_l_b.pdb B F
-DockQ 0.824 iRMSD 0.625 LRMSD 3.994 fnat 0.800 fnonnat 0.000 clashes 0.000 F1 0.889 DockQ_F1 0.853 mapping AG:BH examples/1EXB_r_l_b.model.pdb A G -> examples/1EXB_r_l_b.pdb B H
-DockQ 0.687 iRMSD 1.161 LRMSD 3.757 fnat 0.600 fnonnat 0.000 clashes 0.000 F1 0.750 DockQ_F1 0.737 mapping CF:DE examples/1EXB_r_l_b.model.pdb C F -> examples/1EXB_r_l_b.pdb D E
-DockQ 0.477 iRMSD 1.425 LRMSD 3.994 fnat 0.087 fnonnat 0.000 clashes 0.000 F1 0.160 DockQ_F1 0.502 mapping CG:DH examples/1EXB_r_l_b.model.pdb C G -> examples/1EXB_r_l_b.pdb D H
-DockQ 0.775 iRMSD 0.711 LRMSD 2.831 fnat 0.609 fnonnat 0.125 clashes 0.000 F1 0.718 DockQ_F1 0.812 mapping DH:CG examples/1EXB_r_l_b.model.pdb D H -> examples/1EXB_r_l_b.pdb C G
-DockQ 0.914 iRMSD 0.547 LRMSD 3.426 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 0.914 mapping DE:CF examples/1EXB_r_l_b.model.pdb D E -> examples/1EXB_r_l_b.pdb C F
-DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping FH:EG examples/1EXB_r_l_b.model.pdb F H -> examples/1EXB_r_l_b.pdb E G
-DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping FG:EH examples/1EXB_r_l_b.model.pdb F G -> examples/1EXB_r_l_b.pdb E H
-DockQ 0.992 iRMSD 0.001 LRMSD 0.001 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping HE:GF examples/1EXB_r_l_b.model.pdb H E -> examples/1EXB_r_l_b.pdb G F
-DockQ 1.000 iRMSD 0.001 LRMSD 0.001 fnat 1.000 fnonnat 0.024 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping EG:FH examples/1EXB_r_l_b.model.pdb E G -> examples/1EXB_r_l_b.pdb F H
+DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping BC:AD examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb A D
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping BD:AC examples/1EXB_r_l_b.model.pdb B D -> examples/1EXB_r_l_b.pdb A C
+DockQ 0.552 iRMSD 1.458 LRMSD 3.757 fnat 0.304 fnonnat 0.000 F1 0.467 clashes 0 mapping BF:AE examples/1EXB_r_l_b.model.pdb B F -> examples/1EXB_r_l_b.pdb A E
+DockQ 0.694 iRMSD 0.793 LRMSD 2.831 fnat 0.400 fnonnat 0.000 F1 0.571 clashes 0 mapping BH:AG examples/1EXB_r_l_b.model.pdb B H -> examples/1EXB_r_l_b.pdb A G
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping AC:BD examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb B D
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping AD:BC examples/1EXB_r_l_b.model.pdb A D -> examples/1EXB_r_l_b.pdb B C
+DockQ 0.742 iRMSD 0.850 LRMSD 3.426 fnat 0.609 fnonnat 0.176 F1 0.700 clashes 0 mapping AE:BF examples/1EXB_r_l_b.model.pdb A E -> examples/1EXB_r_l_b.pdb B F
+DockQ 0.824 iRMSD 0.625 LRMSD 3.994 fnat 0.800 fnonnat 0.000 F1 0.889 clashes 0 mapping AG:BH examples/1EXB_r_l_b.model.pdb A G -> examples/1EXB_r_l_b.pdb B H
+DockQ 0.687 iRMSD 1.161 LRMSD 3.757 fnat 0.600 fnonnat 0.000 F1 0.750 clashes 0 mapping CF:DE examples/1EXB_r_l_b.model.pdb C F -> examples/1EXB_r_l_b.pdb D E
+DockQ 0.477 iRMSD 1.425 LRMSD 3.994 fnat 0.087 fnonnat 0.000 F1 0.160 clashes 0 mapping CG:DH examples/1EXB_r_l_b.model.pdb C G -> examples/1EXB_r_l_b.pdb D H
+DockQ 0.775 iRMSD 0.711 LRMSD 2.831 fnat 0.609 fnonnat 0.125 F1 0.718 clashes 0 mapping DH:CG examples/1EXB_r_l_b.model.pdb D H -> examples/1EXB_r_l_b.pdb C G
+DockQ 0.914 iRMSD 0.547 LRMSD 3.426 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping DE:CF examples/1EXB_r_l_b.model.pdb D E -> examples/1EXB_r_l_b.pdb C F
+DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping FH:EG examples/1EXB_r_l_b.model.pdb F H -> examples/1EXB_r_l_b.pdb E G
+DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping FG:EH examples/1EXB_r_l_b.model.pdb F G -> examples/1EXB_r_l_b.pdb E H
+DockQ 0.992 iRMSD 0.001 LRMSD 0.001 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping HE:GF examples/1EXB_r_l_b.model.pdb H E -> examples/1EXB_r_l_b.pdb G F
+DockQ 1.000 iRMSD 0.001 LRMSD 0.001 fnat 1.000 fnonnat 0.024 F1 0.988 clashes 0 mapping EG:FH examples/1EXB_r_l_b.model.pdb E G -> examples/1EXB_r_l_b.pdb F H
diff --git a/testdata/1EXB_.ABC.dockq b/testdata/1EXB_.ABC.dockq
@@ -1,3 +1,3 @@
 Total DockQ over 2 native interfaces: 0.998 with ABC:ABC model:native mapping
-DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping AC:AC examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb A C
-DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 1.000 mapping BC:BC examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb B C
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping AC:AC examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb A C
+DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping BC:BC examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb B C
diff --git a/testdata/1EXB_AB.BA.dockq b/testdata/1EXB_AB.BA.dockq
@@ -1,17 +1,17 @@
 Total DockQ over 16 native interfaces: 0.852 with ABCDFHEG:BADCEGFH model:native mapping
-DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping AC:BD examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb B D
-DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping AD:BC examples/1EXB_r_l_b.model.pdb A D -> examples/1EXB_r_l_b.pdb B C
-DockQ 0.742 iRMSD 0.850 LRMSD 3.426 fnat 0.609 fnonnat 0.176 clashes 0.000 F1 0.700 DockQ_F1 0.772 mapping AE:BF examples/1EXB_r_l_b.model.pdb A E -> examples/1EXB_r_l_b.pdb B F
-DockQ 0.824 iRMSD 0.625 LRMSD 3.994 fnat 0.800 fnonnat 0.000 clashes 0.000 F1 0.889 DockQ_F1 0.853 mapping AG:BH examples/1EXB_r_l_b.model.pdb A G -> examples/1EXB_r_l_b.pdb B H
-DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 1.000 mapping BC:AD examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb A D
-DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping BD:AC examples/1EXB_r_l_b.model.pdb B D -> examples/1EXB_r_l_b.pdb A C
-DockQ 0.552 iRMSD 1.458 LRMSD 3.757 fnat 0.304 fnonnat 0.000 clashes 0.000 F1 0.467 DockQ_F1 0.606 mapping BF:AE examples/1EXB_r_l_b.model.pdb B F -> examples/1EXB_r_l_b.pdb A E
-DockQ 0.694 iRMSD 0.793 LRMSD 2.831 fnat 0.400 fnonnat 0.000 clashes 0.000 F1 0.571 DockQ_F1 0.751 mapping BH:AG examples/1EXB_r_l_b.model.pdb B H -> examples/1EXB_r_l_b.pdb A G
-DockQ 0.687 iRMSD 1.161 LRMSD 3.757 fnat 0.600 fnonnat 0.000 clashes 0.000 F1 0.750 DockQ_F1 0.737 mapping CF:DE examples/1EXB_r_l_b.model.pdb C F -> examples/1EXB_r_l_b.pdb D E
-DockQ 0.477 iRMSD 1.425 LRMSD 3.994 fnat 0.087 fnonnat 0.000 clashes 0.000 F1 0.160 DockQ_F1 0.502 mapping CG:DH examples/1EXB_r_l_b.model.pdb C G -> examples/1EXB_r_l_b.pdb D H
-DockQ 0.775 iRMSD 0.711 LRMSD 2.831 fnat 0.609 fnonnat 0.125 clashes 0.000 F1 0.718 DockQ_F1 0.812 mapping DH:CG examples/1EXB_r_l_b.model.pdb D H -> examples/1EXB_r_l_b.pdb C G
-DockQ 0.914 iRMSD 0.547 LRMSD 3.426 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 0.914 mapping DE:CF examples/1EXB_r_l_b.model.pdb D E -> examples/1EXB_r_l_b.pdb C F
-DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping FH:EG examples/1EXB_r_l_b.model.pdb F H -> examples/1EXB_r_l_b.pdb E G
-DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping FG:EH examples/1EXB_r_l_b.model.pdb F G -> examples/1EXB_r_l_b.pdb E H
-DockQ 0.992 iRMSD 0.001 LRMSD 0.001 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping HE:GF examples/1EXB_r_l_b.model.pdb H E -> examples/1EXB_r_l_b.pdb G F
-DockQ 1.000 iRMSD 0.001 LRMSD 0.001 fnat 1.000 fnonnat 0.024 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping EG:FH examples/1EXB_r_l_b.model.pdb E G -> examples/1EXB_r_l_b.pdb F H
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping AC:BD examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb B D
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping AD:BC examples/1EXB_r_l_b.model.pdb A D -> examples/1EXB_r_l_b.pdb B C
+DockQ 0.742 iRMSD 0.850 LRMSD 3.426 fnat 0.609 fnonnat 0.176 F1 0.700 clashes 0 mapping AE:BF examples/1EXB_r_l_b.model.pdb A E -> examples/1EXB_r_l_b.pdb B F
+DockQ 0.824 iRMSD 0.625 LRMSD 3.994 fnat 0.800 fnonnat 0.000 F1 0.889 clashes 0 mapping AG:BH examples/1EXB_r_l_b.model.pdb A G -> examples/1EXB_r_l_b.pdb B H
+DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping BC:AD examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb A D
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping BD:AC examples/1EXB_r_l_b.model.pdb B D -> examples/1EXB_r_l_b.pdb A C
+DockQ 0.552 iRMSD 1.458 LRMSD 3.757 fnat 0.304 fnonnat 0.000 F1 0.467 clashes 0 mapping BF:AE examples/1EXB_r_l_b.model.pdb B F -> examples/1EXB_r_l_b.pdb A E
+DockQ 0.694 iRMSD 0.793 LRMSD 2.831 fnat 0.400 fnonnat 0.000 F1 0.571 clashes 0 mapping BH:AG examples/1EXB_r_l_b.model.pdb B H -> examples/1EXB_r_l_b.pdb A G
+DockQ 0.687 iRMSD 1.161 LRMSD 3.757 fnat 0.600 fnonnat 0.000 F1 0.750 clashes 0 mapping CF:DE examples/1EXB_r_l_b.model.pdb C F -> examples/1EXB_r_l_b.pdb D E
+DockQ 0.477 iRMSD 1.425 LRMSD 3.994 fnat 0.087 fnonnat 0.000 F1 0.160 clashes 0 mapping CG:DH examples/1EXB_r_l_b.model.pdb C G -> examples/1EXB_r_l_b.pdb D H
+DockQ 0.775 iRMSD 0.711 LRMSD 2.831 fnat 0.609 fnonnat 0.125 F1 0.718 clashes 0 mapping DH:CG examples/1EXB_r_l_b.model.pdb D H -> examples/1EXB_r_l_b.pdb C G
+DockQ 0.914 iRMSD 0.547 LRMSD 3.426 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping DE:CF examples/1EXB_r_l_b.model.pdb D E -> examples/1EXB_r_l_b.pdb C F
+DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping FH:EG examples/1EXB_r_l_b.model.pdb F H -> examples/1EXB_r_l_b.pdb E G
+DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping FG:EH examples/1EXB_r_l_b.model.pdb F G -> examples/1EXB_r_l_b.pdb E H
+DockQ 0.992 iRMSD 0.001 LRMSD 0.001 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping HE:GF examples/1EXB_r_l_b.model.pdb H E -> examples/1EXB_r_l_b.pdb G F
+DockQ 1.000 iRMSD 0.001 LRMSD 0.001 fnat 1.000 fnonnat 0.024 F1 0.988 clashes 0 mapping EG:FH examples/1EXB_r_l_b.model.pdb E G -> examples/1EXB_r_l_b.pdb F H