---
title: AiZynthFinder outputs & interpretation
description: 'Read AiZynthFinder routes.json and routes.csv — route_id, score, length, is_purchasable, template_ids, starting_materials — and what a red tree node means.'
---

AiZynthFinder returns ranked retrosynthetic routes as JSON and CSV, each with a score, step count, and a purchasability flag showing whether every starting material is in your selected stocks. Filter for purchasable, high-scoring routes first — those tell you which candidates are worth advancing to procurement (a ZINC purchasability check) or a Compound Passport synthesis section.

## Output artifacts

AiZynthFinder generates multiple output files containing route information, scoring data, and metadata. All outputs are available for download from the job page or via API.

## Primary artifacts

### Routes JSON (`routes.json`)
**Format**: Hierarchical JSON structure containing complete retrosynthetic trees
**Contents**:
- Full route trees with intermediates and reactions
- Template IDs and probabilities for each step
- Stock availability information for starting materials
- Route metadata (scores, lengths, purchasability)

**Structure**:
```json
{
  "routes": [
    {
      "route_id": "route_001",
      "score": 0.85,
      "length": 3,
      "is_purchasable": true,
      "tree": {
        "smiles": "CCc1ccc(cc1)C(C)C(=O)O",
        "children": [
          {
            "smiles": "CCc1ccc(cc1)C(C)C(=O)Cl",
            "template_id": "ester_hydrolysis_rev",
            "template_prob": 0.92,
            "children": [...]
          }
        ]
      }
    }
  ]
}
```

### Routes CSV (`routes.csv`)
**Format**: Tabular format with one row per route
**Columns**:
- `route_id`: Unique identifier for the route
- `score`: Overall route score (0.0-1.0)
- `length`: Number of reaction steps
- `is_purchasable`: Boolean indicating if all starting materials are available
- `template_ids`: Comma-separated list of template IDs used
- `target_smiles`: Target molecule SMILES
- `starting_materials`: SMILES of required starting materials

**Example**:
```
route_id,score,length,is_purchasable,template_ids,target_smiles,starting_materials
route_001,0.85,3,true,ester_hydrolysis_rev,coupling,Cc1ccc(cc1)C(C)C(=O)O,Cc1ccc(cc1)C(C)C(=O)Cl.CO
route_002,0.72,4,false,suzuki_coupling_rev,ester_hydrolysis_rev,Cc1ccc(cc1)C(C)C(=O)O,Cc1ccc(cc1)B.O=C(Cl)C(C)C,CCO
```

### Route analysis JSON (`analysis.json`)
**Format**: Detailed analysis of route characteristics
**Contents**:
- Route complexity metrics
- Starting material availability breakdown
- Template usage statistics
- Stock coverage analysis

## Metadata and logs

### Job metadata (`metadata.json`)
**Format**: Complete configuration and runtime information
**Contents**:
- Input parameters (SMILES, stocks, policies, filters)
- Model versions and policy information
- Search statistics (nodes explored, time taken)
- Stock database versions
- Template database information

**Example**:
```json
{
  "input": {
    "smiles": "CCc1ccc(cc1)C(C)C(=O)O",
    "stocks": ["zinc", "emolecules"],
    "policy": ["uspto_50k"],
    "filters": ["price"]
  },
  "versions": {
    "aizynthfinder": "2.3.1",
    "policy": "uspto_50k_v1.2",
    "templates": "uspto_2023_q4"
  },
  "runtime": {
    "duration_seconds": 245.3,
    "nodes_explored": 15420,
    "routes_found": 67
  }
}
```

### Search logs (`search.log`)
**Format**: Detailed execution log with timestamps
**Contents**:
- Search progress and milestones
- Template application attempts
- Stock availability checks
- Performance metrics and warnings

## Key metrics and fields

### Route scoring
- **Overall score**: Composite metric (0.0-1.0) balancing:
  - Template probabilities (how likely each reaction is)
  - Route length (shorter routes preferred)
  - Stock availability (purchasable materials boost score)
- **Score interpretation**:
  - > 0.8: High-confidence routes
  - 0.6-0.8: Moderate confidence
  - < 0.6: Low confidence, may need manual validation

### State score vs. route score
- **State score**: Measures search tree node quality during exploration (used internally by MCTS/search algorithms)
- **Route score**: Final composite metric for completed routes, combining template probabilities across all steps
- **Tree search metrics**: The underlying Monte Carlo Tree Search (or alternative algorithms like Nested MCTS or Greedy Best First) use state scores to guide exploration

### Success rate context
In published benchmarks, AiZynthFinder achieves 80-86% success rates for finding at least one route with all starting materials available in commercial stock databases. Routes with higher scores and shorter step counts generally correlate with experimental success.

### Purchasability assessment
- **is_purchasable**: Boolean flag indicating complete stock coverage
- **Stock checking**: Each starting material verified against specified stock sources
- **Partial availability**: Routes may be partially purchasable if some materials are missing

### Route complexity
- **num_steps** (length): Number of reaction steps required
- **Template diversity**: Number of different reaction types used
- **Intermediate complexity**: Molecular weight and synthetic complexity of intermediates

### Template information
- **template_ids**: Machine-readable identifiers for applied reaction templates
- **Template metadata**: Reaction class, substrate scope, literature references
- **Probability scores**: Confidence in template applicability

## Interpreting results

## Route prioritization

1. **Filter for purchasability**: Focus on `is_purchasable: true` routes first
2. **Sort by score**: Higher scores indicate more reliable routes
3. **Consider length**: Shorter routes are generally preferred for simplicity
4. **Review intermediates**: Check for synthetic feasibility of key intermediates

## Quality assessment

### High-quality routes
- Score &gt; 0.8 and purchasable
- 2-4 reaction steps
- Common reaction types (esterification, coupling, etc.)
- Commercially available starting materials

### Moderate-quality routes
- Score 0.6-0.8 or partially purchasable
- May require custom synthesis of one intermediate
- Uncommon reactions but literature precedent exists

### Low-quality routes
- Score &lt; 0.6 or non-purchasable
- Very long sequences (>6 steps)
- Novel reactions without clear precedent
- Require rare or expensive starting materials

## Common patterns to watch for

### Realistic disconnections
- **Good**: Breaking at functional groups with clear synthetic precedent
- **Questionable**: Breaking stable rings or introducing unusual functionality
- **Poor**: Routes requiring protection/deprotection of every functional group

### Starting material quality
- **Good**: Common building blocks, catalog compounds, natural products
- **Questionable**: Complex intermediates requiring multi-step synthesis
- **Poor**: Hypothetical compounds not available commercially

## Export and sharing

## Download options
- **Individual files**: Download specific artifacts from job page
- **Bulk download**: ZIP archive containing all outputs
- **API access**: The finished job record from `GET /api/v1/jobs/{jobId}` lists each artifact

## Sharing for collaboration
- **Job links**: Include complete job URL in ELN entries
- **Configuration export**: Share exact parameters used for reproducibility
- **Route visualization**: Export routes as images or interactive viewers

## Integration with other tools
- **CRO packages**: Include purchasable routes with cost estimates
- **ELN integration**: Embed route information in electronic lab notebooks
- **Literature search**: Use intermediate SMILES for patent/ literature checks

## Troubleshooting outputs

## Empty results
- **Cause**: No valid routes found within search constraints
- **Solutions**:
  - Expand stock sources
  - Use less restrictive policies
  - Increase search depth/limits
  - Check input SMILES validity

## All routes non-purchasable
- **Cause**: Target requires intermediates not in selected stocks
- **Solutions**:
  - Add more comprehensive stock sources
  - Consider custom synthesis of key intermediates
  - Review if target molecule is synthetically accessible

## Unexpectedly low scores
- **Cause**: Molecule outside training data scope or unusual chemistry
- **Solutions**:
  - Try different policies
  - Manually validate high-scoring routes
  - Consider alternative retrosynthesis tools

## Performance issues
- **Cause**: Large search spaces or complex molecules
- **Solutions**:
  - Reduce search breadth
  - Use faster policies
  - Increase computational resources

## Canvas Visualization

When an AiZynthFinder job completes, a result card appears on the canvas.

- **Visualization**: Interactive retrosynthetic tree diagram

### Tier 2 Metrics

- Number of routes found
- Best route score (0-1, closer to 1.0 = more feasible)
- Step count
- Complexity score
- Building block availability

### Interpreting the Tree

- **Nodes**: Molecules (target -> intermediates -> building blocks)
- **Green nodes**: Building blocks that are commercially available (in stock)
- **Yellow nodes**: Available to order from vendors
- **Red nodes**: Not commercially available -- may need custom synthesis
- **Edges**: Reaction steps connecting molecules

## Read next