---
title: RXNFP troubleshooting
description: 'Resolve reaction SMILES parsing failures and similarity-search issues.'
tags:
  - rxnfp
  - troubleshooting
---

This page helps you diagnose reaction SMILES parsing failures, unexpectedly similar fingerprints, and empty similarity-search results.

## RXNFP troubleshooting

## Invalid reaction SMILES

**Symptom**: a reaction in your batch has `is_valid: false` with a parsing error.

**Fixes**:

- Ensure the reaction contains `>>` separating reactants from products.
- Validate each component as a valid SMILES string.
- Remove whitespace and newlines from the SMILES.
- Check for balanced parentheses and ring closures.
- A failed reaction doesn't fail the whole batch — the other reactions in the same call still return fingerprints; fix or drop the failed row and resubmit if you need it.

## Fingerprints look too similar

**Symptom**: cosine similarity between reactions you'd expect to be unrelated comes back high.

**Causes**:

- **Very short SMILES**: simple reactions with few atoms produce sparse transformer representations that overlap more than expected.
- **Same functional groups**: reactions sharing major functional groups will have partial fingerprint overlap even when the transformation differs.
- There's no alternative model to switch to — the fingerprint is always generated by the same fixed RXNBERT model, so a similarity result you don't trust needs to be checked against [Reaction Classifier](/docs/reaction-classifier)'s named classification instead of a different RXNFP setting.

## Similarity search returns no results

**Symptom**: `similar_reactions` comes back empty.

**Fixes**:

- Lower `min_similarity` — the default (0.7) can exclude everything for a genuinely novel transformation.
- Raise `top_k` if you suspect matches exist just below the current cutoff.
- Remember similarity search only matches against the platform's reference index (built from ORDerly reaction data); a transformation with no close analog there will legitimately return few or no matches.

## Query reaction fails to fingerprint

**Symptom**: the similarity-search job fails before returning any matches.

**Fix**: the query reaction SMILES has the same validity requirements as fingerprinting — confirm it parses on its own with a plain fingerprint call first, then retry the similarity search.

## Getting help

If issues persist:

1. Check the job logs for the specific error message.
2. Validate your reaction SMILES format.
3. Describe the issue to Ivy.

## Read next