SynthI

SynthI is a open-source tool for synthons-based library design written by Laboratoire-de-Chemoinformatique from University of Strasbourg

Setup

Anaconda3 and a copy of SynthI are already install on /nfs/soft2/. To activate:

$ source /nfs/soft2/anaconda3/bin/activate SynthI-env

Install Anaconda3 on your computer

$ wget https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh 

$ sh Anaconda3-2021.11-Linux-x86_64.sh
  Welcome to Anaconda3 5.3.1
  In order to continue the installation process, please review the license
  agreement.
  Please, press ENTER to continue
  .
  .
  .
  Anaconda3 will now be installed into this location:
  /home/khtang/anaconda3
  [/home/khtang/anaconda3] >>> /nfs/home/khtang/anaconda3
  PREFIX=/mnt/nfs/home/khtang/anaconda3
  .
  .
  .
  Do you wish the installer to initialize Anaconda3
  in your /nfs/home/khtang/.bashrc ? [yes|no]
  [no] >>> no
  Do you wish to proceed with the installation of Microsoft VSCode? [yes|no]
  >>> no

$ source /<path to anaconda3>/bin/activate

Download and setup SynthI

Install dependencies

If you are on the cluster, SynthI is installed on /nfs/soft2/SynthI

$ source /nfs/soft2/anaconda3/bin/activate SynthI-env
$ conda deactivate //to exit environment

Install stand-alone

$ git clone https://github.com/Laboratoire-de-Chemoinformatique/SynthI.git
$ cd SynthI
$ source /<path to anaconda3>/bin/activate
(base) $ conda env create -f SynthI_environment.yml  -p /home/user/anaconda3/envs/synthI_env
(base) $ conda activate /home/user/anaconda3/envs/synthI_env
(synthI_env) $

Usage

The scripts are to be use as a Python library inside of customized script as in you can package it up using setuptools and install the package into your virtual environment or copy into the directory where your script is and import it as a module.

Please note: Prior to BBs synthonization the SMILES should be preprocessed and conterions and solvents should be removed. SynthI-BBs consider every molecule while processing mixture SMILES and for each of them synthons will be generated if possible, therefore take care of them before synthonization.

Detailed guide is here