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CGRs, molecules and reactions manipulation
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README.md

CGRTools

Tools for processing of reactions based on Condensed Graph of Reaction (CGR) approach.

Basic opertions:

  • Read /write /convert formats MDL .RDF and .SDF, SMILES, .MRV
  • Standardize reactions and valid structures checker.
  • Produce CGRs.
  • Perfrom subgraph search.
  • Build /correct molecules and reactions.
  • Produce template based reactions.

INSTALL

Linux Debian based

  • Install python3.7, virtualenv and git

    sudo apt install python3.7 python3.7-dev git python3-virtualenv
    
  • Create new environment and activate it.

    virtualenv -p python3.7 venv
    source venv/bin/activate
    

Mac

  • Install python3.7 and git using brew

    brew install git
    brew install python3
    
  • Install virtualenv.

    pip install virtualenv
    
  • Create new environment and activate it.

    virtualenv -p python3.7 venv
    source venv/bin/activate
    

Windows

  • Install python3.7 and git using Chocolately

    choco install git
    choco install python3
    
  • Install virtualenv.

    pip install virtualenv
    
  • Create new environment and activate it.

    virtualenv venv
    venv\Scripts\activate
    

General part

  • stable version will be available through PyPI

    pip install CGRTools
    
  • Install CGRtools library DEV version for features that are not well tested

    pip install -U git+https://github.com/cimm-kzn/CGRtools.git@master#egg=CGRtools
    
  • Jupyter integration:

    pip install jupyter
    jupyter notebook
    
  • Download tutorial files to same directory

    https://github.com/cimm-kzn/CGRtools/tree/master/tutorial

  • Open .ipynb files from tutorial directory in Jupyter browser

If you still have questions, please open issue within github.

COPYRIGHT

2014-2019 Ramil Nugmanov stsouko@live.ru main developer
2014-2019 Timur Madzhidov tmadzhidov@gmail.com atom ordering algorithm and API discussion
2014-2019 Alexandre Varnek varnek@unistra.fr base idea of CGR approach

CONTRIBUTORS

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