From 8ab0f8668d7fb3c0d4eddca620270d53932604fd Mon Sep 17 00:00:00 2001
From: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
Date: Mon, 1 Dec 2025 10:01:33 -0800
Subject: [PATCH] pull names directly from ligandmapping (#1702)

* pull names directly from ligandmapping

* update news entry
---
 news/gather_by_gufe.rst              |   2 +-
 openfecli/commands/gather.py         |  20 ++-
 openfecli/tests/commands/conftest.py | 200 +++++++++++++++++++++++++++
 3 files changed, 210 insertions(+), 12 deletions(-)

diff --git a/news/gather_by_gufe.rst b/news/gather_by_gufe.rst
index c34d7200..32cc0b3a 100644
--- a/news/gather_by_gufe.rst
+++ b/news/gather_by_gufe.rst
@@ -4,7 +4,7 @@
 
 **Changed:**
 
-* ``openfe gather`` is now more rigorous in extracting ligand names and run types. These are now determined directly from component attributes, rather than relying on naming conventions. See `PR #1691 <https://github.com/OpenFreeEnergy/openfe/pull/1691>`_ for more details.
+* ``openfe gather`` is now more rigorous in extracting ligand names and run types. These are now determined directly from component attributes, rather than relying on naming conventions. See `PR #1691 <https://github.com/OpenFreeEnergy/openfe/pull/1702>`_ for more details.
 
 **Deprecated:**
 
diff --git a/openfecli/commands/gather.py b/openfecli/commands/gather.py
index c8cb251f..4c37a6e5 100644
--- a/openfecli/commands/gather.py
+++ b/openfecli/commands/gather.py
@@ -221,25 +221,23 @@ def _get_names(result: dict) -> tuple[str, str]:
 
     # TODO: I don't like this [0][0] indexing, but I can't think of a better way currently
     protocol_data = list(result["protocol_result"]["data"].values())[0][0]
-    ligand_A = gufe.SmallMoleculeComponent.from_dict(
-        protocol_data["inputs"]["stateA"]["components"]["ligand"]
-    )
-    ligand_B = gufe.SmallMoleculeComponent.from_dict(
-        protocol_data["inputs"]["stateB"]["components"]["ligand"]
-    )
 
-    return ligand_A.name, ligand_B.name
+    name_A = protocol_data["inputs"]["ligandmapping"]["componentA"]["molprops"]["ofe-name"]
+    name_B = protocol_data["inputs"]["ligandmapping"]["componentB"]["molprops"]["ofe-name"]
+
+    return name_A, name_B
 
 
 def _get_type(result: dict) -> Literal["vacuum", "solvent", "complex"]:
     """Determine the simulation type based on the component types."""
 
     protocol_data = list(result["protocol_result"]["data"].values())[0][0]
-    chem_sys_A = gufe.ChemicalSystem.from_dict(protocol_data["inputs"]["stateA"])
-
-    if not chem_sys_A.contains(gufe.SolventComponent):
+    component_types = [
+        x["__module__"] for x in protocol_data["inputs"]["stateA"]["components"].values()
+    ]
+    if "gufe.components.solventcomponent" not in component_types:
         return "vacuum"
-    elif chem_sys_A.contains(gufe.ProteinComponent):
+    elif "gufe.components.proteincomponent" in component_types:
         return "complex"
     else:
         return "solvent"
diff --git a/openfecli/tests/commands/conftest.py b/openfecli/tests/commands/conftest.py
index 197a03c2..00fa3382 100644
--- a/openfecli/tests/commands/conftest.py
+++ b/openfecli/tests/commands/conftest.py
@@ -207,6 +207,206 @@ def min_result_json():
                                 "__qualname__": "ChemicalSystem",
                                 "__module__": "gufe.chemicalsystem",
                             },
+                            "ligandmapping": {
+                                "componentA": {
+                                    "atoms": [
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [17, 0, 0, False, 0, 0, {}],
+                                        [6, 0, 0, False, 0, 0, {}],
+                                        [8, 0, 0, False, 0, 0, {}],
+                                        [7, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [7, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [7, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [6, 0, 0, False, 0, 0, {}],
+                                        [8, 0, 0, False, 0, 0, {}],
+                                        [6, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [17, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                    ],
+                                    "bonds": [
+                                        [0, 1, 1, 0, {}],
+                                        [1, 6, 12, 0, {}],
+                                        [1, 2, 12, 0, {}],
+                                        [2, 3, 12, 0, {}],
+                                        [2, 31, 1, 0, {}],
+                                        [3, 4, 12, 0, {}],
+                                        [3, 30, 1, 0, {}],
+                                        [4, 5, 12, 0, {}],
+                                        [4, 9, 1, 0, {}],
+                                        [5, 6, 12, 0, {}],
+                                        [5, 8, 1, 0, {}],
+                                        [6, 7, 1, 0, {}],
+                                        [9, 10, 2, 0, {}],
+                                        [9, 11, 1, 0, {}],
+                                        [11, 12, 1, 0, {}],
+                                        [11, 13, 1, 0, {}],
+                                        [13, 18, 12, 0, {}],
+                                        [13, 14, 12, 0, {}],
+                                        [14, 15, 12, 0, {}],
+                                        [14, 29, 1, 0, {}],
+                                        [15, 16, 12, 0, {}],
+                                        [15, 28, 1, 0, {}],
+                                        [16, 17, 12, 0, {}],
+                                        [17, 18, 12, 0, {}],
+                                        [17, 20, 1, 0, {}],
+                                        [18, 19, 1, 0, {}],
+                                        [20, 21, 1, 0, {}],
+                                        [20, 22, 1, 0, {}],
+                                        [22, 23, 2, 0, {}],
+                                        [22, 24, 1, 0, {}],
+                                        [24, 25, 1, 0, {}],
+                                        [24, 26, 1, 0, {}],
+                                        [24, 27, 1, 0, {}],
+                                    ],
+                                    "conformer": [
+                                        "\u0093NUMPY\u0001\u0000v\u0000{'descr': '<f8', 'fortran_order': False, 'shape': (32, 3), }                                                         \n\u00f3\u008eSt$\u0017\u0013\u00c0W[\u00b1\u00bf\u00ec\u009e\u0006\u00c09\u00b4\u00c8v\u00be\u007f0\u00c05\u00ef8EGr\u0015\u00c0P\u008d\u0097n\u0012\u0083\r\u00c0b\u00a1\u00d64\u00ef80\u00c0\u0095e\u0088c]\u001c\u0013\u00c0\u0096!\u008euq\u00db\u0013\u00c0\u00a5,C\u001c\u00eb20\u00c0j\u00deq\u008a\u008e$\u0016\u00c0\u00b4\u00c8v\u00be\u009fZ\u0018\u00c0+\u00f6\u0097\u00dd\u0093\u00a7/\u00c0_\u0007\u00ce\u0019Q\u009a\u001b\u00c0d\u00cc]K\u00c8\u00c7\u0017\u00c0m\u00c5\u00fe\u00b2{\u00f2.\u00c0\u009e\u00ef\u00a7\u00c6K\u00f7\u001d\u00c0p\u00ce\u0088\u00d2\u00de\u00a0\u0012\u00c0\u00e7\u00fb\u00a9\u00f1\u00d2\r/\u00c0r\u008a\u008e\u00e4\u00f2\u00df\u001a\u00c0\u00e1\u000b\u0093\u00a9\u0082Q\f\u00c0\t\u001b\u009e^)\u00cb/\u00c0\u00f7\u00e4a\u00a1\u00d6\u00b4\u001c\u00c0\u0017\u00b7\u00d1\u0000\u00de\u0082\u0004\u00c0\u00e2X\u0017\u00b7\u00d1\u00e0/\u00c0)\u00cb\u0010\u00c7\u00baX\"\u00c0a2U0*\u00a9\u0011\u00c0V\u009f\u00ab\u00ad\u00d8_.\u00c0C\u001c\u00eb\u00e26\u00da\u001e\u00c0\u0083/L\u00a6\n\u0086\u001c\u00c0\u00de\u0093\u0087\u0085Z\u0013.\u00c0\u00d3\u00bc\u00e3\u0014\u001dI \u00c0\u00ec/\u00bb'\u000f\u00cb\u001c\u00c0h\"lxz\u00c5+\u00c0\u009f\u00cd\u00aa\u00cf\u00d5\u0096\u001f\u00c0\u0094\u0087\u0085Z\u00d3\u001c \u00c0t$\u0097\u00ff\u0090\u00fe/\u00c0r\u00f9\u000f\u00e9\u00b7\u00af\u001d\u00c0Gr\u00f9\u000f\u00e9w\u001f\u00c0Zd;\u00dfO\u00dd0\u00c0p_\u0007\u00ce\u0019q!\u00c0!\u00b0rh\u0091m\"\u00c0\u008c\u00dbh\u0000o\u00010\u00c0H\u00e1z\u0014\u00ae'#\u00c0\u008a\u00b0\u00e1\u00e9\u00952#\u00c0\u009e^)\u00cb\u0010\u00e7-\u00c0\u0085\u00ebQ\u00b8\u001e\u00c5$\u00c0I.\u00ff!\u00fdv%\u00c0M\u00f3\u008eStD.\u00c0\\\u008f\u00c2\u00f5(\u00bc$\u00c0\nh\"lx\u00fa&\u00c0\u00ff\u00b2{\u00f2\u00b0@0\u00c0Nb\u0010X9\u0014#\u00c0?5^\u00baIL&\u00c0i\u0000o\u0081\u0004E1\u00c0=\u009bU\u009f\u00abm!\u00c0\u008euq\u001b\r\u0000$\u00c0[\u00b1\u00bf\u00ec\u009e,1\u00c0%\u0006\u0081\u0095C+ \u00c0\u0088\u0085Z\u00d3\u00bcc#\u00c0\u0003x\u000b$(\u00fe1\u00c0\u0012\u00a5\u00bd\u00c1\u0017&#\u00c0\u00cb\u00a1E\u00b6\u00f3\u00dd'\u00c0io\u00f0\u0085\u00c9t2\u00c0\u00ea\u0095\u00b2\fq\u00cc$\u00c0\u0018\u0095\u00d4\th\u0002)\u00c0vO\u001e\u0016j\u008d2\u00c0\u00bb\u00b8\u008d\u0006\u00f0V!\u00c0\u00c1\u00ca\u00a1E\u00b6\u0013(\u00c0\u00deq\u008a\u008e\u00e4r3\u00c0\u00c5 \u00b0rhQ\u001e\u00c0\u00c5\u00fe\u00b2{\u00f2\u00f0&\u00c0\u00d1\u0091\\\u00feCz3\u00c0B>\u00e8\u00d9\u00ac\u001a\"\u00c0\u0080\u00b7@\u0082\u00e2\u00e7)\u00c0\b=\u009bU\u009f\u009b4\u00c0r\u00f9\u000f\u00e9\u00b7O\"\u00c0\u00de\u0093\u0087\u0085Z\u00f3+\u00c0o\u0012\u0083\u00c0\u00caA4\u00c0\u008a\u008e\u00e4\u00f2\u001f\u0092 \u00c0\u00aa`TR'\u00e0)\u00c0n4\u0080\u00b7@b5\u00c0\u00e8j+\u00f6\u0097\u00fd#\u00c0\u00b3{\u00f2\u00b0PK)\u00c0:#J{\u0083\u000f5\u00c0\u008c\u00dbh\u0000o!&\u00c0\u00d9=yX\u00a8\u0015&\u00c0\u0012\u0014?\u00c6\u00dc\u00b5,\u00c0\u00a5\u00bd\u00c1\u0017&S#\u00c0io\u00f0\u0085\u00c9\u0014\"\u00c0\u00ab\u00cf\u00d5V\u00ec\u000f,\u00c0\u00e0\u009c\u0011\u00a5\u00bd\u0001\u0013\u00c0\u00ad\u00fa\\m\u00c5~\u001e\u00c0L7\u0089A`\u00a5/\u00c0\u0002\u009a\b\u001b\u009e\u00de\r\u00c0\u00c8\u0098\u00bb\u0096\u0090O\u0014\u00c0N\u00d1\u0091\\\u00fes0\u00c0",
+                                        {},
+                                    ],
+                                    "molprops": {"ofe-name": "lig_ejm_31"},
+                                    "__qualname__": "SmallMoleculeComponent",
+                                    "__module__": "gufe.components.smallmoleculecomponent",
+                                },
+                                "componentB": {
+                                    "atoms": [
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [17, 0, 0, False, 0, 0, {}],
+                                        [6, 0, 0, False, 0, 0, {}],
+                                        [8, 0, 0, False, 0, 0, {}],
+                                        [7, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [7, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [6, 0, 0, True, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [7, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [6, 0, 0, False, 0, 0, {}],
+                                        [8, 0, 0, False, 0, 0, {}],
+                                        [6, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [6, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                        [17, 0, 0, False, 0, 0, {}],
+                                        [1, 0, 0, False, 0, 0, {}],
+                                    ],
+                                    "bonds": [
+                                        [0, 1, 1, 0, {}],
+                                        [1, 6, 12, 0, {}],
+                                        [1, 2, 12, 0, {}],
+                                        [2, 3, 12, 0, {}],
+                                        [2, 34, 1, 0, {}],
+                                        [3, 4, 12, 0, {}],
+                                        [3, 33, 1, 0, {}],
+                                        [4, 5, 12, 0, {}],
+                                        [4, 9, 1, 0, {}],
+                                        [5, 6, 12, 0, {}],
+                                        [5, 8, 1, 0, {}],
+                                        [6, 7, 1, 0, {}],
+                                        [9, 10, 2, 0, {}],
+                                        [9, 11, 1, 0, {}],
+                                        [11, 12, 1, 0, {}],
+                                        [11, 13, 1, 0, {}],
+                                        [13, 18, 12, 0, {}],
+                                        [13, 14, 12, 0, {}],
+                                        [14, 15, 12, 0, {}],
+                                        [14, 32, 1, 0, {}],
+                                        [15, 16, 12, 0, {}],
+                                        [15, 31, 1, 0, {}],
+                                        [16, 17, 12, 0, {}],
+                                        [17, 18, 12, 0, {}],
+                                        [17, 20, 1, 0, {}],
+                                        [18, 19, 1, 0, {}],
+                                        [20, 21, 1, 0, {}],
+                                        [20, 22, 1, 0, {}],
+                                        [22, 23, 2, 0, {}],
+                                        [22, 24, 1, 0, {}],
+                                        [24, 25, 1, 0, {}],
+                                        [24, 26, 1, 0, {}],
+                                        [24, 27, 1, 0, {}],
+                                        [27, 28, 1, 0, {}],
+                                        [27, 29, 1, 0, {}],
+                                        [27, 30, 1, 0, {}],
+                                    ],
+                                    "conformer": [
+                                        "\u0093NUMPY\u0001\u0000v\u0000{'descr': '<f8', 'fortran_order': False, 'shape': (35, 3), }                                                         \n\u00ac\u00ad\u00d8_v\u000f\u0013\u00c0\u009a\b\u001b\u009e^\u00a9\u0006\u00c0\u0019\u0004V\u000e-\u00820\u00c0\u00b0\u0003\u00e7\u008c(m\u0015\u00c0]\u00dcF\u0003x\u008b\r\u00c0C\u001c\u00eb\u00e26:0\u00c0io\u00f0\u0085\u00c9\u0014\u0013\u00c0\u00c5\u008f1w-\u00e1\u0013\u00c03333330\u00c0\u0001\u00de\u0002\t\u008a\u001f\u0016\u00c0\u00fee\u00f7\u00e4aa\u0018\u00c0a2U0*\u00a9/\u00c0\u00f8\u00c2d\u00aa`\u0094\u001b\u00c0\u0004\u00e7\u008c(\u00ed\u00cd\u0017\u00c0\u00a85\u00cd;N\u00f1.\u00c0\u00db\u00f9~j\u00bc\u00f4\u001d\u00c0e\u00aa`TR\u00a7\u0012\u00c0\u0091~\u00fb:p\u000e/\u00c0\u00cc\u007fH\u00bf}\u00dd\u001a\u00c0>\u00e8\u00d9\u00ac\u00fa\\\f\u00c0\u00aeG\u00e1z\u0014\u00ce/\u00c0\u0001M\u0084\rO\u00af\u001c\u00c0\u00d5x\u00e9&1\u0088\u0004\u00c0M\u00f3\u008eSt\u00e4/\u00c0\u009c3\u00a2\u00b47X\"\u00c0\u0088\u00f4\u00db\u00d7\u0081\u00b3\u0011\u00c0U\u00c1\u00a8\u00a4N`.\u00c0q\u001b\r\u00e0-\u00d0\u001e\u00c0\u00af%\u00e4\u0083\u009e\u008d\u001c\u00c0\u0002+\u0087\u0016\u00d9\u000e.\u00c0-!\u001f\u00f4l6 \u00c0\u009bU\u009f\u00ab\u00ad\u00d8\u001c\u00c0xz\u00a5,C\u00bc+\u00c0T\u00e3\u00a5\u009b\u00c4\u00a0\u001f\u00c0\u0099\u00bb\u0096\u0090\u000f\u001a \u00c09\u00b4\u00c8v\u00be\u00ff/\u00c0:\u0092\u00cb\u007fH\u00bf\u001d\u00c0:#J{\u0083o\u001f\u00c0\u001f\u0085\u00ebQ\u00b8\u00de0\u00c0\u00f8\u00c2d\u00aa`t!\u00c0\t\u001b\u009e^)k\"\u00c0\u00fee\u00f7\u00e4a\u00010\u00c0b\u0010X9\u00b4(#\u00c0\u0006\u0081\u0095C\u008b,#\u00c0h\"lxz\u00e5-\u00c0\u0016\u00fb\u00cb\u00ee\u00c9\u00c3$\u00c0\u00c1\u00ca\u00a1E\u00b6s%\u00c0\u00cd;N\u00d1\u0091<.\u00c0\u0093\u00a9\u0082QI\u00bd$\u00c0xz\u00a5,C\u00fc&\u00c0\u00ec/\u00bb'\u000f;0\u00c0\u00b6\u0084|\u00d0\u00b3\u0019#\u00c0\u0002+\u0087\u0016\u00d9N&\u00c0\u008c\u00dbh\u0000oA1\u00c0\u00fc\u0018s\u00d7\u0012r!\u00c0R'\u00a0\u0089\u00b0\u0001$\u00c0A\u00f1c\u00cc]+1\u00c04\u00116<\u00bd2 \u00c0\u0010\u00e9\u00b7\u00af\u0003g#\u00c0 c\u00eeZB\u00fe1\u00c0\u00b2\u009d\u00ef\u00a7\u00c6+#\u00c0\u00b8\u00af\u0003\u00e7\u008c\u00e8'\u00c0V\u000e-\u00b2\u009do2\u00c00\u00bb'\u000f\u000b\u00d5$\u00c0\u00e8\u00d9\u00ac\u00fa\\\r)\u00c0+\u00f6\u0097\u00dd\u0093\u00872\u00c0\u00ac\u001cZd;_!\u00c0\u00b8\u00af\u0003\u00e7\u008c((\u00c0X\u00ca2\u00c4\u00b1n3\u00c0\u00deq\u008a\u008e\u00e4r\u001e\u00c0\u00a0\u0089\u00b0\u00e1\u00e9\u00f5&\u00c0\"\u00fd\u00f6u\u00e0|3\u00c0yX\u00a85\u00cd\u001b\"\u00c0(\u000f\u000b\u00b5\u00a6\u0019*\u00c0\u00e3\u00a5\u009b\u00c4 \u00904\u00c01\b\u00ac\u001cZ\u00e4\"\u00c0Y\u00868\u00d6\u00c5\u00ed(\u00c0\u00a2E\u00b6\u00f3\u00fdd5\u00c0\u00d5\u00e7j+\u00f6\u00b7#\u00c0\u008cJ\u00ea\u00044q+\u00c0\u00e0\u00be\u000e\u009c3B4\u00c0\u00b3{\u00f2\u00b0Pk\u001f\u00c0\u00bb'\u000f\u000b\u00b5\u00c6+\u00c0\u00b6\u00f3\u00fd\u00d4x\t5\u00c0vq\u001b\r\u00e0M \u00c0\u008c\u00dbh\u0000o!-\u00c0\u00bc\u0096\u0090\u000fz\u00d65\u00c0_\u0098L\u0015\u008c\u00ca\u001d\u00c0\u00d1\u0091\\\u00feC\u00fa,\u00c0a\u00c3\u00d3+e94\u00c0K\u00ea\u00044\u00116\u001c\u00c0\u00a2\u00b47\u00f8\u00c2\u0084*\u00c0[\u00b1\u00bf\u00ec\u009el5\u00c0X9\u00b4\u00c8v\u001e&\u00c0p_\u0007\u00ce\u0019\u0011&\u00c0\u00ce\u0088\u00d2\u00de\u00e0\u00ab,\u00c0\u00d5\u00e7j+\u00f6W#\u00c0^\u00baI\f\u0002\u000b\"\u00c08gDio\u0010,\u00c0\u00c6m4\u0080\u00b7\u0000\u0013\u00c0\\ A\u00f1c\u008c\u001e\u00c0\u009e^)\u00cb\u0010\u00a7/\u00c0\u00e7\u00fb\u00a9\u00f1\u00d2\u00cd\r\u00c0\u009d\u0011\u00a5\u00bd\u00c1W\u0014\u00c0\u00f7\u00e4a\u00a1\u00d6t0\u00c0",
+                                        {},
+                                    ],
+                                    "molprops": {"ofe-name": "lig_ejm_42"},
+                                    "__qualname__": "SmallMoleculeComponent",
+                                    "__module__": "gufe.components.smallmoleculecomponent",
+                                },
+                                "componentA_to_componentB": {
+                                    "0": 0,
+                                    "1": 1,
+                                    "2": 2,
+                                    "3": 3,
+                                    "4": 4,
+                                    "5": 5,
+                                    "6": 6,
+                                    "7": 7,
+                                    "8": 8,
+                                    "9": 9,
+                                    "10": 10,
+                                    "11": 11,
+                                    "12": 12,
+                                    "13": 13,
+                                    "14": 14,
+                                    "15": 15,
+                                    "16": 16,
+                                    "17": 17,
+                                    "18": 18,
+                                    "19": 19,
+                                    "20": 20,
+                                    "21": 21,
+                                    "22": 22,
+                                    "23": 23,
+                                    "24": 24,
+                                    "25": 26,
+                                    "27": 25,
+                                    "28": 31,
+                                    "29": 32,
+                                    "30": 33,
+                                    "31": 34,
+                                },
+                                "annotations": '{"score": 0.09516258196404048}',
+                                "__qualname__": "LigandAtomMapping",
+                                "__module__": "gufe.mapping.ligandatommapping",
+                            },
                         },
                     }
                 ]