Graph-to-vector reaction application in molecular fingerprint space.
This repository contains tools to represent chemical reactions as signed transformations between counted molecular ECFP vectors. It focuses on the link between graph-level reaction templates and vector-space reaction operators.
The project provides utilities to:
- compute molecular ECFPs;
- compute reaction ECFPs as product-minus-substrate fingerprint differences;
- compute reaction-center ECFPs for fast applicability filtering;
- build ECFP-compatible reaction templates from mapped reactions;
- analyze and compare reaction representations across datasets such as MetaNetX and USPTO;
- run benchmark tasks such as reaction-class and EC-number prediction.
For a reaction S -> P, the reaction ECFP is represented as:
reaction ECFP = ECFP(P) - ECFP(S)
Reaction-center ECFPs encode the local molecular environments required for a reaction to be applicable. They can be used as fast coordinate-wise filters before graph-level template validation.
This repository is under active development and accompanies ongoing research on reaction representations in molecular fingerprint space.
Citation information will be added with the associated manuscript.