CompRet

Description

Repository for "CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration"

Requirement

Java

• ChemAxon (liscenced, academic free)

Python

• rdkit
• networkx

Set up

1. Clone this repository

2. Download ChemAxon to your home directory

3. Put liscence certification file (liscence.cxl) under ~/.chemaxon

4. Install anaconda and create environment for extractor

$ cd ~
$ wget https://repo.anaconda.com/archive/Anaconda3-2019.07-Linux-x86_64.sh
$ sha256sum Anaconda3-2019.07-Linux-x86_64.sh
$ bash Anaconda3-2019.07-Linux-x86_64.sh

5. Create python environment

$ conda create -c rdkit -n compret-env rdkit
$ conda activate compret-env
$ conda install tqdm
$ conda install IPython
$ conda install pydot
$ pip install networkx
$ pip install bs4

6. Clone scscore repository

$ cd CompRet
$ git clone https://github.com/connorcoley/scscore.git

7. Prepare your own chemical reaction dataset under ./reactions and building blocks as blocks.smi. ChemAxon provides example set of basic chemical reaction in their website.

reactions
    |-rxn1.smarts
    |-rxn2.smarts
    |-.
      .
      .

8. Edit run_all.sh and run!

License

This edition of CompRet is for evaluation, learning, and non-profit academic research purposes only, and a license is needed for any other uses. Please send requests on license or questions to rs1018bio8.utokyo@gmail.com