From 31ccc299c9161ba0ab912bb65135937759581c73 Mon Sep 17 00:00:00 2001 From: Nathan Miller Date: Wed, 21 Jan 2026 11:52:59 -0500 Subject: [PATCH 1/2] Predicted updates --- .gitignore | 5 +- api/draw_utils.py | 79 +- api/environment.yml | 2 +- api/server.py | 47 +- data/hybrid_routes_example.json | 2 +- data/merged_example.json | 6605 +++++++++++++++++ .../GraphRetrieval/ExampleGraphs.jsx | 1 + ui/src/components/NetworkSearchMenu.jsx | 8 +- ui/src/helpers/commonHelpers.js | 2 +- 9 files changed, 6693 insertions(+), 58 deletions(-) create mode 100644 data/merged_example.json diff --git a/.gitignore b/.gitignore index ab3512e..104b5e3 100644 --- a/.gitignore +++ b/.gitignore @@ -26,4 +26,7 @@ api/data/ # Test files tests/.env -.pytest_cache \ No newline at end of file +.pytest_cache + +# Temp +temp/ \ No newline at end of file diff --git a/api/draw_utils.py b/api/draw_utils.py index cf14e78..9410efd 100644 --- a/api/draw_utils.py +++ b/api/draw_utils.py @@ -252,7 +252,7 @@ def mol_to_image( [a.SetAtomMapNum(0) for a in mol.GetAtoms()] if show_atom_indices: mol.UpdatePropertyCache(False) - if abbreviate and not highlight_atoms and not highlight_bonds and clear_map: + if abbreviate and not highlight_atoms and not highlight_bonds and clear_map and not show_atom_indices: mol.UpdatePropertyCache(False) mol = rdAbbreviations.CondenseMolAbbreviations(mol, ABBREVIATIONS) if update: @@ -494,7 +494,7 @@ def molecule_smiles_to_image( """ if not highlight and split: mols = [Chem.MolFromSmarts(smi) if show_atom_indices else Chem.MolFromSmiles(smi) for smi in smiles.split(".")] - images = [mol_to_image(mol, svg=svg, transparent=transparent, abbreviate=abbreviate, reference=reference, **kwargs) for mol in mols] + images = [mol_to_image(mol, svg=svg, transparent=transparent, abbreviate=abbreviate, reference=reference, show_atom_indices=show_atom_indices, **kwargs) for mol in mols] return combine_images_horizontally(images, transparent=transparent, return_png=return_png) mol = Chem.MolFromSmarts(smiles) if show_atom_indices else Chem.MolFromSmiles(smiles) @@ -539,51 +539,63 @@ def molecule_smiles_to_image( print("Unable to determine atom highlights using specified reacting atoms. Drawing without highlights.") tb.print_exc() - return mol_to_image(mol, svg=svg, transparent=transparent, return_png=return_png, abbreviate=abbreviate, reference=reference, **kwargs) + return mol_to_image(mol, svg=svg, transparent=transparent, return_png=return_png, abbreviate=abbreviate, reference=reference, show_atom_indices=show_atom_indices, **kwargs) def determine_highlight_colors(mol, frag_map, frag_idx=None): """ Determine highlight colors for reactants and products based on atom map. - Adapted from RDKit MolDraw2D.DrawReaction - https://github.com/rdkit/rdkit/blob/Release_2020_09_5/Code/GraphMol/MolDraw2D/MolDraw2D.cpp#L547 - - If ``frag_idx`` is specified: - * The molecule is considered a reactant fragment - * All atoms in the molecule will be highlighted using the same color - * ``frag_map`` will be updated in place - - Otherwise: - * The molecule is considered a product fragment - * Atoms will be colored based the contents of ``frag_map`` - * ``frag_map`` will not be altered + More robust behavior: + - When frag_idx is provided (building phase): assign every mapped atom's mapno + to frag_idx in frag_map (overwriting if already present). + - When frag_idx is None (drawing phase): only highlight atoms whose mapno exists + in frag_map (skip unknown map numbers instead of raising KeyError). Args: mol (Chem.Mol): molecule object to analyze - frag_map (dict): mapping from atom map number to fragment index - frag_idx (int, optional): current fragment index + frag_map (dict[int, int]): mapping from atom map number -> fragment index + frag_idx (int, optional): current fragment index when building frag_map Returns: - dict: containing highlight kwargs for ``mol_to_image`` + dict: highlight kwargs for mol_to_image """ highlight_atoms = [] highlight_bonds = [] highlight_atom_colors = {} highlight_bond_colors = {} + for atom in mol.GetAtoms(): mapno = atom.GetAtomMapNum() - if mapno: - idx = atom.GetIdx() - if frag_idx is not None: - frag_map[mapno] = frag_idx - highlight_atoms.append(idx) - highlight_atom_colors[idx] = HIGHLIGHT_COLORS[frag_map[mapno] % len(HIGHLIGHT_COLORS)] - for atom2 in atom.GetNeighbors(): - if atom2.GetIdx() < idx and highlight_atom_colors.get(atom2.GetIdx()) == highlight_atom_colors[idx]: - bond_idx = mol.GetBondBetweenAtoms(idx, atom2.GetIdx()).GetIdx() - highlight_bonds.append(bond_idx) - highlight_bond_colors[bond_idx] = highlight_atom_colors[idx] + if not mapno: + continue # RDKit uses 0 for "no mapping" + + # Build-phase: record map number -> fragment index + if frag_idx is not None: + frag_map[mapno] = frag_idx + + # Draw-phase: if we don't know this map number, skip it (don't crash) + frag = frag_map.get(mapno) + if frag is None: + continue + + idx = atom.GetIdx() + color = HIGHLIGHT_COLORS[frag % len(HIGHLIGHT_COLORS)] + + highlight_atoms.append(idx) + highlight_atom_colors[idx] = color + + # Highlight bonds between same-colored neighboring atoms + for atom2 in atom.GetNeighbors(): + j = atom2.GetIdx() + if j < idx and highlight_atom_colors.get(j) == color: + bond = mol.GetBondBetweenAtoms(idx, j) + if bond is None: + continue + bond_idx = bond.GetIdx() + highlight_bonds.append(bond_idx) + highlight_bond_colors[bond_idx] = color + return { "highlight_atoms": highlight_atoms, "highlight_bonds": highlight_bonds, @@ -591,8 +603,7 @@ def determine_highlight_colors(mol, frag_map, frag_idx=None): "highlight_bond_colors": highlight_bond_colors, } - - + def reaction_smiles_to_image(smiles, svg=True, transparent=True, return_png=True, retro=False, highlight=False, align=False, plus=True, update=True, show_atom_indices=False,**kwargs): """ Create image of the provided reaction SMILES string. Omits agents. @@ -637,10 +648,12 @@ def reaction_smiles_to_image(smiles, svg=True, transparent=True, return_png=True if plus and i > 0: images.append(draw_plus(svg=svg, transparent=transparent)) smiles = Chem.MolToSmarts(mol) if show_atom_indices else Chem.MolToSmiles(mol) - if smiles.count(".") > 1: + # Only split when NOT highlighting; splitting breaks highlight atom indices + if (not highlight) and smiles.count(".") > 1: images.append(molecule_smiles_to_image(smiles, svg=svg, transparent=transparent, **kwargs)) else: - images.append(mol_to_image(mol, svg=svg, transparent=transparent, update=update, show_atom_indices=show_atom_indices, **kwargs)) + images.append(mol_to_image(mol, svg=svg, transparent=transparent, update=update, + show_atom_indices=show_atom_indices, **kwargs)) images.append(draw_arrow(retro=retro, svg=svg, transparent=transparent)) diff --git a/api/environment.yml b/api/environment.yml index f8dcbf7..54cde61 100644 --- a/api/environment.yml +++ b/api/environment.yml @@ -5,7 +5,7 @@ channels: dependencies: - svgutils - python=3.12 - - rdkit=2024.3.5 + - rdkit=2025.03.2 - networkx - pip - pip: diff --git a/api/server.py b/api/server.py index 2f94b74..957319b 100644 --- a/api/server.py +++ b/api/server.py @@ -268,7 +268,8 @@ class Availability(BaseModel): class InputFile(BaseModel): synth_graph: Optional[SynthGraph] = None evidence_synth_graph: Optional[SynthGraph] = None - predictive_synth_graph: Optional[SynthGraph] = None + predicted_synth_graph: Optional[SynthGraph] = None + predictive_synth_graph: Optional[SynthGraph] = None # Deprecated: Use predicted_synth_graph routes: Optional[List[Route]] = None availability: Optional[list[Availability]] = None @@ -521,6 +522,7 @@ async def rxsmiles_to_svg_endpoint(rxsmiles: str = 'CCO.CC(=O)O>>CC(=O)OCC.O', h Unable to generate reaction SVG """.strip() + logger.error(f"Error generating SVG for rxsmiles {rxsmiles}: {e}") if base64_encode: svg = base64.b64encode(svg.encode('utf-8')).decode('utf-8') @@ -669,7 +671,7 @@ def flatten_dict(d, parent_key='', sep='_'): return dict(items) -def convert_to_cytoscape_json(aicp_graph, synth_graph_key="synth_graph", convert_route=False, predicted_route=False, route_index=0): +def convert_to_cytoscape_json(aicp_graph, synth_graph_key="synth_graph", convert_route=False, is_predicted=False, route_index=0): # Try to get the specified graph, with fallback logic similar to frontend synth_graph = None @@ -679,10 +681,12 @@ def convert_to_cytoscape_json(aicp_graph, synth_graph_key="synth_graph", convert synth_graph = aicp_graph["synth_graph"] elif "evidence_synth_graph" in aicp_graph and aicp_graph["evidence_synth_graph"] is not None: synth_graph = aicp_graph["evidence_synth_graph"] + elif "predicted_synth_graph" in aicp_graph and aicp_graph["predicted_synth_graph"] is not None: + synth_graph = aicp_graph["predicted_synth_graph"] elif "predictive_synth_graph" in aicp_graph and aicp_graph["predictive_synth_graph"] is not None: - synth_graph = aicp_graph["predictive_synth_graph"] + synth_graph = aicp_graph["predictive_synth_graph"] # Backward compatibility else: - raise ValueError(f"No synthesis graph found. Looked for: {synth_graph_key}, synth_graph, evidence_synth_graph, predictive_synth_graph") + raise ValueError(f"No synthesis graph found. Looked for: {synth_graph_key}, synth_graph, evidence_synth_graph, predicted_synth_graph, predictive_synth_graph") if convert_route: routes = aicp_graph.get("routes", []) @@ -724,7 +728,7 @@ def convert_to_cytoscape_json(aicp_graph, synth_graph_key="synth_graph", convert ] aggregated_yield = "N/A" - if predicted_route: + if is_predicted: for node in filtered_nodes: node_type = node["data"].get("node_type", "") if isinstance(node_type, str) and node_type.lower() == "substance": @@ -758,11 +762,11 @@ def convert_to_cytoscape_json(aicp_graph, synth_graph_key="synth_graph", convert # Generate name based on whether this is a route or full graph if convert_route: # Route name: Include reaction steps, index, and type - route_type = "Predicted" if predicted_route else "Evidence" + route_type = "Predicted" if is_predicted else "Evidence" cytoscape_name = f"{target_inchikey}_SD_{reaction_steps} - Route {route_index} - {route_type}" else: # Full graph name: Simple format - graph_type = "Predicted Graph" if predicted_route else "Evidence Graph" + graph_type = "Predicted Graph" if is_predicted else "Evidence Graph" cytoscape_name = f"{target_inchikey} - {graph_type}" return { @@ -820,7 +824,7 @@ def send_to_cytoscape( layout_type: str = "hierarchical", send_all_routes: bool = True, synth_graph_key: str = "synth_graph", - predicted_route: bool = False, + is_predicted: bool = False, convert_route: bool = False, route_index: int = 0, ): @@ -834,7 +838,7 @@ def send_to_cytoscape( - layout_type (str, optional): Layout algorithm name (e.g., "hierarchical"). Defaults to "hierarchical". - send_all_routes (bool, optional): If True, sends all routes as separate networks. If False, uses single route/graph mode. Defaults to True. - synth_graph_key (str, optional): Key in the input JSON containing the synthesis graph. Defaults to "synth_graph". Auto-detects if not present. - - predicted_route (bool, optional): If True, relabels substance nodes (e.g., by InChIKey) and marks network as predicted. Only used when send_all_routes=False. + - is_predicted (bool, optional): If True, relabels substance nodes (e.g., by InChIKey) and marks network as predicted. Only used when send_all_routes=False. - convert_route (bool, optional): If True, filters the graph to a single route. Only used when send_all_routes=False. Defaults to False. - route_index (int, optional): Index into the 'routes' array to select a route. Only used when send_all_routes=False and convert_route=True. Defaults to 0. @@ -863,7 +867,7 @@ def send_to_cytoscape( network_json, synth_graph_key, convert_route, - predicted_route, + is_predicted, route_index ) return _send_single_network_to_cytoscape(converted_json, layout_type) @@ -876,14 +880,16 @@ def send_to_cytoscape( routes = network_json.get("routes", []) results = [] - # First, send all available full graphs (synth_graph, evidence_synth_graph, predictive_synth_graph) + # First, send all available full graphs (synth_graph, evidence_synth_graph, predicted_synth_graph) graph_types = [] if "synth_graph" in network_json and network_json["synth_graph"] is not None: graph_types.append(("synth_graph", False, "Evidence Synthesis Graph")) if "evidence_synth_graph" in network_json and network_json["evidence_synth_graph"] is not None: graph_types.append(("evidence_synth_graph", False, "Evidence Synthesis Graph")) - if "predictive_synth_graph" in network_json and network_json["predictive_synth_graph"] is not None: - graph_types.append(("predictive_synth_graph", True, "Predictive Synthesis Graph")) + if "predicted_synth_graph" in network_json and network_json["predicted_synth_graph"] is not None: + graph_types.append(("predicted_synth_graph", True, "Predicted Synthesis Graph")) + elif "predictive_synth_graph" in network_json and network_json["predictive_synth_graph"] is not None: + graph_types.append(("predictive_synth_graph", True, "Predicted Synthesis Graph")) # Backward compatibility # Send each full graph for graph_key, is_predicted, graph_name in graph_types: @@ -894,7 +900,7 @@ def send_to_cytoscape( network_json, graph_key, convert_route=False, - predicted_route=is_predicted, + is_predicted=is_predicted, route_index=0 ) @@ -940,13 +946,20 @@ def send_to_cytoscape( logger.info(f"Processing route {idx}: {route_name}") # Use the correct graph key based on route type - route_graph_key = "predictive_synth_graph" if is_predicted else synth_graph_key + # Check predicted_synth_graph first, fallback to predictive_synth_graph for backward compatibility + if is_predicted: + if "predicted_synth_graph" in network_json and network_json["predicted_synth_graph"] is not None: + route_graph_key = "predicted_synth_graph" + else: + route_graph_key = "predictive_synth_graph" # Backward compatibility + else: + route_graph_key = synth_graph_key converted_json = convert_to_cytoscape_json( network_json, route_graph_key, convert_route=True, - predicted_route=is_predicted, + is_predicted=is_predicted, route_index=idx ) @@ -1168,7 +1181,7 @@ async def _convert_to_aicp(request: ConvertToAicpRequest) -> dict: # Return converted graph return { - "predictive_synth_graph": { + "predicted_synth_graph": { "nodes": nodes, "edges": edges }, diff --git a/data/hybrid_routes_example.json b/data/hybrid_routes_example.json index 22ef22f..1d4f6af 100644 --- a/data/hybrid_routes_example.json +++ b/data/hybrid_routes_example.json @@ -2707,7 +2707,7 @@ } ] }, - "predictive_synth_graph": { + "predicted_synth_graph": { "nodes": [ { "node_label": "45427382-fde3-4163-8315-468e47f1ebab", diff --git a/data/merged_example.json b/data/merged_example.json new file mode 100644 index 0000000..63414c7 --- /dev/null +++ b/data/merged_example.json @@ -0,0 +1,6605 @@ +{ + "target_molecule_inchikey": "BACODVKOMBXPLL-UHFFFAOYSA-N", + "target_molecule_smiles": "O=C(O)c1cc(-c2ccccc2)cc2cc[nH]c12", + "reaction_steps": 2, + "evidence_routes_success": true, + "predicted_routes_success": true, + "routes": [ + { + "aggregated_yield": 58.84784878828043, + "predicted": false, + "route_index": 1, + "route_status": "Viable Synthesis Route", + "method": "AICP", + "route_node_labels": [ + "RYHBNJHYFVUHQT-UHFFFAOYSA-N", + "YSFZPMNRVJTVIV-UHFFFAOYSA-N", + "FJDQFPXHSGXQBY-UHFFFAOYSA-L", + "HXITXNWTGFUOAU-UHFFFAOYSA-N", + "ASPIRE-6958145032533313838", + "YJVFFLUZDVXJQI-UHFFFAOYSA-L", + "LFQSCWFLJHTTHZ-UHFFFAOYSA-N", + "ASPIRE-2097084335487425141", + "OKKJLVBELUTLKV-UHFFFAOYSA-N", + "BACODVKOMBXPLL-UHFFFAOYSA-N", + "XLYOFNOQVPJJNP-UHFFFAOYSA-N", + "VZYDZTIPNOBVNC-UHFFFAOYSA-N", + "WMFOQBRAJBCJND-UHFFFAOYSA-M", + "OTOSIXGMLYKKOW-UHFFFAOYSA-M", + "PCHJSUWPFVWCPO-UHFFFAOYSA-N", + "AUVSUPMVIZXUOG-UHFFFAOYSA-N", + "ASPIRE-4105087716800423292" + ] + }, + { + "aggregated_yield": 57.61799729751479, + "predicted": false, + "route_index": 2, + "route_status": "Viable Synthesis Route", + "method": "AICP", + "route_node_labels": [ + "RYHBNJHYFVUHQT-UHFFFAOYSA-N", + "YSFZPMNRVJTVIV-UHFFFAOYSA-N", + "NHDIQVFFNDKAQU-UHFFFAOYSA-N", + "FJDQFPXHSGXQBY-UHFFFAOYSA-L", + "HXITXNWTGFUOAU-UHFFFAOYSA-N", + "ASPIRE-6958145032533313838", + "YJVFFLUZDVXJQI-UHFFFAOYSA-L", + "MZRVEZGGRBJDDB-UHFFFAOYSA-N", + "ASPIRE-2672521253083458424", + "BACODVKOMBXPLL-UHFFFAOYSA-N", + "OKKJLVBELUTLKV-UHFFFAOYSA-N", + "XLYOFNOQVPJJNP-UHFFFAOYSA-N", + "VZYDZTIPNOBVNC-UHFFFAOYSA-N", + "OTOSIXGMLYKKOW-UHFFFAOYSA-M", + "VLKZOEOYAKHREP-UHFFFAOYSA-N", + "WMFOQBRAJBCJND-UHFFFAOYSA-M", + "ASPIRE-4105087716800423292" + ] + }, + { + "aggregated_yield": 57.61799729751479, + "predicted": false, + "route_index": 3, + "route_status": "Viable Synthesis Route", + "method": "AICP", + "route_node_labels": [ + "RYHBNJHYFVUHQT-UHFFFAOYSA-N", + "YSFZPMNRVJTVIV-UHFFFAOYSA-N", + "NHDIQVFFNDKAQU-UHFFFAOYSA-N", + "FJDQFPXHSGXQBY-UHFFFAOYSA-L", + "ANUZKYYBDVLEEI-UHFFFAOYSA-N", + "HXITXNWTGFUOAU-UHFFFAOYSA-N", + "ASPIRE-6958145032533313838", + "YJVFFLUZDVXJQI-UHFFFAOYSA-L", + "BACODVKOMBXPLL-UHFFFAOYSA-N", + "OKKJLVBELUTLKV-UHFFFAOYSA-N", + "XLYOFNOQVPJJNP-UHFFFAOYSA-N", + "VZYDZTIPNOBVNC-UHFFFAOYSA-N", + "OTOSIXGMLYKKOW-UHFFFAOYSA-M", + "WMFOQBRAJBCJND-UHFFFAOYSA-M", + "ASPIRE-4105087716800423292", + "ASPIRE-8090828743022637323" + ] + }, + { + "predicted": true, + "source": "ASKCOS v2", + "route_index": 4, + "route_node_labels": [ + "NJSFLYKFAHEEET-UHFFFAOYSA-N", + "287c4669-a6a7-42b4-9cd8-403259dc7e36", + "BACODVKOMBXPLL-UHFFFAOYSA-N" + ] + }, + { + "predicted": true, + "source": "ASKCOS v2", + "route_index": 5, + "route_node_labels": [ + "YVPFHVKOHMYAHB-UHFFFAOYSA-N", + "NTIQTKXSDRUAOC-UHFFFAOYSA-M", + "659dbbdc-9182-49f0-b217-5978e482cd70", + "AAJMEFMGYGSJPA-UHFFFAOYSA-N", + "e2b32b2f-925c-44e6-bd73-4a305d8b0b75", + "BACODVKOMBXPLL-UHFFFAOYSA-N" + ] + }, + { + "predicted": true, + "source": "ASKCOS v2", + "route_index": 6, + "route_node_labels": [ + "SDMOTXWDDFBAMM-UHFFFAOYSA-N", + "HXITXNWTGFUOAU-UHFFFAOYSA-N", + "3d609715-c3d8-4ad1-a5b0-00f49bd8544b", + "VMTPCPGYOUPMEU-UHFFFAOYSA-N", + "a71404ab-ef31-4341-b11a-c1f0338c0666", + "BACODVKOMBXPLL-UHFFFAOYSA-N" + ] + } + ], + "synth_graph": { + "nodes": [ + { + "node_label": "BACODVKOMBXPLL-UHFFFAOYSA-N", + "node_type": "substance", + "uuid": "substance_da2a646a25fc5aa2427dd50c68cc4b86da7fafdd2c912d65e67d2a4db9892a65", + "inchikey": "BACODVKOMBXPLL-UHFFFAOYSA-N", + "canonical_smiles": "O=C(O)c1cc(-c2ccccc2)cc2cc[nH]c12", + "srole": "tm", + "route_assembly_type": { + "is_predicted": false, + "is_evidence": true + }, + "provenance": { + 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"/data/hybrid_routes_example.json" }, + { name: "Merged Routes Example", path: "/data/merged_example.json" }, ]; const ExampleGraphs = () => { diff --git a/ui/src/components/NetworkSearchMenu.jsx b/ui/src/components/NetworkSearchMenu.jsx index 763548a..a564936 100644 --- a/ui/src/components/NetworkSearchMenu.jsx +++ b/ui/src/components/NetworkSearchMenu.jsx @@ -45,7 +45,7 @@ const NetworkSearchMenu = () => { setEvidenceSynthGraph( aicpGraph.synth_graph || aicpGraph.evidence_synth_graph || null ); - setPredictedSynthGraph(aicpGraph.predictive_synth_graph || null); + setPredictedSynthGraph(aicpGraph.predicted_synth_graph || aicpGraph.predictive_synth_graph || null); // Check predicted first, fallback to predictive setRouteOptions(aicpGraph.routes || null); } }, [aicpGraph]); @@ -69,7 +69,7 @@ const NetworkSearchMenu = () => { } else if (evidenceSynthGraph) { onRouteChange("SynthGraph"); } else if (predictedSynthGraph) { - onRouteChange("PredictiveGraph"); + onRouteChange("PredictedGraph"); // Updated from PredictiveGraph } } }, [evidenceSynthGraph, predictedSynthGraph, routeOptions]); @@ -82,7 +82,7 @@ const NetworkSearchMenu = () => { preserveSubgraphIndexRef.current = true; resetReagentOriginalGraph.current = true; setUsePredictedGraph(false); - } else if (value == "PredictiveGraph") { + } else if (value == "PredictedGraph") { // Updated from PredictiveGraph setSubgraphIndex(-2); preserveSubgraphIndexRef.current = true; resetReagentOriginalGraph.current = true; @@ -130,7 +130,7 @@ const NetworkSearchMenu = () => { )} {aicpGraph && predictedSynthGraph && ( - + Predicted Synth Graph )} diff --git a/ui/src/helpers/commonHelpers.js b/ui/src/helpers/commonHelpers.js index c1ee7e3..124424c 100644 --- a/ui/src/helpers/commonHelpers.js +++ b/ui/src/helpers/commonHelpers.js @@ -92,7 +92,7 @@ export const mapGraphDataToCytoscape = (data, routeIndex = 0) => { // Extract evidenceSynthGraph and predictedSynthGraph const evidenceSynthGraph = data.synth_graph || data.evidence_synth_graph || {}; - const predictedSynthGraph = data.predictive_synth_graph || {}; + const predictedSynthGraph = data.predicted_synth_graph || data.predictive_synth_graph || {}; // Check predicted first, fallback to predictive // Extract route_node_labels from the selected subgraph const routes = data.routes; From 3ebdd1bca88b629c2199f868c5af5c5051e98be3 Mon Sep 17 00:00:00 2001 From: Nathan Miller Date: Wed, 21 Jan 2026 15:03:44 -0500 Subject: [PATCH 2/2] predicted route updates --- ui/src/App.js | 2 +- ui/src/components/NetworkSearchMenu.jsx | 42 ++++++++++++++++---- ui/src/helpers/commonHelpers.js | 53 ++++++++++++++++++++----- 3 files changed, 78 insertions(+), 19 deletions(-) diff --git a/ui/src/App.js b/ui/src/App.js index 3658823..14510b0 100644 --- a/ui/src/App.js +++ b/ui/src/App.js @@ -335,7 +335,7 @@ function App() { subgraphIndex < aicpGraph.routes.length ) { let data = aicpGraph; - const mappedData = mapGraphDataToCytoscape(data, subgraphIndex); + const mappedData = mapGraphDataToCytoscape(data, subgraphIndex, usePredictedGraph); updateCytoscapeGraph(mappedData); resetReagentOriginalGraph.current = true; } diff --git a/ui/src/components/NetworkSearchMenu.jsx b/ui/src/components/NetworkSearchMenu.jsx index a564936..0c9614a 100644 --- a/ui/src/components/NetworkSearchMenu.jsx +++ b/ui/src/components/NetworkSearchMenu.jsx @@ -23,6 +23,7 @@ const NetworkSearchMenu = () => { const [selectedRetrievalOption, setSelectedRetrievalOption] = useState( "json" ); + const [primarySynthGraph, setPrimarySynthGraph] = useState(null); const [evidenceSynthGraph, setEvidenceSynthGraph] = useState(null); const [predictedSynthGraph, setPredictedSynthGraph] = useState(null); const [routeOptions, setRouteOptions] = useState(null); @@ -42,10 +43,22 @@ const NetworkSearchMenu = () => { // When aicpGraph changes, update the synth graph states useEffect(() => { if (aicpGraph) { - setEvidenceSynthGraph( - aicpGraph.synth_graph || aicpGraph.evidence_synth_graph || null - ); - setPredictedSynthGraph(aicpGraph.predicted_synth_graph || aicpGraph.predictive_synth_graph || null); // Check predicted first, fallback to predictive + const primary = aicpGraph.synth_graph || null; + const evidence = aicpGraph.evidence_synth_graph || null; + const predicted = aicpGraph.predicted_synth_graph || aicpGraph.predictive_synth_graph || null; + + setPrimarySynthGraph(primary); + + // Only show evidence graph if it exists AND differs from primary synth_graph + // (or if primary doesn't exist) + const showEvidence = evidence && (!primary || JSON.stringify(evidence) !== JSON.stringify(primary)); + setEvidenceSynthGraph(showEvidence ? evidence : null); + + // Only show predicted graph if it exists AND differs from primary synth_graph + // (or if primary doesn't exist) + const showPredicted = predicted && (!primary || JSON.stringify(predicted) !== JSON.stringify(primary)); + setPredictedSynthGraph(showPredicted ? predicted : null); + setRouteOptions(aicpGraph.routes || null); } }, [aicpGraph]); @@ -53,6 +66,7 @@ const NetworkSearchMenu = () => { // Update dropdownDisabled based on the updated state values useEffect(() => { const shouldDisable = + primarySynthGraph == null && evidenceSynthGraph == null && predictedSynthGraph == null && routeOptions == null; @@ -66,23 +80,30 @@ const NetworkSearchMenu = () => { if (routeOptions) { onRouteChange("Route 0"); + } else if (primarySynthGraph) { + onRouteChange("PrimarySynthGraph"); } else if (evidenceSynthGraph) { onRouteChange("SynthGraph"); } else if (predictedSynthGraph) { - onRouteChange("PredictedGraph"); // Updated from PredictiveGraph + onRouteChange("PredictedGraph"); } } - }, [evidenceSynthGraph, predictedSynthGraph, routeOptions]); + }, [primarySynthGraph, evidenceSynthGraph, predictedSynthGraph, routeOptions]); // On route change const onRouteChange = (value) => { setSelectedOption(value); - if (value == "SynthGraph") { + if (value == "PrimarySynthGraph") { + setSubgraphIndex(-3); + preserveSubgraphIndexRef.current = true; + resetReagentOriginalGraph.current = true; + setUsePredictedGraph(false); + } else if (value == "SynthGraph") { setSubgraphIndex(-1); preserveSubgraphIndexRef.current = true; resetReagentOriginalGraph.current = true; setUsePredictedGraph(false); - } else if (value == "PredictedGraph") { // Updated from PredictiveGraph + } else if (value == "PredictedGraph") { setSubgraphIndex(-2); preserveSubgraphIndexRef.current = true; resetReagentOriginalGraph.current = true; @@ -124,6 +145,11 @@ const NetworkSearchMenu = () => { onChange={(value) => onRouteChange(value)} data-testid="SynthesisRouteDropdown" > + {aicpGraph && primarySynthGraph && ( + + Synth Graph + + )} {aicpGraph && evidenceSynthGraph && ( Evidence Synth Graph diff --git a/ui/src/helpers/commonHelpers.js b/ui/src/helpers/commonHelpers.js index 124424c..89e0ce2 100644 --- a/ui/src/helpers/commonHelpers.js +++ b/ui/src/helpers/commonHelpers.js @@ -75,7 +75,7 @@ export const mapGraphData = (data) => { }; }; -export const mapGraphDataToCytoscape = (data, routeIndex = 0) => { +export const mapGraphDataToCytoscape = (data, routeIndex = 0, usePredictedGraph = false) => { const flattenObject = (obj) => { return Object.keys(obj).reduce((acc, key) => { const value = obj[key]; @@ -89,10 +89,10 @@ export const mapGraphDataToCytoscape = (data, routeIndex = 0) => { }, {}); }; - // Extract evidenceSynthGraph and predictedSynthGraph - const evidenceSynthGraph = - data.synth_graph || data.evidence_synth_graph || {}; - const predictedSynthGraph = data.predicted_synth_graph || data.predictive_synth_graph || {}; // Check predicted first, fallback to predictive + // Extract the different graph types + const primarySynthGraph = data.synth_graph || {}; + const evidenceSynthGraph = data.evidence_synth_graph || {}; + const predictedSynthGraph = data.predicted_synth_graph || data.predictive_synth_graph || {}; // Extract route_node_labels from the selected subgraph const routes = data.routes; @@ -105,7 +105,20 @@ export const mapGraphDataToCytoscape = (data, routeIndex = 0) => { const route = routes[routeIndex]; const predictedRoute = route["predicted"] || false; - const graph = predictedRoute ? predictedSynthGraph : evidenceSynthGraph; + // Select the appropriate graph: + // 1. If predicted route, try predictedSynthGraph first, then fall back to primarySynthGraph + // 2. If evidence route, try evidenceSynthGraph first, then fall back to primarySynthGraph + let graph; + if (predictedRoute) { + graph = (predictedSynthGraph.nodes && predictedSynthGraph.nodes.length > 0) + ? predictedSynthGraph + : primarySynthGraph; + } else { + graph = (evidenceSynthGraph.nodes && evidenceSynthGraph.nodes.length > 0) + ? evidenceSynthGraph + : primarySynthGraph; + } + filteredNodes = graph.nodes || []; filteredEdges = graph.edges || []; @@ -123,11 +136,23 @@ export const mapGraphDataToCytoscape = (data, routeIndex = 0) => { routeNodeLabels.has(edge.end_node) ); } else if (routeIndex === -1) { - filteredNodes = evidenceSynthGraph.nodes; - filteredEdges = evidenceSynthGraph.edges; + // Evidence synth graph, fall back to primary if needed + const graph = (evidenceSynthGraph.nodes && evidenceSynthGraph.nodes.length > 0) + ? evidenceSynthGraph + : primarySynthGraph; + filteredNodes = graph.nodes; + filteredEdges = graph.edges; } else if (routeIndex === -2) { - filteredNodes = predictedSynthGraph.nodes; - filteredEdges = predictedSynthGraph.edges; + // Predicted synth graph, fall back to primary if needed + const graph = (predictedSynthGraph.nodes && predictedSynthGraph.nodes.length > 0) + ? predictedSynthGraph + : primarySynthGraph; + filteredNodes = graph.nodes; + filteredEdges = graph.edges; + } else if (routeIndex === -3) { + // Use the primary synth_graph + filteredNodes = primarySynthGraph.nodes; + filteredEdges = primarySynthGraph.edges; } else { throw new Error("Invalid subgraph index."); } @@ -162,6 +187,8 @@ export const mapGraphDataToCytoscape = (data, routeIndex = 0) => { evidence_conditions_info: flatNode.evidence_conditions_info ?? {}, predicted_conditions_info: flatNode.predicted_conditions_info ?? {}, }, + // Add class for predicted target molecules + classes: flatNode.srole === "tm" && usePredictedGraph ? "predicted-tm" : "", }; }); @@ -473,6 +500,12 @@ export const cyStyles = [ "border-width": 3, }, }, + { + selector: 'node.predicted-tm', + style: { + "border-style": "dashed", + }, + }, { selector: 'node[is_predicted="true"]', style: {