Benchling

Benchling Molecule API

A Molecule represents a small molecule chemical compound in Benchling that is imported either as a MolFile or using SMILES (Simplified Molecular Input Line Entry System) notation. Molecules are registry entities that can be registered, searched, and linked to other items. When present, the `canonicalSmiles` field provides a standardized SMILES representation for comparison, while originalSmiles preserves the user-provided SMILES and may be null if SMILES was not provided at creation. Molecules support custom fields via schemas and can be organized in folders and projects.

GitHub OpenAPI
Business capability
Compound & Library Management BC-1500.60

Operations 9

POST /molecule Create Molecule #
GET /molecule/items List Molecule items #
GET /molecule/{molecule_id} Get Molecule by ID #
PATCH /molecule/{molecule_id} Update Molecule #
GET /molecule/{molecule_id}/authors/items List Principal items #
POST /molecule:batch-create Batch create Molecule #
PATCH /molecule:batch-update Batch update Molecule #
POST /molecule:bulk-create Bulk create Molecule #
PATCH /molecule:bulk-update Bulk update Molecule #

Documentation

📖
Documentation
https://docs.benchling.com/docs/developer-platform-overview
📖
APIReference
https://benchling.com/api/v3/reference
📖
Authentication
https://raw.githubusercontent.com/api-evangelist/benchling/refs/heads/main/authentication/benchling-authentication.yml
📖
RateLimits
https://raw.githubusercontent.com/api-evangelist/benchling/refs/heads/main/rate-limits/benchling-rate-limits.yml

Specifications

⚙
OpenAPI
https://raw.githubusercontent.com/api-evangelist/benchling/refs/heads/main/openapi/benchling-molecule-api-openapi.yml

Other Resources

🔗
OpenAPIRemote
https://benchling.com/api/v3/openapi.yaml
🔗
OAuthScopes
https://raw.githubusercontent.com/api-evangelist/benchling/refs/heads/main/scopes/benchling-scopes.yml
🔗
Conventions
https://raw.githubusercontent.com/api-evangelist/benchling/refs/heads/main/conventions/benchling-conventions.yml
🔗
ErrorCatalog
https://raw.githubusercontent.com/api-evangelist/benchling/refs/heads/main/errors/benchling-problem-types.yml
🔗
DataModel
https://raw.githubusercontent.com/api-evangelist/benchling/refs/heads/main/data-model/benchling-data-model.yml
🔗
Webhooks
https://raw.githubusercontent.com/api-evangelist/benchling/refs/heads/main/asyncapi/benchling-webhooks.yml
🔗
Lifecycle
https://raw.githubusercontent.com/api-evangelist/benchling/refs/heads/main/lifecycle/benchling-lifecycle.yml
🔗
ChangeLog
https://raw.githubusercontent.com/api-evangelist/benchling/refs/heads/main/changelog/benchling-changelog.yml
🔗
StabilityPolicy
https://docs.benchling.com/docs/stability-guidelines
🔗
SDKs
https://raw.githubusercontent.com/api-evangelist/benchling/refs/heads/main/packages/benchling-packages.yml

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OpenAPI Specification

benchling-molecule-api-openapi.yml Raw ↑ 
openapi: 3.2.0
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling Molecule API
  version: 2.0.0
  description: 'A Molecule represents a small molecule chemical compound in Benchling that is imported either as a MolFile or

    using SMILES (Simplified Molecular Input Line Entry System) notation.'
servers:
- url: /api/v3
security:
- oAuth: []
- basicApiKeyAuth: []
tags:


# --- truncated at 32 KB (63 KB total) ---
# Full source: https://raw.githubusercontent.com/api-evangelist/benchling/refs/heads/main/openapi/benchling-molecule-api-openapi.yml