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.gitattributes

@@ -102,3 +102,8 @@ checkpoints/retrochimera_template/uspto_full/aux/template_lib.json filter=lfs di
 checkpoints/retrochimera_transformer/uspto_full/benchmarks/native/tgt-test.txt filter=lfs diff=lfs merge=lfs -text
 checkpoints/retrochimera_transformer/uspto_full/benchmarks/default_test.jsonl filter=lfs diff=lfs merge=lfs -text
 checkpoints/retrochimera_transformer/uspto_full/benchmarks/native/src-test.txt filter=lfs diff=lfs merge=lfs -text
+paroutes2/single_step/reference_route_reactions.jsonl filter=lfs diff=lfs merge=lfs -text
+paroutes2/route_benchmarks/n1/reference_routes.json filter=lfs diff=lfs merge=lfs -text
+paroutes2/route_benchmarks/n5/reference_routes.json filter=lfs diff=lfs merge=lfs -text
+paroutes2/single_step/native/selected_reactions.csv filter=lfs diff=lfs merge=lfs -text
+paroutes2/single_step/selected_reactions_full.jsonl filter=lfs diff=lfs merge=lfs -text

paroutes2/SHA256SUMS

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paroutes2/manifest.json

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+  "bundle_type": "benchmark_bundle",
+  "format_version": 1,
+  "generated_at": "1970-01-01T00:00:00+00:00",
+  "route_benchmarks": [
+    {
+      "benchmark_id": "paroutes2_n1",
+      "benchmark_variant": "n1",
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+      "num_stock": 13432,
+      "num_targets": 10000,
+      "reference_reaction_hashes_path": "shared/ref_routes_reaction_hashes.txt",
+      "reference_routes_path": "route_benchmarks/n1/reference_routes.json",
+      "stock_path": "route_benchmarks/n1/stock.txt",
+      "targets_path": "route_benchmarks/n1/targets.txt"
+    },
+    {
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+      "benchmark_variant": "n5",
+      "format": "route_tree_json",
+      "metadata_path": "route_benchmarks/n5/metadata.json",
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+      "num_stock": 13328,
+      "num_targets": 10000,
+      "reference_reaction_hashes_path": "shared/ref_routes_reaction_hashes.txt",
+      "reference_routes_path": "route_benchmarks/n5/reference_routes.json",
+      "stock_path": "route_benchmarks/n5/stock.txt",
+      "targets_path": "route_benchmarks/n5/targets.txt"
+    }
+  ],
+  "single_step_datasets": [
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+      "default": true,
+      "format": "jsonl",
+      "metadata_path": "single_step/reference_route_reactions.metadata.json",
+      "native_source_paths": [
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+      ],
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+      "path": "single_step/reference_route_reactions.jsonl",
+      "split": "test",
+      "usage": [
+        "single_step_benchmark",
+        "route_reference_subset"
+      ]
+    },
+    {
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+      "default": false,
+      "format": "jsonl",
+      "metadata_path": "single_step/selected_reactions_full.metadata.json",
+      "native_source_paths": [
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+      ],
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+      "path": "single_step/selected_reactions_full.jsonl",
+      "split": "test",
+      "usage": [
+        "single_step_corpus",
+        "fine_tuning_source"
+      ]
+    }
+  ],
+  "source_dataset": {
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+    "public_record": "7341155",
+    "source_root": "/mnt/HDD/syntheseus-bundle-builder/datasets/paroutes_public_data",
+    "source_urls_path": "shared/urls.txt"
+  }
+}

paroutes2/provenance.json

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+{
+  "builder_module": "bundle_builder.paroutes",
+  "bundle_id": "paroutes2",
+  "generated_at": "1970-01-01T00:00:00+00:00",
+  "source_dataset": {
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+    "local_source_root": "/mnt/HDD/syntheseus-bundle-builder/datasets/paroutes_public_data",
+    "public_record": "7341155",
+    "source_files": [
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+      },
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+        "source_url": "https://zenodo.org/records/7341155/files/ref_routes_n1.json?download=1"
+      },
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+        "included_in_bundle": true,
+        "source_url": "https://zenodo.org/records/7341155/files/ref_routes_n5.json?download=1"
+      },
+      {
+        "bundle_paths": [
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+        ],
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+        "included_in_bundle": true,
+        "source_url": "https://zenodo.org/records/7341155/files/ref_routes_reaction_hashes.txt?download=1"
+      },
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+        ],
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+        "source_url": "https://zenodo.org/records/7341155/files/selected_reactions.csv?download=1"
+      },
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+      },
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+      },
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+        "source_url": "https://zenodo.org/records/7341155/files/stock_n5.txt?download=1"
+      },
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+        "source_url": "https://zenodo.org/records/7341155/files/targets_n5.txt?download=1"
+      },
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+      },
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+      },
+      {
+        "bundle_paths": [],
+        "filename": "uspto_ringbreaker_template_library.csv",
+        "included_in_bundle": false,
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+      },
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+        "source_url": "https://zenodo.org/records/7341155/files/uspto_unique_templates.csv.gz?download=1"
+      }
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+  },
+  "validation": {
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+      "path": "shared/ref_routes_reaction_hashes.txt"
+    },
+    "route_benchmarks": {
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+        "num_stock": 13432,
+        "num_targets": 10000,
+        "route_root_targets_match": true
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+        "num_stock": 13328,
+        "num_targets": 10000,
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+    "single_step": {
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+      "reference_route_hashes": 56657,
+      "reference_route_rows": 56657,
+      "selected_reactions_rows": 1198554
+    }
+  }
+}

paroutes2/route_benchmarks/n1/metadata.json

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+{
+  "benchmark_id": "paroutes2_n1",
+  "benchmark_variant": "n1",
+  "built_at": "1970-01-01T00:00:00+00:00",
+  "format": "route_tree_json",
+  "notes": [
+    "Targets are aligned 1:1 and in-order with the top-level route roots in reference_routes.json.",
+    "reference_reaction_hashes_path points to the shared reaction-hash list spanning the bundled PaRoutes reference routes."
+  ],
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+  "num_stock": 13432,
+  "num_targets": 10000,
+  "reaction_node_metadata_keys": [
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+    "RingBreaker",
+    "reaction_hash",
+    "rsmi",
+    "smiles"
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+  "reference_reaction_hashes_path": "shared/ref_routes_reaction_hashes.txt",
+  "reference_route_root_keys": [
+    "children",
+    "in_stock",
+    "smiles",
+    "type"
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+  "route_root_targets_match": true,
+  "source_files": {
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+      "source_url": "https://zenodo.org/records/7341155/files/ref_routes_n1.json?download=1"
+    },
+    "stock": {
+      "path": "route_benchmarks/n1/stock.txt",
+      "source_url": "https://zenodo.org/records/7341155/files/stock_n1.txt?download=1"
+    },
+    "targets": {
+      "path": "route_benchmarks/n1/targets.txt",
+      "source_url": "https://zenodo.org/records/7341155/files/targets_n1.txt?download=1"
+    }
+  },
+  "stock_input_format": "smiles_txt",
+  "targets_input_format": "smiles_txt"
+}

paroutes2/route_benchmarks/n1/reference_routes.json

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paroutes2/route_benchmarks/n5/metadata.json

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+{
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+  "benchmark_variant": "n5",
+  "built_at": "1970-01-01T00:00:00+00:00",
+  "format": "route_tree_json",
+  "notes": [
+    "Targets are aligned 1:1 and in-order with the top-level route roots in reference_routes.json.",
+    "reference_reaction_hashes_path points to the shared reaction-hash list spanning the bundled PaRoutes reference routes."
+  ],
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+  "num_stock": 13328,
+  "num_targets": 10000,
+  "reaction_node_metadata_keys": [
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+    "RingBreaker",
+    "reaction_hash",
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+  "reference_route_root_keys": [
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+    "in_stock",
+    "smiles",
+    "type"
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+  "route_root_targets_match": true,
+  "source_files": {
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+    },
+    "stock": {
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+      "source_url": "https://zenodo.org/records/7341155/files/stock_n5.txt?download=1"
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+      "source_url": "https://zenodo.org/records/7341155/files/targets_n5.txt?download=1"
+    }
+  },
+  "stock_input_format": "smiles_txt",
+  "targets_input_format": "smiles_txt"
+}

paroutes2/route_benchmarks/n5/reference_routes.json

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paroutes2/shared/urls.txt

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+https://zenodo.org/records/7341155/files/ref_routes_n1.json?download=1
+https://zenodo.org/records/7341155/files/ref_routes_n5.json?download=1
+https://zenodo.org/records/7341155/files/ref_routes_reaction_hashes.txt?download=1
+https://zenodo.org/records/7341155/files/selected_reactions.csv?download=1
+https://zenodo.org/records/7341155/files/selected_reactions_all.csv?download=1
+https://zenodo.org/records/7341155/files/stock_n1.txt?download=1
+https://zenodo.org/records/7341155/files/stock_n5.txt?download=1
+https://zenodo.org/records/7341155/files/targets_n1.txt?download=1
+https://zenodo.org/records/7341155/files/targets_n5.txt?download=1
+https://zenodo.org/records/7341155/files/uspto_keras_model.hdf5?download=1
+https://zenodo.org/records/7341155/files/uspto_lookup.json?download=1
+https://zenodo.org/records/7341155/files/uspto_ringbreaker_keras_model.hdf5?download=1
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+https://zenodo.org/records/7341155/files/uspto_template_library.csv?download=1
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paroutes2/single_step/native/selected_reactions.csv

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+size 582648364

paroutes2/single_step/reference_route_reactions.jsonl

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+size 78882207

paroutes2/single_step/reference_route_reactions.metadata.json

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+{
+  "built_at": "1970-01-01T00:00:00+00:00",
+  "dataset_id": "paroutes2_reference_route_reactions",
+  "format": "jsonl",
+  "native_input_format": "tab_delimited_reactants_reagents_product_rows",
+  "native_source": {
+    "path": "single_step/native/selected_reactions.csv",
+    "source_url": "https://zenodo.org/records/7341155/files/selected_reactions.csv?download=1"
+  },
+  "notes": [
+    "Records are normalized from selected_reactions.csv into syntheseus-compatible JSONL with product and expected_reactants fields.",
+    "reaction_smiles removes reagents to match current single-step wrapper inputs, while reaction_smiles_with_reagents preserves the original PaRoutes row.",
+    "This subset contains exactly the reactions referenced by ref_routes_reaction_hashes.txt and is the default single-step benchmark view in this bundle."
+  ],
+  "num_examples": 56657,
+  "record_fields": [
+    "product",
+    "expected_reactants",
+    "reaction_smiles",
+    "reaction_smiles_with_reagents",
+    "reagents",
+    "reaction_hash",
+    "classification",
+    "ringbreaker",
+    "source_row",
+    "route_reference_reaction"
+  ],
+  "route_reference_hashes_complete": true,
+  "route_reference_hashes_path": "shared/ref_routes_reaction_hashes.txt",
+  "split": "test"
+}

paroutes2/single_step/selected_reactions_full.jsonl

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paroutes2/single_step/selected_reactions_full.metadata.json

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+{
+  "built_at": "1970-01-01T00:00:00+00:00",
+  "dataset_id": "paroutes2_selected_reactions_full",
+  "format": "jsonl",
+  "native_input_format": "tab_delimited_reactants_reagents_product_rows",
+  "native_source": {
+    "path": "single_step/native/selected_reactions.csv",
+    "source_url": "https://zenodo.org/records/7341155/files/selected_reactions.csv?download=1"
+  },
+  "notes": [
+    "Records are normalized from selected_reactions.csv into syntheseus-compatible JSONL with product and expected_reactants fields.",
+    "reaction_smiles removes reagents to match current single-step wrapper inputs, while reaction_smiles_with_reagents preserves the original PaRoutes row.",
+    "This full reaction table can be used as a broad single-step evaluation corpus or as a starting point for separate fine-tuning workflows."
+  ],
+  "num_examples": 1198554,
+  "record_fields": [
+    "product",
+    "expected_reactants",
+    "reaction_smiles",
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+    "reagents",
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+    "classification",
+    "ringbreaker",
+    "source_row",
+    "route_reference_reaction"
+  ],
+  "route_reference_hashes_path": "shared/ref_routes_reaction_hashes.txt",
+  "route_reference_num_examples": 56657,
+  "split": "test"
+}