chore(validation-output): add gt3 fragment export

Track refreshed validation outputs and add a filtered fragment
library export that retains only side-chain fragments with more
than 3 heavy atoms.

validation_output/README.md

@@ -8,6 +8,7 @@ This directory contains validation results for MacrolactoneDB 12-20 membered rin
 validation_output/
 ├── README.md                    # This file
 ├── fragments.db                 # SQLite database with all data
+├── fragment_library.csv         # Unified fragment library export
 ├── summary.csv                  # Summary of all processed molecules
 ├── summary_statistics.json      # Statistical summary
 │
@@ -37,6 +38,7 @@ validation_output/
 - **parent_molecules**: Original molecule information
 - **ring_numberings**: Ring atom numbering details
 - **side_chain_fragments**: Fragmentation results with isotope tags
+- **fragment_library_entries**: Unified fragment library rows for downstream design
 - **validation_results**: Manual validation records
 
 ### Key Fields
@@ -44,6 +46,8 @@ validation_output/
 - `classification`: standard_macrolactone | non_standard_macrocycle | not_macrolactone
 - `dummy_isotope`: Cleavage position stored as isotope value for reconstruction
 - `cleavage_position`: Position on ring where side chain was attached
+- `has_dummy_atom`: Whether the fragment contains a dummy atom for splicing
+- `dummy_atom_count`: Number of dummy atoms in the fragment
 
 ## Ring Numbering Convention
 
@@ -61,13 +65,21 @@ Fragments use isotope values to mark cleavage position:
 
 ### summary.csv
 
-- `source_id`: Original molecule ID from MacrolactoneDB
+- `ml_id`: MacrolactoneDB unique ID (e.g., ML00000001)
+- `chembl_id`: Original CHEMBL ID (if available)
 - `classification`: Classification result
 - `ring_size`: Detected ring size (12-20)
 - `num_sidechains`: Number of side chains detected
 - `cleavage_positions`: JSON array of cleavage positions
 - `processing_status`: pending | success | failed | skipped
 
+### fragment_library.csv
+
+- `source_type`: validation_extract | supplemental (reserved)
+- `has_dummy_atom`: Whether the fragment contains a dummy atom
+- `dummy_atom_count`: Number of dummy atoms
+- `splice_ready`: Whether the fragment is directly compatible with single-anchor splicing
+
 ## Querying the Database
 
 ```bash

validation_output/summary_statistics.json

@@ -1,24 +1,23 @@
 {
-  "total_molecules": 1097,
+  "total_molecules": 11036,
   "by_classification": {
-    "non_standard_macrocycle": 617,
-    "standard_macrolactone": 459,
-    "not_macrolactone": 21
+    "non_standard_macrocycle": 6336,
+    "standard_macrolactone": 4482,
+    "not_macrolactone": 218
   },
   "by_ring_size": {
-    "14.0": 301,
-    "16.0": 187,
-    "15.0": 161,
-    "12.0": 141,
-    "19.0": 85,
-    "18.0": 80,
-    "13.0": 67,
-    "20.0": 24,
-    "17.0": 19
+    "14.0": 3017,
+    "16.0": 1879,
+    "15.0": 1613,
+    "12.0": 1419,
+    "19.0": 855,
+    "18.0": 809,
+    "13.0": 679,
+    "20.0": 243,
+    "17.0": 196
   },
   "by_status": {
-    "skipped": 638,
-    "success": 367,
-    "failed": 92
+    "skipped": 6554,
+    "success": 4482
   }
 }