Overview
The Algorithmic Building Block Survey tool automates the process of sourcing commercially available starting materials for chemical synthesis. It queries multiple vendor inventory databases simultaneously using structure similarity, applies configurable filters, and consolidates results into a single standardized report — dramatically accelerating the procurement step of any synthesis campaign.
The Problem
Identifying available commercial building blocks for a target synthesis requires manually searching multiple vendor websites (eMolecules, Chemspace, Enamine, etc.) with varying interfaces, different data formats, and inconsistent inventory information. This is tedious, error-prone, and creates bottlenecks in synthesis planning.
The Solution
Multi-Vendor API Integration
The tool queries three major commercial building block distributors simultaneously via their APIs:
| Vendor | Specialty |
|---|---|
| eMolecules | Broad commercial catalog |
| Chemspace | Screening & building blocks |
| Enamine | Make-on-demand compounds |
Queries are made by structure similarity using SMILES inputs, allowing chemists to find close analogs when exact matches are unavailable.
Configurable Inventory Filters
The search tool supports granular commercial inventory filtering:
- Amount available — minimum quantity thresholds
- Estimated lead times — exclude compounds outside project timelines
- Price limits — budget-aware procurement
- Atom alternatives — specify equivalent functional group substitutions (e.g., alkyl bromide OR chloride for amine alkylations)
Data Standardization & Consolidation
Raw vendor hit data returned via API is reformatted into a single, standardized table with consistent field naming, unit normalization, and deduplication — eliminating the need for manual cross-referencing.
Vendor Performance Tracking
The tool was later extended with the ability to track specific vendors’ price and lead time performance over time, building an empirical record used to preferentially weight vendor selection in the algorithm’s scoring logic.
Deployment
The complete tool was:
- Wrapped with a lightweight Flask GUI for non-programmer accessibility
- Containerized via Docker for seamless deployment across the chemistry team’s workstations
Impact
- Reduced building block sourcing from hours to minutes per campaign
- Enabled data-driven vendor selection based on historical performance
- Eliminated cross-platform manual searching and data reconciliation
- Made the tool accessible to all chemists, regardless of programming background