lingyuzeng
f6bf9e85a3
Track refreshed validation outputs and add a filtered fragment library export that retains only side-chain fragments with more than 3 heavy atoms.
98 lines
3.5 KiB
Markdown
98 lines
3.5 KiB
Markdown
# MacrolactoneDB Validation Output
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This directory contains validation results for MacrolactoneDB 12-20 membered rings.
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## Directory Structure
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```
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validation_output/
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├── README.md # This file
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├── fragments.db # SQLite database with all data
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├── fragment_library.csv # Unified fragment library export
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├── summary.csv # Summary of all processed molecules
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├── summary_statistics.json # Statistical summary
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│
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├── ring_size_12/ # 12-membered rings
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├── ring_size_13/ # 13-membered rings
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...
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└── ring_size_20/ # 20-membered rings
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├── molecules.csv # Molecules in this ring size
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├── standard/ # Standard macrolactones
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│ ├── numbered/ # Numbered ring images
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│ │ └── {id}_numbered.png
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│ └── sidechains/ # Fragment images
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│ └── {id}/
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│ └── {id}_frag_{n}_pos{pos}.png
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├── non_standard/ # Non-standard macrocycles
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│ └── original/
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│ └── {id}_original.png
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└── rejected/ # Not macrolactones
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└── original/
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└── {id}_original.png
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```
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## Database Schema
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### Tables
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- **parent_molecules**: Original molecule information
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- **ring_numberings**: Ring atom numbering details
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- **side_chain_fragments**: Fragmentation results with isotope tags
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- **fragment_library_entries**: Unified fragment library rows for downstream design
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- **validation_results**: Manual validation records
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### Key Fields
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- `classification`: standard_macrolactone | non_standard_macrocycle | not_macrolactone
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- `dummy_isotope`: Cleavage position stored as isotope value for reconstruction
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- `cleavage_position`: Position on ring where side chain was attached
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- `has_dummy_atom`: Whether the fragment contains a dummy atom for splicing
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- `dummy_atom_count`: Number of dummy atoms in the fragment
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## Ring Numbering Convention
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1. Position 1 = Lactone carbonyl carbon (C=O)
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2. Position 2 = Ester oxygen (-O-)
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3. Positions 3-N = Sequential around ring
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## Isotope Tagging
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Fragments use isotope values to mark cleavage position:
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- `[5*]CCO` = Fragment from position 5, dummy atom has isotope=5
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- This enables precise reconstruction during reassembly
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## CSV Columns
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### summary.csv
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- `ml_id`: MacrolactoneDB unique ID (e.g., ML00000001)
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- `chembl_id`: Original CHEMBL ID (if available)
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- `classification`: Classification result
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- `ring_size`: Detected ring size (12-20)
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- `num_sidechains`: Number of side chains detected
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- `cleavage_positions`: JSON array of cleavage positions
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- `processing_status`: pending | success | failed | skipped
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### fragment_library.csv
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- `source_type`: validation_extract | supplemental (reserved)
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- `has_dummy_atom`: Whether the fragment contains a dummy atom
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- `dummy_atom_count`: Number of dummy atoms
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- `splice_ready`: Whether the fragment is directly compatible with single-anchor splicing
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## Querying the Database
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```bash
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# List tables
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sqlite3 fragments.db ".tables"
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# Get standard macrolactones with fragments
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sqlite3 fragments.db "SELECT * FROM parent_molecules WHERE classification='standard_macrolactone' LIMIT 5;"
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# Get fragments for a specific molecule
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sqlite3 fragments.db "SELECT * FROM side_chain_fragments WHERE parent_id=1;"
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# Count by ring size
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sqlite3 fragments.db "SELECT ring_size, COUNT(*) FROM parent_molecules GROUP BY ring_size;"
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```
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