lucy-ng:dereplicate

Dereplication only - match observed 13C shifts against reference databases to identify known compounds.

Purpose

This skill performs ONLY dereplication (database matching). It does NOT proceed to full structure elucidation. Use this when you want to:

• •Quickly check if a compound is already known
• •Identify a natural product from a database
• •Get candidate matches before deciding whether full CASE is needed

Domain Knowledge: For dereplication score interpretation and ranking thresholds, see skill/SKILL.md Section 4 (Dereplication).

Prerequisites

lucy --version || pip install lucy-ng

Database: lucy-ng-derep.db

The SQLite compound database lucy-ng-derep.db contains 928K compounds:

• •COCONUT: 895,099 natural products with predicted 13C shifts
• •NMRShiftDB: 33,344 compounds with experimental 13C shifts
• •111,493 unique molecular formulas indexed for fast lookup

The CLI automatically discovers the database by searching:

1. •LUCY_DATABASE environment variable
2. •data/reference/lucy-ng-derep.db (project location)
3. •Common paths (~/.lucy/, ~/lucy-ng/, ~/.local/share/lucy-ng/)
4. •macOS Spotlight (mdfind) for fast discovery

If not found, download with:

lucy database download

Workflow

Step 1: Identify Available Data

Check what NMR experiments are available:

# List experiments and identify 13C spectrum
for dir in */; do
    if [ -f "$dir/acqus" ]; then
        nuc=$(grep "##\$NUC1=" "$dir/acqus" | head -1)
        echo "Experiment $dir: $nuc"
    fi
done

Dereplication requires:

• •13C spectrum (essential) - either binary data or peak list
• •Molecular formula (essential) - from user (simulating HRMS)

Step 2: Request Molecular Formula

Always ask the user for the molecular formula. Do not extract from metadata.

"Please provide the molecular formula for this compound (typically from HRMS)."

Step 3: Run Dereplication

From Bruker spectrum (preferred)

lucy dereplicate c13 <bruker_13c_path> <formula> -n 10

The CLI automatically discovers and uses lucy-ng-derep.db.

From peak list (Python API)

from lucy_ng.database import DatabaseQueryService
from lucy_ng.dereplication import DereplicationService

shifts = [187.81, 152.55, 135.73, 123.41, 120.68, 120.09, 118.99, 113.45]

# db_path auto-discovered or specify explicitly
with DatabaseQueryService(db_path) as query:
    service = DereplicationService(query)
    result = service.dereplicate_from_shifts(shifts, "C16H10N2O2", top_n=10)

    for match in result.top_matches:
        print(f"{match.entry.name}: score={match.score:.3f}")

Step 4: Interpret Results

For dereplication score interpretation thresholds and recommendations, see skill/SKILL.md Section 4 (Dereplication).

Step 5: Report Results

For strong/possible matches:

## Dereplication Results

**Molecular Formula:** C16H10N2O2
**Database:** lucy-ng-derep.db (928K compounds)

### Top Matches

| Rank | Compound | Score | Avg Deviation |
|------|----------|-------|---------------|
| 1 | [Name] | 0.XX | X.X ppm |
| 2 | [Name] | 0.XX | X.X ppm |

### Assessment

[Strong/Possible/Weak/No] match found.

**Top candidate:** [Name]
**Confidence:** [High/Medium/Low]
**SMILES:** [if available]

### Recommendation

[Either "Compound likely identified as X" or "Consider full CASE for confirmation"]

For no matches:

## Dereplication Results

**Molecular Formula:** C16H10N2O2
**Database:** lucy-ng-derep.db (928K compounds)

No strong matches found (best score: 0.XX)

This suggests:
1. Novel compound not in database
2. Known compound with different stereochemistry
3. Compound not yet added to reference database

### Recommendation

Proceed to full CASE: `/lucy-ng:CASE`

Important Notes

1. •This skill does NOT perform full structure elucidation
2. •Molecular formula must come from user, not metadata
3. •Symmetry affects matching - if formula has 16 carbons but only 8 signals, the compound has symmetry
4. •Database is ~100x faster than SD file scanning due to formula-based indexing

Quick Reference

# Quick dereplication with CLI (auto-discovers database)
lucy dereplicate c13 ./2 C16H10N2O2 -n 10

# Check database status
lucy database info lucy-ng-derep.db

# Download database if missing
lucy database download