NeoChemSynthWave: Chemistry

Welcome to the NeoChemSynthWave: Chemistry project !!!

Over the last decade, computer-assisted chemical synthesis has re-emerged as a heavily researched subject in Chemoinformatics. Even though the idea of utilizing computers to assist chemical synthesis has existed for nearly as long as computers themselves, the expected blend of reliability and innovation has repeatedly been proven difficult to achieve. Nevertheless, recent machine learning approaches have exhibited the potential to address these shortcomings. Considering the interdisciplinary nature of such approaches, providing essential programming utilities to researchers from various backgrounds is paramount to maximizing success. The main objective of the NeoChemSynthWave: Chemistry project is to provide chemistry programming utilities that are easy to understand and easy to utilize regardless of background and skill level.

Installation

A standalone environment can be created using the git and conda commands as follows:

git clone https://github.com/neo-chem-synth-wave/ncsw-chemistry.git

cd ncsw-chemistry

conda env create -f environment.yaml

conda activate ncsw-chemistry-env

The ncsw_chemistry package can be installed using the pip command as follows:

pip install --no-build-isolation -e .

Utilization

The purpose of the scripts directory is to illustrate how to utilize the ncsw_chemistry package in the following scenarios:

1. Extraction of Chemical Reaction Retro Templates
2. Application of Chemical Reaction Retro Templates
3. Extraction of Chemical Reaction Reactive Sites and Synthons

Scenario 1: Extraction of Chemical Reaction Retro Templates

The chemical reaction retro templates can be extracted as follows:

python scripts/extract_reaction_retro_template.py \
  --mapped_reactant_compounds_smiles "[CH3:9][CH2:8][O:7][C:6](=[O:10])[CH2:5][N:4]1[CH2:3][CH2:2][C:1](=O)[CH2:12][CH2:11]1.[CH2:18]([N:19]1[CH2:20][CH2:21][NH:22][CH2:23][CH2:24]1)[c:17]1[cH:16][cH:15][cH:14][cH:26][cH:25]1" \
  --mapped_product_compound_smiles "[CH3:9][CH2:8][O:7][C:6](=[O:10])[CH2:5][N:4]1[CH2:3][CH2:2][CH:1]([CH2:12][CH2:11]1)[N:22]1[CH2:21][CH2:20][N:19]([CH2:18][c:17]2[cH:16][cH:15][cH:14][cH:26][cH:25]2)[CH2:24][CH2:23]1"

Scenario 2: Application of Chemical Reaction Retro Templates

The chemical reaction retro templates can be applied as follows:

python scripts/apply_reaction_retro_template.py \
  --reaction_retro_template_smarts "[#16:4]=[N;H0;D2;+0:5]-[C;H0;D3;+0:1](-[C;D1;H3:2])=[O;D1;H0:3]>>Cl-[C;H0;D3;+0:1](-[C;D1;H3:2])=[O;D1;H0:3].[#16:4]=[NH;D1;+0:5]" \
  --compound_smiles "CCOC(=O)CN1CCC(CC1)N1CCN(Cc2ccccc2)CC1"

Scenario 3: Extraction of Chemical Reaction Reactive Sites and Synthons

The chemical reaction reactive sites and synthons can be extracted as follows:

python scripts/apply_reaction_retro_template.py \
  --mapped_reaction_smiles "[CH3:9][CH2:8][O:7][C:6](=[O:10])[CH2:5][N:4]1[CH2:3][CH2:2][C:1](=O)[CH2:12][CH2:11]1.[CH2:18]([N:19]1[CH2:20][CH2:21][NH:22][CH2:23][CH2:24]1)[c:17]1[cH:16][cH:15][cH:14][cH:26][cH:25]1>>[CH3:9][CH2:8][O:7][C:6](=[O:10])[CH2:5][N:4]1[CH2:3][CH2:2][CH:1]([CH2:12][CH2:11]1)[N:22]1[CH2:21][CH2:20][N:19]([CH2:18][c:17]2[cH:16][cH:15][cH:14][cH:26][cH:25]2)[CH2:24][CH2:23]1"

License Information

The contents of this repository are published under the MIT license. Please refer to individual references for more details regarding the license information of external resources utilized within this repository.

Contact

If you are interested in contributing to this repository by reporting bugs, suggesting improvements, or submitting feedback, feel free to use GitHub Issues.