CGRTools

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

Basic operations:

• Read/write/convert formats: MDL .RDF and .SDF, .MRV, SMILES, INCHI (Linux and Windows), .XYZ, .PDB
• Standardize molecules and reactions and valid structures checker.
• Produce CGRs.
• Perform subgraph search.
• Build/edit molecules and reactions.
• Produce template based reactions and molecules.
• Atom-to-atom mapping checker and rule-based fixer.
• Perform MCS search.
• 2d depiction.

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 Chocolatey

  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
  

• Install CGRtools with MRV files parsing support

  pip install CGRTools[mrv]
  

• Install CGRtools with structures clean2d support [only DEV] optimized version [numba and numpy used]

  pip install -U git+https://github.com/cimm-kzn/CGRtools.git@master#egg=CGRTools[clean2djit]
  

• Install CGRtools with structures clean2d support [only DEV] slow version [numpy used]

  pip install -U git+https://github.com/cimm-kzn/CGRtools.git@master#egg=CGRtools[clean2d]
  

• 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.

PACKAGING

For wheel generation just type next command in source root

python setup.py bdist_wheel

On Linux additionally do repairing of package

pip install auditwheel
auditwheel repair dist/CGRtools-<version>-<python_version>-linux_x86_64.whl

COPYRIGHT

2014-2020 Ramil Nugmanov nougmanoff@protonmail.com main developer
2014-2019 Timur Madzhidov tmadzhidov@gmail.com features and API discussion
2014-2019 Alexandre Varnek varnek@unistra.fr base idea of CGR approach

CONTRIBUTORS

• Dinar Batyrshin batyrshin-dinar@mail.ru
• Timur Gimadiev timur.gimadiev@gmail.com
• Adelia Fatykhova adelik21979@gmail.com
• Tagir Akhmetshin tagirshin@gmail.com
• Ravil Mukhametgaleev sonic-mc@mail.ru